Principal supervisor - Jeremy Derrick, co-supervisors Ian Kimber (Faculty of Life Sciences), Meenu Wadhwa and Robin Thorpe (NIBSC - industrial partner).

4 year BBSRC Bioprocessing Research Industry Club (BRIC) Industrial CASE Studentship

The production of anti-drug antibodies against recombinant human therapeutics can have a detrimental effect on drug efficacy and safety. Although this is generally regarded as a matter for concern within the industry, the precise immunological mechanisms responsible for generation of anti-drug antibodies remain poorly defined. Protein aggregates are believed to play an important part in this process. However, despite this, there have been comparatively few comprehensive studies of this phenomenon. Specifically, systematic investigations are lacking into how the extent and quality of protein aggregation impacts on the induction of immune responses to protein therapeutics. It is the objective, therefore, of this project to characterise the relationships between the structural characteristics of protein aggregates and the vigour and quality of induced immune responses. To address this objective we will use two independent, but complementary, experimental strategies. In the first of these we will use selected human proteins into which different extents and forms of aggregation have been engineered. Protein preparations in which aggregation patterns have been defined and confirmed by structural/biophysical characterisation will then be used for immunisation. At various periods thereafter, the vigour and quality of induced immune responses will be measured. The second experimental strategy will be to examine the influence of aggregation patterns on the recognition, internalisation and presentation of protein antigens by cultured dendritic cells (DC).  The hypothesis is that the ability of proteins with different aggregation patterns to stimulate immune responses of different vigour of quality will, at least in part, be determined by the nature of their interactions with DC. The project will provide training in immunology and protein chemistry relating to aggregate formation in biopharmaceuticals, and would suit a student with an interest in a career in the biotherapeutics industry.

Applications should be submitted no later than Friday 15 June 2012

1.         Rosenberg, A.S. The AAPS Journal 8, E501-7 (2006).

2.         Sauerborn, M. et al. Trends Pharmacol. Sci. 31, 53-59 (2009).

3.         Holgate, R.G.E. et al. Idrugs 12, 233-237 (2009).

4.         Porter, S. J. Pharm. Sci. 90, 1-11 (2001).

5.         Casadevall, N. et al. N. Engl. J. Med. 346, 469-475 (2002).

• Biochemistry
• Biomolecular Sciences
• Biotechnology
• Immunology
• Molecular Biology

4 year BBSRC Bioprocessing Research Industry Club (BRIC) Industrial CASE Studentship, starting September 2012.

 Principle supervisor – Alexander Golovanov, co-supervisor - Rebecca Dearman

Protein-based biopharmaceuticals, such as antibodies, can treat ever increasing range of diseases, from autoimmune disorders to cancer [1,2]. This emerging new type of treatment has many advantages over the traditional small-molecule drugs. The number of licensed biopharmaceuticals is predicted to grow at a rate of 20% a year. Protein biopharmaceuticals however often suffer from aggregation, precipitation and instability: these may affect all stages of the preparation process, from bioprocessing to formulation [3]. Therefore, protein aggregation and instability currently presents a major problem for Biopharmaceutical Industry, and a bottleneck for many further developments. It is known that protein aggregation can be reduced by choosing the buffer excipients [4].  Looking for new effective and safe excipients is a significant part of efforts to bring new biopharmaceuticals to the market.

The aim of the current project is to explore the applicability of arginine-glutamate (Arg+Glu) [5] for preventing aggregation of pharmaceutically-relevant proteins and increasing their stability in the industrially-relevant protocols and procedures. The possible effect of Arg+Glu in cell-based toxicity assays will be also assessed. The project offers extensive training opportunities for the student, who will get experience working both in an Academic environment (University of Manchester) and in the Industrial environment. As part of this training, the student will undergo research placement in MedImmune (Cambridge). The project will suit candidates with strong interest in research career at the Academic-Industry interface, or Industry-led research and development in the area related to protein science and biopharmaceuticals.

The deadline for applications is Monday 18 June 2012.

[1] Wang W et al, Antibody Structure, Instability, and Formulation. (2007) J. Pharm. Sci, 96:1–26

[2] Elvin et al., Therapeutic antibodies: Market considerations, disease targets and bioprocessing (2012) Int. J. Pharm. Published ahead of print doi:10.1016/j.ijpharm.2011.12.039

[3] Kamerzell TJ et al, Protein–excipient interactions: Mechanisms and biophysical characterization applied to protein formulation development. (2011). Adv. Drug Deliv. Rev. 63:1118–1159.

[4] Jorgensen L et al. Recent trends in stabilising peptides and proteins in pharmaceutical formulation – considerations in the choice of excipients. (2009) Expert Opin. Drug Deliv. 6(11):1219-1230.

[5] Golovanov AP et al. A Simple Method for Improving Protein Solubility and Long-Term Stability (2004). J. Amer. Chem. Soc., 126(29): 8933–8939.

• Biochemistry
• Biomolecular Sciences
• Biotechnology
• Immunology
• Molecular & Cellular Neuroscience
• Molecular Biology
• Molecular Cancer Studies
• Neuroscience
• Pharmacology
• Structural Biology
• Toxicology

Lead Supervisor: Dr Sam Hay

This PhD studentship is one of up to three available within the MIB (Manchester Interdisciplinary Biocentre).
Applicants should hold (or be expected to obtain) a minimum upper-second degree (or equivalent) in a related area.  Funding is available to support UK/EU tuition fees plus stipend ONLY. International applicants must be able to pay the difference between the home and overseas fee.
 
 Information on how to apply can be found here: www.ls.manchester.ac.uk/phdprogrammes

Please include with your online application the following information:

• A personal statement (750 words maximum) outlining the project you are applying for, your suitability for the study, what you hope to achieve from the PhD and your research experience to date.

Applicants are encouraged to discuss suitability for the project with the lead supervisor of their chosen project by contacting the lead supervisor directly.

Project Outline

In this application, we propose to develop a novel NMR-based assay capable of measuring, with unparalleled precision, 13C competitive kinetic isotope effects (KIEs) on enzymatic methyl transfer reactions. The model system is catechol-O-methyl transferase (COMT), a medically important enzyme involved in the breakdown of catecholamine neurotransmitters and a drug target for disorders such as Parkinson’s disease. We wish to measure KIEs on methyl transfer in COMT as a means of probing the reaction mechanism. Additionally, as barrier compression has been implicated in this reaction, it has been suggested that quantum mechanical tunnelling of the carbon (C-tunnelling) may play a role in methyl transfer. While C-tunnelling has neither been observed nor rigorously studied in any biological system, it has been demonstrated in model (chemical) systems at room temperature. The COMT methyl transfer reaction is our current ‘best bet’ for demonstrating enzymatic C-tunnelling. Unequivocal evidence for C-tunnelling – e.g. a 13C KIE that is significantly larger than the semiclassical limit or strongly temperature and/or pressure- (p-T) dependent – would provide further, high-profile, evidence for the importance of non trivial quantum effects in biology.
We have shown that 13C KIE on the COMT reaction are readily derived by measuring NMR intensities of methyl group resonances assigned to the methyl donor and/or acceptor. The challenge now is to refine this assay and develop and refine a suitable data analysis approach. With these in place, we will use this methodology to measure the p-T dependence of the COMT reaction with a range of physiological substrates and/or active site mutants and polymorphic variants. Reaction rates will be benchmarked against rate constants determined using more conventional approaches (e.g. steady state and stopped-flow assays). These data will be used to screen for evidence of C-tunnelling and/or barrier compression. If we find evidence of either, we will develop new numerical models that can accommodate barrier compression and heavy atom tunnelling in such enzymatic reactions.
 

Good vibrations in enzyme catalysed reactions (2011) Hay, S & Scrutton N. S. Nature Chemistry, in press

Barrier compression and its contribution to both classical and quantum mechanical aspects of enzyme catalysis (2010). Hay, S., Johannissen, L. O., Sutcliffe, M. J. & Scrutton, N. S. Biophys. J. 98, 121-128

Hay S, Sutcliffe MJ, Scrutton NS. (2007). Promoting motions in enzyme catalysis probed by pressure studies of kinetic isotope effects. Proc Natl Acad Sci USA, 104, 507-512.

Enzymatic methyl transfer: Role of an active site residue in generating active site compaction that correlates with catalytic efficiency (2011). Zhang, J. & Klinman, J.P. J. Am. Chem. Soc., in press [DOI: 10.1021/ja207467d]

Alpha-deuterium and C-13 isotope effects for methyl transfer catalyzed by catechol O-methyltransferase - SN2-like transition-state (1979). Hegazi, M.F., Borchardt, R.T. & Schowen, R.L. J. Am. Chem. Soc. 101, 4359-4365

Biochemistry
Biophysics
Structural Biology

Humanity is currently facing one of its greatest ever challenges – how are we to increase food production to support the growing global population at a time when climates are changing and becoming more unpredictable. If we are to meet this challenge, it is essential that we develop new crops that are able to maintain productivity when stressed and optimise their growth under changing conditions.

This project focuses on how plants are able to optimise photosynthesis under changing conditions. Recent work in our lab has defined a process we call dynamic acclimation of photosynthesis and shown that plants lacking this have substantially reduced yield when grown under natural conditions. Crop plants have only limited acclimation and therefore a better understanding of this process will allow us to develop novel crop varieties though breeding of biotechnological approaches.

In this project you will examine the process of dynamic acclimation using a combination of physiological, metabolomic and proteomic approaches. You will investigate plants of the model species Arabidopsis thaliana that are either able to or lack the ability to acclimate. Changes in metabolite pool and protein content will be investigated in order to unravel molecular processes involved in acclimation and to identify genes required for plants to sense and respond to environmental change.
 

Athanasiou K., Dyson B.C., Webster R.E. and Johnson G.N. (2009) Dynamic acclimation of photosynthesis increases plant fitness in changing environments. Plant Physiology 152, 366-373

• Adaptive Organismal Biology
• Biochemistry
• Biotechnology
• Cell Biology
• Environmental Biology
• Gene Expression
• Plant Sciences

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Drug-resistant and Multidrug-resistant (MDR) strains of the human pathogen Mycobacterium tuberculosis (Mtb) are widespread across the globe, and tuberculosis (TB) is the leading cause of human mortality amongst bacterial diseases. New strategies are desperately needed to address a problem that the World Health Organization considers to be a “Global Emergency”. The Mtb genome sequence revealed numerous unusual features and novel proteins involved in several biochemical pathways important to viability and pathogenicity of the bacterium. Our laboratory focuses on several of these enzyme systems, with particular emphasis on the Mtb cytochrome P450 (P450) enzymes. The Mtb H37Rv genome sequence exposed an unprecedented array of P450s (20 in all) and highlighted the importance of these enzymes. P450s catalyse introduction of oxygen atoms into their substrates, and it is clear that several of the Mtb P450s are essential genes for Mtb viability and/or are involved in important pathways essential for infectivity or pathogenicity of Mtb. Ourselves and others have demonstrated effectiveness of azole-based P450 inhibitors as anti-mycobacterial drugs, and we have shown tight binding of several azoles to Mtb P450s. PhD projects available would focus on the expression/characterization of Mtb P450 and redox partner enzymes critical to viability/infectivity of the pathogen, and would involve a combination of gene expression, protein isolation and characterization, structural and mechanistic studies aimed at deconvoluting biochemical functions of the key Mtb P450 enzymes. Particular focus is currently on Mtb P450s crucial for infecting the human host and responsible for metabolizing host cholesterol as an energy source and to generate immunomodulatory metabolites. The student will join the Molecular Enzymology Group at the new Manchester Interdisciplinary Biocentre at the University of Manchester, and will receive a broad training in molecular biology, protein chemistry, cellular and structural biology, enabling them to tackle an important project with great relevance to human health.

1. Driscoll, M. D., McLean, K. J., Cheesman, M. R., Jowitt, T. A., Howard, M., Carroll, P., Parish, T. and Munro, A. W. (2010). Expression and characterization of Mycobacterium tuberculosis CYP144: Common themes and lessons learned in the M. tuberculosis P450 enzyme family. Biochim. Biophys. Acta (in press).
2. Driscoll, M.D., McLean, K. J., Levy, C., Mast, N., Pikuleva, I.A., Lafite, P., Rigby, S.E.J., Leys, D. and Munro, A. W. (2010). Structural and biochemical characterization of Mycobacterium tuberculosis CYP142: A novel cholesterol oxidase. J. Biol. Chem. (in press).
3. McLean, K. J., Belcher, J., Driscoll, M. D., Fernandez, C. C., Le van, D., Bui, S., Golovanova, M. and Munro, A. W. (2010). The Mycobacterium tuberculosis cytochromes P450: physiology, biochemistry & molecular intervention. Future Med. Sci. 2, 1339-1353.
4. McLean, K.J., Lafite, P., Levy, C.W., Cheesman, M.R., Mast, N., Pikuleva, I.A., Leys, D. and Munro, A.W. (2009). The Structure of Mycobacterium tuberculosis CYP125: molecular basis for cholesterol binding in a P450 needed for host infection. J. Biol. Chem. 284, 35524-35534.
5. McLean K. J., Carroll, P., Lewis, D. G., Dunford, A. J., Seward, H. E., Neeli, R., Cheesman, M.R., Marsollier, L., Douglas, P., Smith, W. E., Rosenkrands, I., Cole, S. T., Leys, D., Parish, T. and Munro, A. W. (2008). Characterization of active site structure in CYP121. A cytochrome P450 essential for viability of Mycobacterium tuberculosis H37Rv. J. Biol. Chem. 283, 33406-33416.
6. Sabri, M., Dunford, A. J., McLean, K. J., Neeli, R., Scrutton, N. S., Leys, D. and Munro, A. W. (2009). Characterization of coenzyme binding and selectivity determinants in Mycobacterium tuberculosis flavoprotein reductase A: analysis of Arg199 and Arg200 mutants at the NADP(H) 2'-phosphate binding site. Biochem. J. 417, 103-112.
7. Mclean, K. J. and Munro, A. W. (2008). Structural biology and biochemistry of cytochrome P450 systems in Mycobacterium tuberculosis. Drug Metab. Rev. 40, 427-446.
8. Neeli, R., Sabri, M., McLean, K. J., Dunford, A. J., Scrutton, N. S., Leys, D. and Munro, A. W. Trp359 regulates flavin thermodynamics and coenzyme selectivity in Mycobacterium tuberculosis FprA. Biochem J. 411, 563-70.
9. Dunford, A.J., Mclean, K.J., Sabri, M., Seward, H.E., Heyes, D.J., Scrutton, N.S. and Munro, A.W. (2007). Rapid P450 heme iron reduction by laser photoexcitation of Mycobacterium tuberculosis CYP121 and CYP51B1. Analysis of CO complexation reactions and reversibility of the P450/P420 equilibrium. J. Biol. Chem. 282, 24816-24824.
10. McLean, K.J., Dunford, A.J., Neeli, R., Driscoll, M.D. and Munro, A.W. (2007). Structure, function and drug targeting in Mycobacterium tuberculosis cytochrome P450 systems. Arch. Biochem. Biophys. 464, 228-240.
11. McLean, K.J., Dunford, A.J., Sabri, M., Neeli, R., Girvan, H.M., Balding, P.R., Leys, D., Seward, H.E., Marshall, K.R. and Munro, A.W. (2006). CYP121, CYP51 and associated redox systems in Mycobacterium tuberculosis: towards deconvoluting enzymology of P450 systems in a human pathogen. Biochem. Soc. Trans. 34, 1178-1182.
12. Seward, H.E., Roujeinikova, A., McLean, K.J., Munro, A.W. and Leys, D. (2006). Crystal structure of the Mycobacterium tuberculosis P450 CYP121-fluconazole complex reveals new azole drug-P450 binding mode. J. Biol. Chem. 281, 39437-39443.
13. McLean, K.J., Warman, A.J., Seward, H.E., Marshall, K.R., Girvan, H.M., Cheesman, M.R., Waterman, M.R. and Munro, A.W. (2006). Biophysical characterization of the sterol demethylase P450 from Mycobacterium tuberculosis, its cognate ferredoxin, and their interactions. Biochemistry 45, 8427-8443.
14. Gong, M., Hay, S., Marshall, K.R., Munro, A.W. (2007). DNA binding suppresses human AIF-M2 activity and provides a connection between redox chemistry, reactive oxygen species, and apoptosis. J. Biol. Chem. 282, 30331-30340.
15. McLean, K.J., Clift,

• Biochemistry
• Biomolecular Sciences
• Biotechnology
• Cell Biology
• Gene Expression
• Genetics
• Microbiology
• Molecular Biology
• Pharmacology
• Toxicology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Mitochondrion, a vitally important organelle, plays crucial roles during many biological processes (e.g. cell growth and apoptosis), and is implicated in several human diseases and aging process. Protein import is essential for biogenesis of mitochondria, because about 99% mitochondrial proteins are synthesized in the cytosol and have to be imported into mitochondria for their function. The proteins are imported into mitochondria in unfolded forms through specific import pathways that consist of highly regulated translocase complexes. Consequently, correct import, folding, and protein-protein interactions are fundamentally important for mitochondrial biogenesis. Research in my lab focuses on understanding the molecular mechanisms of import, folding, and function of the mitochondrial intermembrane space (IMS) proteins.

One of the recent most important findings in biology is that disulphide bond formation is essential for the import and function of many mitochondrial IMS proteins. Using Tim9 and Tim10 as model proteins, we have made several important findings and contributions to this currently very hot research field. This project is aiming to understand the import and oxidative folding pathways of Tim9 and Tim10, and how Mia40/Erv1 oxidoreductase system and other biologically relevant factors affect the processes. A wide range of well-defined biophysical techniques, as well as biochemical and biological assays have been established in the lab, which will be used and further developed in this project.
 

• Ang, S.K. & Lu, H (2009). Deciphering structural and functional roles of individual disulfide bonds of the mitochondrial sulfhydryl oxidase Erv1p. The Journal of biological chemistry, 284(42), 28754-61. Full text doi:10.1074/jbc.M109.021113
• Morgan, B., Ang, S.K., Yan, G. & Lu, H (2009). Zinc can play chaperone-like and inhibitor roles during import of mitochondrial small Tim proteins. The Journal of biological chemistry, 284(11), 6818-25. Full text doi:10.1074/jbc.M808691200
• Morgan B, Lu H. (2008). Oxidative folding competes with mitochondrial import of the small Tim proteins. The Biochemical journal, 411(1), 115-22. (Faculty of 1000 Biology). Full text doi:10.1042/BJ20071476
• Lu H, Allen S, Wardleworth L, Savory P, Tokatlidis K. (2004). Functional TIM10 chaperone assembly is redox-regulated in vivo. Journal of Biological Chemistry, 279, 18952-8. Full text doi:10.1074/jbc.M313045200

• Biochemistry
• Biomolecular Sciences
• Biotechnology
• Cell Biology
• Molecular Biology
• Organelle Function
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The ubiquitous polysaccharide hyaluronan (HA) has critical roles in development, inflammatory disease and cancer. The majority of HA’s functions are mediated via its interactions with specific HA-binding proteins, termed hyaladherins, leading to the formation of multi-molecular complexes with a diverse range of structural architectures [1]. We have already made considerable progress in determining the molecular basis of how HA is recognised by human proteins (e.g. the HA receptor CD44 that mediates the migration of leukocytes and metastatic tumour cells) and how these interactions are regulated, e.g. during inflammation [2-4]. One of our main current interests is to understand how HA is organised into higher-order structures that have important functional roles, e.g. during mammalian ovulation and in inflammatory disease. For instance, TSG-6 mediates the formation of HC•HA complexes in which “heavy chains” (HC) derived from the serum protein inter-alpha-inhibitor become covalently attached to HA [1]; these HC•HA then can be cross-linked via their association with the octameric pentraxin 3 (see [5]). This project, which will utilise a combination of high-resolution structural biology, solution-based biophysical analyses and functional studies (e.g. with site-specific mutants), forms part of our ongoing work to characterise these fundamental molecular interactions.

1. Day, A.J. & de la Motte, C.A. Hyaluronan cross-linking: a protective mechanism in inflammation? (2005) Trends Immunol. 26, 637-643.

2. Banerji, S., Wright, A.J., Noble, M., Mahoney, D.J., Campbell, I.D., Day, A.J. & Jackson, D.G. Structures of the CD44-hyaluronan complex and new insight into a fundamental carbohydrate-protein interaction. (2007) Nat. Struct. Mol. Biol. 14, 234-239.

3. Blundell, C.D., Mahoney, D.J., Cordell. M.R., Almond, A., Kahmann, J.D., Perczel, A., Taylor, J.D., Campbell, I.D. & Day, A.J. Determining the molecular basis for the pH-dependent interaction between the Link module of human TSG-6 and hyaluronan. (2007) J. Biol. Chem. 282, 12976-12988.

4. Wolny, P.M., Banerji, S., Gounon, C., Brisson, A.R., Day, A.J., Jackson, D.G. & Richter, R.P. Analysis of CD44-hyaluronan interactions in an artificial membrane system: insights into the distinct binding properties of high and low molecular weight hyaluronan. (2010) J. Biol. Chem., in press. Published as a “Paper in Press” online on 27th July 2010.

5. Inforzato, A., Baldock, C., Jowitt, T.A., Holmes, D.F., Lindstedt, R., Marcellini, M., Rivieccio, V., Briggs, D.C., Kadler, K.E., Verdoliva, A., Bottazzi, B., Mantovani, A., Salvatori, G. & Day, A.J. The angiogenic inhibitor long pentraxin PTX3 forms an asymmetric octamer with two binding sites for FGF2. (2010) J. Biol. Chem. 285, 17681-17692.
 

• Biochemistry
• Biomolecular Sciences
• Cell Matrix Research
• Developmental Biology
• Genetics
• Immunology
• Molecular Biology
• Molecular Cancer Studies
• Stem Cell Research
• Structural Biology
   

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

We propose to search for novel lead compounds for the treatment of cystic fibrosis (CF). We plan to do this by exploiting our collaborative links with Cystic Fibrosis Foundation Therapeutics Inc (CFFT) and building on work we have been carrying out as part of its CFTR 3D structure consortium. This work has led to novel protocols for the production of signifcant amounts of highly purified CFTR protein.

This project will be jointly supervised by Bob Ford (Faculty of Life Sciences) and Jichen Li (School of Physics)

• Huang, P., Stroffekova, K., Cuppoletti, J., Mahanty, S.K. & Scarborough, G.A.
• Biochim. Biophys. Acta 1281, 80-90 (1996).
• Huang, P., Liu, Q. & Scarborough, G.A. Anal. Biochem. 259, 89-97 (1998).
• Kiser, G.L. et al. Arch Biochem Biophys 390, 195-205 (2001).
• Verkman, A.S., Lukacs, G.L. & Galietta, L.J.. Curr Pharm Des 12, 2235-47 (2006).
• Van Goor, F. et al. Am J Physiol Lung Cell Mol Physiol 290, L1117-30 (2006).

• Biochemistry
• Biomolecular Sciences
• Channels & Transporters
• Molecular Biology

If you are applying for this project as a UK/EU applicant and wish to be considered for our first round of studentship awards, then please apply by Friday 25 November 2011.

Interview Days will be held on Wednesday 7 December 2011 (for current UoM students) and Thursday 5 January 2012 (for external applicants). We will contact all shortlisted applicants directly with invitations to an interview day.

If you apply after 25 November 2011, then you will be considered for any remaining projects in the second round of awards which we anticipate being in around February/March.

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Amongst the millions of protein sequences now known from genome projects, many contain intriguing repetitive regions. The repeats confer on their host proteins various properties, including stretchiness, springiness, mechanical strength, adhesion, etc. Structural properties aside, these proteins elicit interest because of their known and suspected roles in mediating certain diseases: e.g., elastins have been implicated in diseases like cutis laxa, where the elasticity of the skin is lost; glutenins have been implicated in food intolerance syndromes like coeliac disease; huntingtin and prion proteins are associated with Huntington’s disease and various human dementias. The repeats vary in complexity, and many of their structures are unknown: some are thought to be disordered, while others are likely to be highly structured (e.g., for binding particular metals, or to form rigid scaffolds or flexible rope-like structures). This project offers interesting opportunities to explore structure-function relationships in repeat-containing proteins using systematic sequence-structure and comparative genome analyses. The results will help to discover whether: 1) the nature of repeats varies across the different kingdoms of life; 2) specific recurrent motifs are indicative of particular types of function or local structure; and 3) there are underlying patterns associated with the onset of different types of disease.

• 1. Coletta A, Pinney JW, Weiss Solis DY, Marsh J, Pettifer SR & Attwood TK (2010) ?Low-complexity regions within protein sequences have position-dependent roles. ?BMC Syst. Biol., 4(1), 43.
• 2. Park H, Huxley-Jones J, Boot-Handford RP, Bishop PN, Attwood TK & Bella J (2008) LRRCE: a leucine-rich repeat cysteine capping motif unique to the chordate lineage. BMC Genomics, 9, 599. doi:10.1186/1471-2164-9-599.
• 3. Nordle AKL, Rios P, Gaulton A, Pulido R, Attwood TK & Tabernero L (2007) ?Functional assignment of MAPK phosphatase domains. ?PROTEINS: Structure, Function & Bioinformatics, 69(1), 19-31.
• 4. Flower DR & Attwood TK (2004) Integrative bioinformatics for functional genome annotation: trawling for G protein-coupled receptors. Semin.Cell Dev.Biol., 15(6), 693-701.
• 5. Attwood TK (2001) A compendium of specific motifs for diagnosing GPCR subtypes. Trends in Pharmacological Sciences, 22(4), 162-165.
   

• Bioinformatics
• Biomolecular Science
• Structural Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Bioenergetics drives life on this planet and is of fundamental importance to the global ecosystem. This project will use computational analysis of tomographic data on bioenergetic systems, bridging our understanding between the molecular and cellular scale organisation of these systems. A 3D modelling of the bioenergetic systems and of the flux of electrons and protons through them will be carried out. The aim is to understand the limits of the productivity of systems and how adaptive evolution can optimise the 3D organisation of the systems to maximise energy production. The conclusions will then be applied for the design of biomimetic nanotechnology devices.The student will be trained in modern electron tomographic techniques, computational analysis and 3D reconstruction.

• Ford, R. C., A. L. Brunkan-LaMontagne, et al. (2009). "Structure-function relationships of the outer membrane translocon Wza investigated by cryo-electron microscopy and mutagenesis." J Struct Biol 166(2): 172-82.
• Ford, R. C., S. V. Ruffle, et al. (2004). "Neutron scattering measurements of intact cells show changes after heat shock consistent with an increase in molecular crowding." J Mol Recognit 17(5): 505-11.
• Ford, R. C., S. V. Ruffle, et al. (2004). "Inelastic incoherent neutron scattering measurements of intact cells and tissues and detection of interfacial water." J Am Chem Soc 126(14): 4682-8
• Ford, R. C., S. S. Stoylova, et al. (2002). "An alternative model for photosystem II/light harvesting complex II in grana membranes based on cryo-electron microscopy studies." Eur J Biochem 269(1): 326-36.
• Ruffle, S. V., A. O. Mustafa, et al. (2002). "The location of plastocyanin in vascular plant photosystem I." J Biol Chem 277(28): 25692-6.

• Biochemistry
• Channels & Transporters
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

G protein-coupled receptors (GPCRs) are a large, functionally diverse group of membrane proteins that regulate vital cellular processes. As targets for >50% of prescription drugs, they are of pivotal interest, particularly to pharmaceutical companies who constantly seek to design new, safer and more efficacious drugs. Despite their importance, much remains unknown about how they function: many are 'orphans' with unknown ligand- and G protein-coupling specificities; many function as oligomers or in association with other protein partners, but the sites of interaction are unknown. In the absence of experimental data, we use patterns of conserved motifs (‘fingerprints’) to help functionally characterise GPCRs - to date, we have created >250 fingerprints to diagnose members of this important class of receptors. Using state-of-the-art bioinformatics analysis and computer visualisation techniques (especially the Utopia suite), this project will investigate such GPCR fingerprints in order to understand their roles in ligand binding, G protein coupling, oligomerisation &/or other protein-protein interactions. In the short term, the results will help us both to discover whether there are specific motifs responsible for receptor-ligand binding, and to identify possible allosteric sites that modulate receptor function; in the longer term, the results may feed into pharmaceutical in silico target- and drug-discovery programmes.

• 1. Pettifer S, Thorne D, McDermott P, Marsh J, Villeger A, Kell DB & Attwood TK (2009)?Visualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics, 10, S18.
• 2. Flower DR & Attwood TK (2004) Integrative bioinformatics for functional genome annotation: trawling for G protein-coupled receptors. Semin.Cell Dev.Biol., 15(6), 693-701.
• 3. Gaulton A & Attwood TK (2003) Bioinformatic approaches for analysing GPCRs. Current opinions in pharmacology, 3(2), 114-120.
• 4. Attwood TK (2001) A compendium of specific motifs for diagnosing GPCR subtypes. Trends in Pharmacological Sciences, 22(4), 162-165.
• 5. Pettifer SR, Sinnott JR & Attwood TK (2004) UTOPIA - User-friendly tools for operating informatics applications. Comp.Funct.Genomics, 5(1), 56-60: http://utopia.cs.man.ac.uk/

• Bioinformatics
• Biomolecular Sciences
• Structural Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

At Manchester we have access to large volumes of mass spectrometry derived data relating to peptide identifications of proteins in the proteome. Although the existing computational tools are good at matching peptide mass spectra to theoretical spectra derived from candidate peptide sequences, few take advantage of the patterns in signal intensity related to the amino acids content. In this project we will exploit our data, building on recent results characterising the distributions of ion intensities, to build better peptide identification pipelines. Similarly, we will exploit machine learning algorithms and multiple search engines to improve peptide identification strategies, testing out our results against annotated genomes. This will include application areas taken from local proteomics projects characterising the proteome of organisms such as E.coli, yeast, chicken and human.

• Lau K, Lynch J, Hart, S, Hubbard SJ, Gaskell. SJ (2009) Observations on the Detection of b- and y-Type Ions in the Collisionally Activated Decomposition Spectra of Protonated Peptides. Rapid Comm Mass Spec. 20, 1508-14.
• Jones A, Siepen JA, Hubbard SJ, Paton NW (2009) A strategy for improving sensitivity in proteome studies, using multiple search engines. Proteomics. 9, 1220-9
• McLaughlin T, Selley J, Lynch J, Siepen JA, Lau KW, Yin H, Gaskell SJ, Hubbard SJ (2006) PepSeeker – a database of proteome peptide identifications. Nucleic Acids Res, 34, D549-D564

• Biochemistry
• Bioinformatics
• Biomolecular Sciences
• Biotechnology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Protein-protein interactions underpin most biological functions and are an essential building block of a systems wide understanding of cellular function. Proteins work by interacting with one another in molecular machines and in metabolic and regulatory pathways. In this project we will apply computational analyses to study structural and evolutionary properties of protein interfaces in order to predict them from sequence information alone. This will build on existing work looking at domain-domain interactions observed in known structures and expected from sequenced genomes (Littler & Hubbard, 2005) and studies on the molecular co-evolution observed generally between interacting protein families (Lee et al.,submitted). We will also look at novel conserved features of oligomeric protein interfaces, based on preliminary data that shows promise in distinguishing different states. We aim to use molecular modelling, sequence and structural conservation, co-evolution and information theory to study candidate protein-protein interactions in order to detect true interactions from false ones and build an accurate predictive system to help build/validate interaction networks.

 Littler SJ and Hubbard SJ (2005) Conservation of orientation and sequence in protein domain-domain interactions J. Mol. Biol. 345: 1265-1279.

• Biochemistry
• Bioinformatics
• Biomolecular Sciences
• Biotechnology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

This project concerns the development of advanced statistical inference techniques for fitting stochastic systems biology models to data from live cell imaging experiments. Such data are being generated in the newly established systems microscopy centre based in Manchester, led by Professor Mike White, a state-of-the-art facility for the quantification of single-cell dynamic processes.

Many cellular processes are highly dynamic and stochastic in nature. For example, extracellular signalling by hormones can lead to the activation of receptors in the cell nucleus which control the transcription of genes and subsequently the production of new proteins and complexes in the cell. These processes are often asynchronous across cell populations and so cannot be observed in data from experimental assays that only measure average protein concentrations over large cell populations. Instead, it is necessary to measure data from individual cells over time (Spiller et al. 2010). Such data are highly stochastic and are therefore best modelled using stochastic process models. The task of fitting alternative models to the data and determining which models best fit the data is often the analysis bottleneck. New computational tools are therefore required to more efficiently automate the process of model building and model comparison.

Tools developed in the project will be used to fit and score alternative stochastic process models describing the intra-cellular dynamics of macromolecules moving between cellular compartments. The lead supervisor, Professor Magnus Rattray, has been appointed to a Chair in Systems Biology and has an international reputation in Bayesian statistical inference and machine learning applied to models of biological systems. We will extend developments in Gaussian process inference for ordinary differential equation models with hidden variables (Honkela et al. 2010; Lawrence et al. 2010, Chapter 9) to single-cell models described by stochastic differential equations. A particular focus will be on efficient methods for iterative model improvement and model selection using Bayesian methods, and we will explore sampling-based methods (MCMC), approximate deterministic methods (message passing, variational inference) and likelihood-free methods (ABC). Efficient computational implementations will be provided to the broader community as open source software, to maximise the benefit and impact of the work.

The applicant should have a strong undergraduate or Masters-level training in a mathematical and/or computational discipline, e.g. Mathematics, Statistics, Physics, Computer Science, Computational Biology.

Note: This project will be jointly supervised by Professor Magnus Rattray and Professor Michael White.  Professor Rattray is moving to the University of Manchester, Faculty of Life Sciences in August 2012. Details of recent research are available at his current website in Sheffield: http://staffwww.dcs.shef.ac.uk/people/M.Rattray. This position is one of four new positions (2 PhD, 2 postdoc) being advertised for September.

D.G. Spiller, C.D. Wood, D.A. Rand and M.R.H.White “Measurement of single-cell dynamics” Nature 465 (2010).

A. Honkela, C Girardot, E.H. Gustafson, Y.-H. Liu, E.E.M. Furlong, N.D. Lawrence and M. Rattray "Model-based method for transcription factor target identification with limited data" Proc. Natl. Acad. Sci. USA 107(17), 7793-7798 (2010).

N.D. Lawrence, M. Girolami, M. Rattray, G.Sanguinetti “Learning and Inference in Computational Systems Biology” (MIT Press, 2010).

• Bioinformatics
• Cell Biology
• Gene Expression
• Molecular Biology

Food security is among the most serious challenges facing humanity in the coming decades. Not only do we need to increase agricultural production because of population growth, but also climate change is predicted to have an adverse impact on crops. Periods of drought and heat waves are expected to become more frequent, but crucially it is environmental variability (in terms of light, temperature, water) that imposes the biggest stress on plants. Even periods of moderate stress can, at crucial stages in the growth cycle, have a significant impact on crop yields. Hence, there is an urgent need to develop crops with better tolerance of environmental stress.

Systems biology and computer modelling are becoming major tools to predict properties of living organisms. We are now able to construct genome-scale models that encompass all known metabolic reactions of a species, and we can use these models to make quantitative predictions about the growth of an organism. These methods open novel perspectives to predict the response of plants to environmental variations and to discover new biotechnological solutions to improve crop yields.

We have so far developed genome-scale metabolic models of the plant Arabidopsis thaliana (Radrich et al., 2010) and identified processes that are crucial to the dynamic acclimation of photosynthesis (Athanasiou et al., 2010). Photosynthesis is particularly sensitive to variations in environmental conditions, and changes in photosynthetic activity impact carbon fixation and the whole plant metabolism. The aim of this project will be to investigate how photosynthesis responds to variable environmental conditions and to construct in silico models of the associated metabolic response. Models will be tested experimentally by carrying out selected measurements of metabolite pools in fluctuating conditions. This project offers an exciting opportunity to work in a highly interdisciplinary environment and acquire training in both wet-lab and computer modelling techniques. The project also addresses a fundamental research priority, food security, with the potential of biotechnological applications.
 

Radrich K, Tsuruoka Y, Dobson P, Gevorgyan A, Swainston N, Baart G, Schwartz JM (2010) Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. BMC Systems Biology 4: 114.

Athanasiou K, Dyson BC, Webster RE, Johnson GN (2010) Dynamic acclimation of photosynthesis increases plant fitness in changing environments. Plant Physiology 152: 366-373.
 

• Biochemistry
• Bioinformatics
• Biotechnology
• Environmental Biology
• Plant Sciences

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

A key objective within synthetic biology is to develop new biocatalysts that can be used either on their own or as components within engineered biological ensembles. The importance of this stems from the need to develop efficient routes to pharmaceuticals and chemical feedstocks derived from biomass. Synthetic biology promises to deliver both sustainable and selective new pathways for synthesis, but there are many challenges to overcome. An important step is to be able to increase the chemical repertoire of engineered enzymes, away from those reactions found in natural biosystems towards the more flexible strategies of the chemical laboratory. This project seeks to apply in vitro evolution techniques, combined with covalent ligation of novel prosthetic groups, to enzyme active sites to either (a) generate new C-C bond forming catalysts, or (b) generate new metalloenzymes capable of catalysing not only new C-C bond forming reactions, but also C-N, C-O or C-H bond forming reactions not currently achievable using native enzymes.
The research will utilise easily expressed (in E. coli) thermostable proteins since these are advantageous for synthesis but also offer ease of purification, even in a library (96-well plate) format. Modern saturation mutagenesis techniques will be applied to generate mutant libraries, and acquisition of new activity assessed through the development of suitable screens, in collaboration with Dr. David Berrisford and Prof. Nick Turner in the School of Chemistry. Ideally, the student should be prepared to engage with some organic synthesis of enzyme substrates and/or prosthetic groups.
The project might extend beyond design of an individual enzyme to linking 2 or more enzymes into a novel synthetic pathway of real utility. Crystallisation of interesting candidate enzymes should also be attempted. The student will benefit from an interdisciplinary training and access to state of the art high-throughput equipment in the Manchester Interdisciplinary Biocentre.
 

Martin, CH, Nielsen, DR, Solomon, KV, & Jones Prather, KL (2009) Synthetic Metabolism: Engineering Biology at the Protein and Pathway Scales. Chemistry & Biology 16, 277-286
(DOI 10.1016/j.chembiol.2009.01.010).
 

• Biochemistry
• Biomolecular Sciences
• Gene Expression
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

A key objective within synthetic biology is to develop new biocatalysts that can be used either on their own or as components within engineered biological ensembles. The importance of this stems from the need to develop efficient routes to pharmaceuticals. Here, we focus on generating an enzyme capable of catalysing an existing abiotic organic reaction known as the Baylis-Hillman reaction. The Baylis-Hillman reaction is a carbon-carbon bond forming reaction of great synthetic utility, generating highly functionalised molecules for further incorporation into drug synthesis pathways. There are no known natural enzymes capable of catalysing this reaction and the available organic catalysts for the abiotic reaction are inefficient. Success in generating a new biocatalyst would thus have significant impact on pharmaceutical programmes, as well as being of high interest with respect to enzyme structure, mechanism and engineering. This project seeks to apply in vitro evolution techniques to generate libraries of new enzymes and to combine this with organic synthesis to generate the Baylis-Hillman substrates and to develop a good screen for product formation. The research will utilise easily expressed (in E. coli) thermostable proteins since these are advantageous for synthesis but also offer ease of purification, even in a library (96-well plate) format. Modern saturation mutagenesis techniques will be applied to generate the mutant libraries. A number of native enzymes will be chosen as starting points for the saturation mutagenesis, based on the similarity of their chemistry and substrate binding to that required for a potential ‘Baylis-Hillmanase’. The project would suit a student from a biochemical or chemical background with interests in enzymology, chemistry and protein engineering. It is a collaboration with Dr. David Berrisford in the School of Chemistry and offers interdisciplinary training and access to state of the art high-throughput equipment in the Manchester Interdisciplinary Biocentre.

• Martin, CH, Nielsen, DR, Solomon, KV, & Jones Prather, KL (2009) Synthetic Metabolism: Engineering Biology at the Protein and Pathway Scales. Chemistry & Biology 16, 277-286(DOI 10.1016/j.chembiol.2009.01.010).
• Reetz MT, Carballeira JD. (2007) Iterative saturation mutagenesis for rapid directed evolution of functional enzymes. Nature Protoc. 2, 891-903.

Biochemistry

Biomolecular Sciences

Gene Expression

Molecular Biology

Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Cystic fibrosis is the most common human inherited disease, affecting ~1 in 4000 births. Drugs targeted to the mutated protein (CFTR) are urgently needed. This project will be aimed at the development of high-throughput drug screening assays for CFTR. The project will involve the expression of the recombinant wild-type and mutated CFTR proteins in microbial systems, followed by their purification and biophysical characterisation. The proteins will be reconstituted into lipid vesicles and their activity checked using a variety of biochemical assays. Finally, fluorescent reporter assays will be developed to monitor the activity of the recombinant proteins in the presence of drugs. In the latter stages, the student will be involved in the translation of the assays to a standard 96-well format for high-throughput screening. This project is linked to Cystic Fibrosis Foundation Therapeutics Inc. (USA) which is sponsoring the research in the Ford laboratory.

• Rosenberg, M. F., A. B. Kamis, et al. (2004). "Purification and crystallization of the cystic fibrosis transmembrane conductance regulator (CFTR)." J Biol Chem 279(37): 39051-7.
• Awayn, N. H., M. F. Rosenberg, et al. (2005). "Crystallographic and single-particle analyses of native- and nucleotide-bound forms of the cystic fibrosis transmembrane conductance regulator (CFTR) protein." Biochem Soc Trans 33(Pt 5): 996-9.
• Zhang, L., L. A. Aleksandrov, et al. (2009). "Architecture of the cystic fibrosis transmembrane conductance regulator protein and structural changes associated with phosphorylation and nucleotide binding." J Struct Biol 167(3): 242-51.
• Kos, V. and R. C. Ford (2009). "The ATP-binding cassette family: a structural perspective." Cell Mol Life Sci 66(19): 3111-26.
   

   

• Biochemistry
• Channels & Transporters
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Electron tomography bridges the gap between cell biology and molecular biology. It also provides the 3D information that is lacking from Systems Biology – derived models and maps of the cell or cellular compartments. Hence it is possible to incorporate information about the 3D organisation of components in a system and hence generate improved models of metabolic flux and protein-protein interactions. This project will generate a 3D model of the major protein complexes in photosynthetic organelles and then incorporate the data into a computer-based model of the flux of the major metabolites through photosynthesis.

Visualizing cells at the nanoscale. Leis A, Rockel B, Andrees L, Baumeister W.Trends Biochem Sci. 2009, 34(2):60-70.

Cryo-electron tomography of cells: connecting structure and function.Lucic V, Leis A, Baumeister W.
Histochem Cell Biol. 2008 Aug;130(2):185-96.

Towards a comprehensive catalog of chloroplast proteins and their interactions.Leister D, Kleine T.
Cell Res. 2008 Nov;18(11):1081-3.

Dynamic simulations on the mitochondrial fatty acid beta-oxidation network. Modre-Osprian R, Osprian I, Tilg B, Schreier G, Weinberger KM, Graber A. BMC Syst Biol. 2009 Jan 6;3:2.

• Biochemistry
• Biomolecular Sciences
• Channels & Transporters
• Molecular Biology
• Plant Sciences
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Protein-protein interactions underpin almost all biological functions, with the majority of proteins making at least one interaction with another. If we are to understand how function arises in the cell, an important prerequisite is to understand how protein-protein interactions arise and evolve.

When we analyse sets of related proteins we find that they vary substantially in the sets of interactions that they make. In other words, the network of interactions “rewires” itself through evolutionary time. This rewiring can give rise to enormous complexity and emergent biological function. We propose to study this process of evolutionary rewiring using computational methods. This will involve the use of protein structure, knowledge of how proteins bind through specific interfaces, and evolutionary models. This approach differs from other techniques that attempt to define specificity and binding surfaces in that it is “function-led” (based on the interaction network and the functional annotation), rather than being “sequence-led” (based one the partitioning of the sequences using a phylogenetic tree).

The majority of the data used will be derived from the yeast Saccharomyces cerevisiae. Since Manchester is a centre for yeast research there is may be a possibility to test computational predictions in collaboration with experimental labs.
 

Bioinformatics

Biomolecular Sciences

Evolutionary Biology

Molecular Biology

Structural Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

This project will be jointly supervised by Lydia Tabernero (Lead Supervisor, Faculty of Life Sciences), William Hope (School of Translational Medicine) and Jen Cavet (Faculty of Life Sciences)

Mycobacterium tuberculosis (Mtb), the causing agent of tuberculosis, is one of the most succesful human pathogens. This intracellualr pathogen is able to survive in host immune cells, macrophages, by defeating the innate immune system and avoiding destruction by the antimicrobial mechanisms within macrophage phagosomes. The molecular mechanims that facilitate such survival are still unclear, but manipulation of the host phosphoinositide metabolism is, in part, responsible for phagosome maturation arrest. MptpB is a secreted phosphatase, essential for survival of Mtb within macrophage phagosomes. The biological substrates of MptpB have not yet been defined, but we discovered that MptpB dephosphorylates phosphoinositides needed for specific membrane attachment of Rab proteins and EEA1 that direct phagosome maturation and fusion to lysosomes associated with bacterial killing. This suggests a potential role for MptpB in host phosphoinositide metabolism and phagosome maturation arrest offering exciting new directions for pharmacological intervention of tuberculosis. We also identified potent inhibitors of MptpB that impair the survival of Mtb in infected macrophages supporting our hypothesis. Next we want to use these inhibitors to further study the role of MptpB in pathogenesis and phagosomal maturation arrests and as targets for drug development to treat tuberculosis.
This project offers an exciting new approach to exploit virulence factors to develop novel therapies to fight tuberculosis. The project will involve a multidisciplinary approach with biochemical and structural analysis together with microbiological, cellular and imaging technologies. The collaborative nature of the project is a unique opportunity to engage in real translational research with the benefits of an interdisciplinary working environment (basic research and clinical pathology). The complementary expertise of groups involved means that the student will have a much broader and rounded up training during the PhD.
 

• Singh R, Rao V, Shakila H et al. Mol Microbiol 50(3), 751–762 (2003).
• Beresford N, Patel S, Armstrong J, Szoor B, Fordham-Skelton AP, Tabernero L. Biochem. J. 406(1), 13–18 (2007).
• Beresford NJ, et al. J. Antimicrob. Chemother. 63(5), 928–936 (2009).
• Lestner J.M., Howard S.J., Goodwin J., Gregson L., Majithiya, J., Jensen G.M., Hope W.W. Antimicrobial Agents and Chemotherapy (2010), 54(8):3432-41.
• Hope W.W., et al., Journal of Infectious Diseases (2007), 1;195(3):455-66.

• Biochemistry
• Biomolecular Sciences
• Microbiology
• Pharmacology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Cell signalling pathways play essential roles in human development and disease. One major signalling pathway, the transforming growth factor (TGF)-β family, plays crucial roles in embryonic development, adult tissue homeostasis and the pathogenesis of a wide-range of diseases from fibrosis to tumour invasion. Therefore, it is critical to understand the different ways in which the TGFβ pathway is regulated, in order that therapeutic strategies can be developed in the future.

The aim of this project is to use a multi-technique approach to understand the extracellular regulation of bone morphogenetic protein (BMP) signalling molecules, which constitute a specific subclass within the TGFβ family. We know that BMPs are regulated by protein antagonists which bind and inhibit BMPs, as well as enzymes which liberate BMP from the inhibitory complex. A variety of structural, biochemical and biophysical approaches will be used to investigate how these molecules interact and impact upon BMP function.

This project offers a unique opportunity to be trained in structural, molecular, and biochemical techniques. Moreover, a structural understanding of how BMP regulators function will be useful for the development of novel medical strategies to improve bone healing and reduce atherosclerosis.
 

• Role of dimerization and substrate exclusion in the regulation of bone morphogenetic protein-1 and mammalian tolloid. Berry R, Jowitt TA, Ferrand J, Roessle M, Grossmann JG, Canty-Laird EG, Kammerer RA, Kadler KE, Baldock C. Proc Natl Acad Sci U S A. (2009) 106:8561-6.
• Structural and functional evidence for a substrate exclusion mechanism in mammalian tolloid like-1 (TLL-1) proteinase. Berry R, Jowitt TA, Garrigue-Antar L, Kadler KE, Baldock C. FEBS Lett. (2010) 584:657-61.

• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Cell Matrix Research
• Developmental Biology
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Redox systems are crucial in metabolic and control processes throughout biology. Intracellular compartmentalisation in eukaryotic cells allows the creation of separate redox environments, with the constituent sets of macro- and small molecules evolved to provide specific functionality [1]. A key component of reduction/oxidation networks is the thiol group of cysteine residues, for which the surrounding protein environment modulates activity. This computational project will predict the redox activity of thiol groups in model organisms, and use these predictions to (i) compare with redox networks in disparate organisms, and (ii) investigate the role of altered redox properties in disease. A hierarchical framework will be employed, in which molecular models for thiol activity [2], refined against experimental data, are coupled with genome-wide modelling and 3D structure in normal and disease-associated proteins. Comparative studies will be made between organelles and between organisms (i.e. comparative genomics). Recent work from our group using a similar comparative approach, in the context of organelle proteomics, uncovered evidence for adaptation of pH-dependence to subcellular pH [3]. A final layer of the hierarchy will place the work in the context of systems biology models for cellular function, so that the project will also provide methods and computer code to parameterise the redox inputs to systems models.

1. Redox compartmentalization in eukaryotic cells. Go YM and Jones DP (2008) Biochim Biophys Acta 1780:1273-1290.
2. Prediction of pKa and redox properties in the thioredoxin superfamily. Moutevelis F and Warwicker J (2004) Protein Sci 13:2744-2752.
3. Evidence for the adaptation of protein pH-dependence to subcellular pH. Chan P and Warwicker J (2009) BMC Biol 7:69.
 

• Biochemistry
• Bioinformatics
• Biomolecular Sciences
• Biotechnology
• Cell Biology
• Organelle Function
• Structural Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

From genome sequences, the total number of genes in several organisms can now be predicted. However, the functions of many of these genes remain unknown. The number and percentage of genes that are required for development and classified as essential varies among organisms. The percentage of genes required for human survival is unknown. However, studies in the mouse allow mammalian essential genes to be identified from experimental data. From these data a subset of essential and non-essential genes have been discovered. The task that remains is to identify all the genes that are likely to be required for mammalian development using the mouse as a model, and comparative genomics to then characterise essential human genes. Incorporating a machine learning approach, we seek to identify characteristics that are over-represented in genes known to be required for development. This will allow us to develop criteria for essential genes. By applying these criteria to the mouse genome, we can then identify regions of the genome that contain high numbers of essential genes, as well as identify the individual genes that are likely to be required for mammalian development.

Hentges KE, Pollock DD, Liu B, Justice MJ. Regional variation in the density of essential genes in mice. PLoS Genet. 2007 May 4;3(5):e72.

Lovell SC, Li X, Weerasinghe NR, Hentges KE. Correlation of microsynteny conservation and disease gene distribution in mammalian genomes. BMC Genomics. 2009 Nov 12;10:521.
 

• Bioinformatics
• Developmental Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

New millennium biology is in crisis, overwhelmed both by data and publications describing those data: with 1.5 billion bases pouring monthly into DNA databases, and a new article appearing in Medline every 30 seconds, it is impossible to keep abreast of developments. As we systematically bury our knowledge in data and literature silos, we no longer know what we know, nor know how to find it!
To address these issues, new approaches are needed to manage, merge, interrogate and exploit 'big data' from modern, high-throughput genomic and proteomic experiments. Next-generation software (including new 'social’ software) is required to turn the rapidly accumulating information into biochemical, biophysical and biomedical knowledge; new approaches are also needed to interface with the research hubs that build the databases on which modern biology now depends.
This project is an opportunity to work at this interface, building on collaborations with the curators of important protein databases (InterPro, UniProt, Gene3D, etc.) and with publishers. The broad aim is to integrate data in articles with information stored in databases, to be able to visualise and seamlessly interact with them in real time. The initial focus is on proteins, their families, their structures and interactions; in time, this will broaden to genes and genomic data.
We have built Utopia [1,2], software that semantically integrates visualisation and data-analysis tools with document-reading/management utilities. Utopia uses Web-services to marshal functionality from the Internet [3,4], gathering new tools within a single, user-friendly interface. Extending this work to focus explicitly on protein families [5] and protein-protein interactions, and taking advantage both of the results of the FEBS Letters experiment with the MINT protein interaction database and our semantic Biochemical Journal Experiment with Portland Press [2], this project will begin by exploring exciting new ways for visualising, analysing and understanding proteins and their interactions.
 

• 1. Pettifer S, Thorne D, McDermott P, Marsh J, Villeger A, Kell DB & Attwood TK (2009) Vis-ualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics, 10, S18.
• 2. Attwood TK, McDermott P, Marsh J, Pettifer S & Thorne D (2009) Calling International Rescue: knowledge lost in data and literature landslide! Biochemical Journal, 424(3), 317-333.
• 3. Stockinger H, Attwood TK, Chohan SN, Cote R, Cudre-Mauroux P, Falquet L, Fernandes P et al. (2008) Experience using Web services for biological sequence analysis. Briefings in Bioinformatics,
• 9(6), 493-505.
• 4. Pettifer S, Thorne D, McDermott P, Attwood T, Baran J, Bryne JC, Hupponen T, Mowbray D & Vriend G (2009) An active registry for bioinformatics Web services. Bioinformatics, 25, 2090-2091
• 5. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res., 37, D211-5.

• Bioinformatics
• Biomolecular Sciences
• Structural Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The human protein TSG-6 is secreted by many cell types (including mesenchymal stem cells) in response to inflammation and has been detected in the context of diseases such as arthritis (see [1]). TSG-6 has been shown to limit inflammation and tissue damage when it is administered to mice with inflammatory arthritis (see [1]) and when it is secreted by stem cells during the treatment of myocardial infarction [2]. We have shown recently that neutrophils store TSG-6 protein in granules and release it in response to inflammatory stimuli [3], indicating that it is an endogenous regulator of inflammation. We have also shown that TSG-6 is involved in regulating the balance between the formation and breakdown of bone and that it can inhibit bone erosion by osteoclasts during inflammation [4]. These properties of TSG-6 might be beneficial in the development of new drugs, e.g. for the treatment of bone diseases.

This project will form part of ongoing work to understand the mechanisms that underlie the anti-inflammatory and tissue-protective effects of TSG-6. In particular it will focus on the molecular interactions that are responsible for the effects of TSG-6 on bone erosion. A combination of site-directed mutagenesis and interaction analyses, coupled with structural and biophysical methods, will be used in addition to protein expression and functional characterisation.
 

[1] Milner, C.M. & Day, A.J. TSG-6: a multifunctional protein associated with inflammation. (2003) J. Cell Sci. 116: 1863-1873.
[2] Lee, R.H., Pulin, A.A., Seo, M.J., Kota, D.J., Ylostalo, J. Larson, B.L., Semprun-Prieto, L., Delafontaine, P. & Prockop, D.J. Intravenous hMSCs improve myocardial infarction in mice because cells embolized in the lung are activated to secrete the anti-inflammatory protein TSG-6. (2009) Cell Stem Cell 5: 54-63.
[3] Maina, V., Cotena, A., Doni, A., Nebuloni, M., Pasqualini, F., Milner, C.M., Day, A.J., Mantovani, A. & Garlanda, C. Co-regulation in leukocytes of the long pentraxin PTX3 and TSG-6, two co-operating molecules involved in the assembly of hyaluronan-rich extracellular matrices. (2009) J. Leukocyte Biology 86:123-132.
[4] Mahoney, D.J., Mikecz, K., Ali, T., Mabilleau, G., Benayahu, D., Plaas, A., Milner, C.M., Day, A.J. & Sabokbar, A. TSG-6 regulates bone remodeling through inhibition of osteoblastogenesis and osteoclast activation. (2008) J. Biol. Chem. 283: 25952-25962.
 

• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Cell Matrix Research
• Immunology
• Molecular Biology
• Stem Cell Research
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The aim of the study is to investigate the organization of ion channels in the membranes of excitable cells by scaffold proteins, and to discover how the properties of the channels are modified by these interactions. The work will encompass major structural and proteomic techniques as well as techniques relevant to biotechnology including biochemical assays, protein over-expression and purification, liquid chromatography and reconstitution. The studentship will therefore use computational and structural biology techniques to investigate the molecular architecture involved in the generation of electrical signals across neuronal membranes.

• Biochemistry
• Bioinformatics
• Biomolecular Sciences
• Biotechnology
• Channels & Transports
• Membrane Trafficking
• Molecular & Cellular Neuroscience
• Molecular Biology
• Neuroscience
• Structural Biology
• Systems Neuroscience

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The human immunodeficiency virus type 1 (HIV-1) interacts with 100s of specific proteins of the host
system to use its cellular machinery in order to replicate. A comprehensive database of HIV-1-tohuman
protein interactions was created recently, comprising over 2500 unique HIV-1-to-human
molecular interactions. So far, however, the HIV-1-to-human protein interaction system has been
analysed as a static network only, with no attempt to integrate temporal and spatial aspects. The aim
of this project is to apply a dynamic model to HIV-1 infection. Logical models are powerful tools to
predict the dynamics of complex biological systems when detailed kinetic parameters are unavailable
or prohibitively difficult to determine experimentally. In a logical model, nodes (proteins) are
connected by edges, which describe the nature of the action occurring between two proteins. Typical
examples of actions are activation, inhibition, binding, catalysis, etc. The model will be used to
simulate different scenarios of perturbations of the host system by viral proteins, in order to better
understand the mechanisms used by the virus to hijack the cellular machinery. The project will involve
training in computational, molecular and systems biology.

• Klamt S, Rodriguez JS and Gilles E (2007) Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology, 1:2.
•  MacPherson JI, Dickerson JE, Pinney JW and Robertson DL (2010) Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PLoS Computational Biology, 6:e1000863.
• Pinney JW, Dickerson JE, Fu W, Sanders-Beer BE, Ptak RG and Robertson DL (2009) HIV-host interactions: a map of viral perturbation of the host system. AIDS, 23:549-554.
• Ptak RG, Fu W, Sanders-Beer BE, Dickerson JE, Pinney JW, Robertson DL, Rozanov MN, Katz KS, Maglott DR, Pruitt KD and Dieffenbach CW (2008) Cataloguing the HIV-Human Protein Interaction Network. AIDS Research and Human Retroviruses, 24:1-6.
• •Schwartz JM and Nacher JC (2009) Local and global modes of drug action in biochemical networks. BMC Chem Biol 9:4.

• Bioinformatics
• Biomolecular Sciences
• Cell Biology
• Genetics
• Immunology
• Microbiology
• Molecular Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

It is known that the use of post-translational modification (PTM) to modulate protein activity is widespread. Improvements in the detection and quantification of PTMs, coupled with genome sequence data, are supplying data in this area faster than can be analysed experimentally on a case by case basis. Taking phosphorylation as a key exemplar PTM, computational approaches are also contributing, helping to give a general picture of kinase specificities and of the properties of target regions. For example, the vast majority of phosphorylation lies outside of (3D) folded regions. This leaves the question: What are the molecular mechanisms by which phosphorylation mediates biological activity? Where a folded region is the target, then a change in conformation and/or binding preferences can often be inferred [1]. This is also the case for linear stretches that bind to specific domains, such as peptides containing phosphorylated tyrosine binding to SH2 domains. However, the accumulated substrate data (e.g. see Phospho.ELM [2]), are much more widespread. An obvious association with phosphorylation is the addition of negative charge, and although modulation of net charge is believed to be a key factor in many cases, there exists no model for predicting such effects. This computational project will address that deficit, through bioinformatics analysis tied to physical chemistry. Bioinformatics will tell us about similarities in the properties of substrates and how they associate with biological and molecular function, whilst physical chemistry provides the tools to develop models based on the delicate charge balances that mediate structure and interactions.

1. Charge environments around phosphorylation sites in proteins. Kitchen J, Saunders RE and Warwicker J (2008) BMC Struct Biol 8:19.
2. Phospho.ELM: a database of phosphorylation sites – update 2008. Diella F, Gould CM, Chica C, Via A and Gibson TJ (2008) Nucl Acids Res36:D240-D244.
 

• Biochemistry
• Bioinformatics
• Biomolecular Sciences
• Biotechnology
• Cell Biology
• Structural Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Collagens are the main proteins of structural tissues such as bone, skin, cartilage or blood vessel walls. Collagens are fibrous proteins characterised by a unique triple helical conformation (the collagen triple helix), which is essential for their cable-like properties. Collagens organise the specialised extracellular matrices to which cells adhere to form different tissues through specific interactions with cell-surface receptors and other extracellular matrix molecules. The cell-collagen interaction sends intracellular signals that impact cell survival, migration, or division. Thus, collagen-based biomaterials are extremely important for tissue engineering and regenerative medicine.
Collagen is typically extracted from animal sources. However, increasing concerns about risks of disease transmission plus ethical, environmental and personal choice considerations, make a strong case for the invention of recombinant methods of collagen biosynthesis. We have made progress towards such technologies in our laboratory, and we can produce recombinant collagens capable of sustaining adhesion of human cells in a controlled and reproducible manner.
The aim of the current project is to optimise these recombinant collagens for use as tissue engineering scaffold materials by improving their thermal stability and its balance with biodegradability, and by enhancing their cell-adhesion characteristics. Techniques will include cell culture and transfection, protein expression and purification, biophysical characterisation, electron microscopy, and light microscopy.
 

• Biochemistry
• Biomolecular Sciences
• Biotechnology
• Cell Matrix Research
• Molecular Biology
• Pharmacology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Glycosaminoglycans are ubiquitous in mammalian extracellular matrices, but their structural organisation at the molecular level is enigmatic; this is hindering progress toward understanding tissue, diseases such as arthritis and neurodegeneration, and also novel biotechnology and pharmaceuticals. To address this, we are developing new techniques for studying hyaluronan, and heparin, chondroitin and dermatan sulphate from the micro- to the macroscopic length-scales. We use a range of computational modelling (e.g., molecular dynamics, coarse-graining, quantum calculations) and experimental techniques (e.g., NMR, bacterial cell-culture, Raman spectroscopy, light scattering). Our aim is to both develop technologies that are capable of deducing the spatial organisation of glycosaminoglycans (in a range of environments, e.g., free, bound to protein and in proteoglycans) and use them to investigate specific biological situations, disease states or in the development of novel biomaterials and pharmaceuticals. A range of PhD projects can be accommodated from exclusively computer-based to lab-based, or a combination. The work is interdisciplinary and students can receive training in a broad range of computational, biophysical and biochemical methods in a world-leading carbohydrate research group.

Students with backgrounds in biochemistry, physics, chemistry, or related areas are welcome to apply.
 

• Sattelle BM, Shakeri J, Roberts IS, Almond A. (2010). A 3D-structural model of unsulfated chondroitin from high-field NMR: 4-sulfation has little effect on backbone conformation.Carbohydrate Research, 345, 291 302. Full text doi:doi:10.1016/j.carres.2009.11.013
• Yaffe NR, Almond A, Blanch EW. (2010). A new route to carbohydrate secondary and tertiary structure using Raman spectroscopy and Raman optical activity. Journal of the American Chemical Society, 132, 10654-10655. Full text doi:10.1021/ja104077n
• Sattelle BM, Hansen SU, Gardner, J, Almond A. (2010). Free energy landscapes of iduronic acid and related monosaccharides. Journal of the American Chemical Society, in press. Full text doi:10.1021/ja1054143
• Almond A, DeAngelis PL, Blundell CD. (2006). Hyaluronan: the local solution conformation determined by NMR and computer modelling is close to a contracted left-handed four-fold helix. Journal of Molecular Biology, 358, 1256-1269. Full text doi:10.1016/j.jmb.2006.02.077
 

Biochemistry

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The greatest impediment to producing effective treatments for HIV is the high rate of viral evolution. HIV’s rapid evolution represents a significant challenge for all types of HIV therapy, including drug therapy and vaccine design.

Although the degree of sequence diversity is extremely high, it is not without limit. In particular mutations have the potential to disrupt the protein structure and so can have a negative effect on the structural integrity, and therefore function, of any of HIV’s constituent molecules. Fortunately, the likely effect of a given substitution can be predicted from the known characteristics of the structure and the particular side chain substituted. We therefore aim to predict whether a given evolutionary trajectory is viable or not, and so predict the likely evolution path of HIV. This will be done using computational models of protein evolution and protein structure.
 

Bioinformatics

Biomolecular Sciences

Evolutionary Biology

Molecular Biology

Structural Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

We are developing novel fast reaction methods to study biological electron transfer reactions. Our aim is to study the role of protein conformational dynamics and ligand exchange in controlling rates of electron transfer in enzymes of biomedical relevance. We have established programmes on mammalian nitric oxide synthases, methionine synthase and methionine synthase reductase, cytochrome P450 reductase and related proteins. Using mutagenesis, structural biology and fast reaction methods we aim to identify regulatory mechanisms for electron transfer reactions in these key model protein systems. The work is interdisciplinary and students will receive training in a broad range of biophysical, molecular biology and biochemical methods in a large group focused on understanding the structures, mechanisms and dynamic properties of redox enzymes.

Students with backgrounds in biochemistry, biophysics, chemistry, (bio)physical chemistry, or related areas are welcome to apply.

• Conformational and thermodynamic control of electron transfer in neuronal nitric oxide synthase (2007). Dunford, A. J., Rigby, S. E. J., Hay, S., Munro, A. W. & Scrutton, N. S. Biochemistry. In press
• Laser photoexcitation of NAD(P)H induces reduction of P450 BM3 heme domain in the microsecond time domain (2007). Girvan, H.M., Heyes, D.J., Scrutton, N.S. & Munro, A.W. J. Am. Chem. Soc. In press
• Protein interactions in the human methionine synthase—methionine synthase reductase complex and implications for the mechanism of enzyme reactivation (2007). Wolthers, K. R. & Scrutton, N. S. Biochemistry In press

• Biomolecular Sciences

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Notch receptors are transmembrane glycoproteins that are of fundamental importance in multiple cell-fate decisions, such as occur during stem cell maintenance and cell differentiation. Notch receptors interact with membrane-tethered ligands (Delta, Serrate, Jagged) presented on neighbouring cells, resulting in downstream events that lead to control over the receiving cell’s differentiation programme. Dysregulation of Notch has been implicated in a myriad of disease states, including cancers. To achieve a signal, the Notch receptor must undergo three proteolytic cleavage events that enable release of the Notch intracellular domain into the cytosol, whereupon it translocates to the nucleus to act as a transcription factor. The second proteolytic cleavage, at a site ‘S2’, is key to Notch activation, triggered by ligand binding. This S2 site is housed with a part of the Notch extracellular domain called the Notch Regulatory Region (NRR). A crystal structure of the NRR reveals that the S2 site is normally buried and that Notch is thus autoinhibited. This S2 site needs to be unmasked to activate Notch. We explore the hypothesis that ligand binds to the extracellular domain of Notch and then exerts sufficient force (upon its endocytosis) to cause exposure of the S2 site through conformational change. Mechanical force has indeed emerged as a factor driving a number of cell processes.

Bridging physics and biology disciplines, we will measure the degree of force required to induce structural changes in the NRR to facilitate protease cleavage, and compare these to the forces that are actually exerted during ligand endocytosis. Using force microscopy on recombinant NRR, we have already demonstrated unfolding of protein domains. This PhD will continue the single molecule work, using AFM to establish whether mechanical unfolding does increase protease susceptibility at the S2 site. The work will extend to analysis of Notch mechanical unfolding and activation on live cells, ideally followed by detection of signalling in the nucleus (new method development). Furthermore, the student will initiate experiments aimed at measuring the force exerted on the Serrate ligand upon its endocytosis, in order to correlate this force with that recorded as sufficient to unravel Notch to expose the S2 site. Such an investigation of endocytic force is unprecedented and will involve both AFM and laser tweezer experimentation.
At the end of the PhD, the intended outcomes are to have proven mechanotransduction of the Notch signal, induced by ligand binding, and to thus provide new insight that could in turn lead to new routes to targeting Notch in anti-cancer (or other Notch-related disease) therapy. Indeed, scope for successful targeting of Notch proteolytic processing at a third (S3) site has recently been demonstrated; inhibitors of S3 (?-secretase) cleavage having reached phase II clinical trials. The skills training will encompass molecular biology, protein expression in bacteria and eukaryotic systems, cell culture, protein chemistry, atomic force microscopy, optical trapping (laser tweezers), spectroscopy and microscopy. Hence, multidisciplinary training is a key feature of the project, supported by the supervisory team.
 

• Hansson EM, Lendahl U, Chapman G (2004) Notch signaling in development and disease . Semin Cancer Biol. 14:, 320-8.
• Chen J, Zolkiewska A (2011) Force-induced unfolding simulations of the human Notch1 negative regulatory region: possible roles of the heterodimerization domain in mechanosensing. PLoS One 6: e22837.
• Gordon WR, Vardar-Ulu D, Histen G, Sanchez-Irizarry C, Aster JC, Blacklow SC. (2007) Structural basis for autoinhibition of Notch . Nat Struct Mol Biol. 14:, 295-300.
• Malecki MJ, Sanchez-Irizarry C, Mitchell JL, Histen G, Xu ML, Aster JC, Blacklow SC. (2006) Leukemia-associated mutations within the NOTCH1 heterodimerization domain fall into at least two distinct mechanistic classes. Mol Cell Biol. 26:, 4642-51.
• Vogel V (2006) Mechanotransduction involving multimodular proteins: converting force into biochemical signals. Annu. Rev Biophys Biomol Struct 35:, 459-488

• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Developmental Biology
• Molecular Biology
• Molecular Cancer Studies
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

In recent years there has been much research on the identification of mutations associated with cancer (Stratton at al., 2009). This includes both mutations that are heritable and predispose an individual to cancer, and those that are at the level of a single cell and so contribute to the emergence of a cancerous lineage. The locations of both types of mutations (heritable and somatic) permit the identification of the proteins and functions associated with cancer.

In this project we propose to use an existing database of mutations associated with cancer (http://www.sanger.ac.uk/genetics/CGP/cosmic/) to identify shared properties of cancer-associated proteins. These will include their essentiality, post-translational modifications, length, biophysical properties, number of subunits, position in the human interaction network, number of protein-protein interactions, whether they are duplicated, level of conservation and expression levels. Proteins associated with both heritable and somatic mutations will be compared to each other and to proteins not known to be involved in cancer. The features will be used for input into machine learning methods which will determine an optimal way to separate the protein classes using their properties. This will allow the assignment of any protein as cancer-associated or not. Using these models, we will be able predict novel proteins not identified to-date as having a role in cancer, after running the entire human proteome, with verification by comparing to the recent literature on new cancer proteins. This work will follow our existing methodology for studying drug target proteins (Bakheet & Doig, 2009), but will use an entirely different data set (i.e. cancer proteins).

Ultimately the project will contribute to our understanding of the properties of proteins that are associated with progression to cancer. This will permit the identification of proteins previously not found to be associated with cancer and, thus, new potential drug targets.
 

TM, Doig AJ. (2009) Properties and Identification of Human Protein Drug Targets. Bioinformatics; 25: 451-457.

Stratton MR, Campbell PJ, Futreal PA. (2009) The cancer genome. Nature;458(7239):719-24.
 

Biochemistry
Bioinformatics
Biomolecular Sciences
Biotechnology
Molecular Cancer Studies
 

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Therapeutic proteins are biological drugs, such as antibodies, hormones, enzymes, synthetic peptides, toxins and cytokines. There are currently over 100 therapeutic proteins in use in humans, with most introduced in the last decade. Their main applications are for imaging and diagnosis, blood coagulation, fertility, hormone replacement, enzyme replacement, cancer or immunomodulation. Features which complicate the use of therapeutic proteins include protein aggregation, immunogenicity and cleavage by proteases, which can lead to a decrease in efficacy and/or increased toxicity. Despite this, therapeutic proteins have a better success rate in drug development than small molecule drugs. Most are human, synthetic or human chimeras which helps minimise unwanted immunogenicity.

In this project we will survey known therapeutic proteins to identify their shared properties. These will include essentiality and location in biochemical pathways, post-translational modifications, biophysical properties, protein structure, number of subunits, protein-protein interactions, whether they are duplicated, level of conservation, immunogenicity and expression levels, amongst others. Therapeutic proteins are frequently modified to improve their behaviour. We will therefore compare modified, unmodified and non-therapeutic proteins. This work will give rules for the identification and design of new therapeutic proteins.

The most important features that we discover will be used for input into machine learning methods, such as random forests or support vector machines, which will determine the optimal way to distinguish therapeutic from non-therapeutic proteins. This will allow the prediction of new potential therapeutic proteins, after running the entire human proteome, with verification by comparing to the recent literature on new therapeutic proteins. This entirely computational project will follow our existing methodology for studying drug target proteins (Bakheet & Doig, 2009; Bakheet & Doig, 2010), but will use an entirely different data set.
 

Bakheet TM, Doig AJ. (2009) Properties and Identification of Human Protein Drug Targets. Bioinformatics; 25: 451-457.

Bakheet, TM, Doig, AJ. (2010). Properties and identification of antibiotic drug targets. BMC Bioinformatics, 11, 195-204.
 

• Biochemistry
• Bioinformatics
• Biomolecular Sciences
• Biotechnology
• Immunology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

High protein concentration and long-term stability are required for numerous applications, including biotechnology, structural and biochemical studies, as well as manufacturing of pharmaceutical and therapeutic liquid preparations such as antibodies and vaccines. Amino acids always surround proteins in their natural environment in vivo, and they are often used to stabilise and solubilise proteins in vitro. The effect of addition of separate amino acids on proteins in vitro has been fairly well characterised [1], however recently we have discovered that simultaneous addition of several amino acids (such as arginine and glutamate) has much more dramatic effect than when amino acids are added separately [2]. The mechanism of such amino acid cooperativity is currently poorly understood. In a real cellular environment the proteins are surrounded by the complex mixtures of co-solutes. The cooperative effect of various solution components thus becomes extremely important for our understanding of how proteins function in vivo. Moreover, new and improved protein-stabilising formulations are sought after by a pharmaceutical industry. Future applications of cooperative amino acid additives also include stabilization of protein-based machines for nanotechnology and synthetic biology. The current project is going to explore the effect of simultaneous addition of several amino acids and osmolytes on the structural, thermodynamic and aggregation properties of proteins and protein assemblies. This project will benefit a bright, thorough and dedicated student with a background in Chemistry, Physics or Physical Chemistry. The work will be conducted in the Manchester Interdisciplinary Biocentre (http://www.mib.manchester.ac.uk/) which currently brings together experts in different areas of Biochemistry, Structural Biology, Enzymology, Physics, Material Science and Chemistry.

1. Arakawa, T., Tsumoto, K., Kita, Y., Chang, B., Ejima, D. Biotechnology applications of amino acids in protein purification and formulations (2007) Amino Acids, 33:587-605
2. Golovanov, A. P., Hautbergue, G. M., Wilson, S. A., Lian, L.-Y. A simple method for improving protein solubility and long-term stability (2004) J. Am. Chem. Soc., 126:8933-8939.
    

• Biomolecular Science
• Biotechnology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The deployment of a battery of orthogonal techniques to a structural problem is the only way to completely describe a complex biomolecule. The project aims to develop integrative methods for the optimal combination of data from scattering and microscopy techniques, with limiting conditions provided by spectroscopy, to develop a coherent image of a protein or complex. In this way ordered and folded domains can be combined with natively disordered regions and placed in the context of a flexible protein, or large macromolecular assemblies can be constructed from high-resolution components in a stepwise fashion.

The project will allow the development of data analysis skills from diverse techniques such as crystallography, small angle scattering, mass spectrometry, and electron microscopy with computational bioinformatics and modelling. The techniques developed will make use of and build upon existing software in the relevant disciplines.
 

• Biochemistry
• Bioinformatics
• Biomolecular Sciences
• Structural Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Mitochondria are essential organelle playing a central role in many biological processes. For example, mitochondria perform a central task in the biogenesis of all cellular iron–sulfur (Fe-S) proteins. Not only mitochondrial Fe-S proteins, all cytosolic and nuclear Fe-S protein maturation depends strictly on the function of the mitochondrial Fe-S cluster assembly and export machineries. However, little is known about how a ‘Fe/S’ cluster is exported from mitochondrial matrix to the cytosol is unknown. Evidence suggests that Erv1, an essential component of the MIA pathway is not only required for protein import into mitochondria, but also involved in export of ‘Fe/S’ from mitochondria. Our preliminary study suggests that Mia40 may be able to bind a Fe-S cluster as well. This PhD project will investigate the correlation between Mia40/Erv1 function and biogenesis of cellular iron–sulfur proteins. A wide range of biological, biochemical, and biophysical methods will be used to address the issue comprehensively. The project will be co-supervised and carried out in well equipped labs in the Manchester Multidisciplinary Biocentre. This study will provide important insights into mitochondrial function that are inextricably linked to many human diseases and ageing process.

Lill R. (2009) Function and biogenesis of iron-sulphur proteins. Nature 460:831-8 (Review) 

Lange H. et al. (2001) An essential function of the mitochondrial sulfhydryl oxidase Erv1p/ALR in the maturation of cytosolic Fe/S proteins. EMBO Rep. 2:715-20. 

Ang, SK. & Lu, H (2009). Deciphering structural and functional roles of individual disulfide bonds of the mitochondrial sulfhydryl oxidase Erv1p. The Journal of biological chemistry, 284: 28754-61.

Biochemistry

Biomolecular Sciences

Biotechnology

Cell Biology

Molecular Biology

Organelle Function

Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Changing climates, due to emissions of CO2 result not simply in an increase in temperature but, more importantly to an increased unpredictability of climates, with heat waves, droughts and floods all becoming more frequent. Even relatively short periods of extreme weather at crucial phases in a plant’s lifecycle can have dramatic effects on final yield and there is an urgent need to develop crops with a greater tolerance of environmental stress.

Regardless of the source of stress, exposure to environmental conditions outside a plant’s normal tolerance range will result in the formation of highly damaging reactive oxygen species (ROS) and the major source of these is the electron transport chain in the chloroplast involved in photosynthesis. We have been examining how this chain can be regulated to avoid ROS production under stress conditions and have identified a number of regulatory processes that interact to control the flow of electrons and avoid oxidative damage. In particular we have identified a novel feedback control whereby if NADPH is produced at a faster rate than it is consumed, it regulates proteins in the thylakoid membrane to limit its own production. We have shown that this regulation plays a crucial role in preventing ROS production when photosynthesis is limited.

In this project you will examine the molecular basis for feedback control of electron transport by NADPH. Using mutants of Arabidopsis thaliana and tobacco, you will investigate possible mechanisms for this regulation. You will receive training in the application of advanced spectroscopic techniques to whole leaves. As the project develops you will also gain experience of protein biochemistry and mass spectrometry, identifying proteins and complexes involved in the regulation.
 

Hald S., Nandha B., Gallois P. and Johnson G.N. (2008) Feedback regulation of photosynthetic electron transport by NADP(H) redox poise. Biochimica et Biophysica Acta 1777 433-440
Nandha B., Finazzi G., Joliot P., Hald S. and Johnson G.N. (2007) The role of PGR5 in the redox poising of photosynthetic electron transport. Biochimica et Biophysica Acta 1767, 1252-1259
 

• Adaptive Organismal Biology
• Biochemistry
• Biotechnology
• Cell Biology
• Environmental Biology
• Gene Expression
• Plant Sciences

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The research in my laboratory is focused on understanding the role of protein tyrosine phosphatases (PTPs) in the regulation of cell signalling pathways (eg. MAPK signalling). PTPs are essential enzymes in controlling a myriad of cellular events involved in cell proliferation and growth, cell adhesion and communication. Recently a number of PTPs have been reported to act as oncogenes in many cancer types. Likewise, PTPs are emerging as unique targets against infectious diseases (tuberculosis, trypanosomiasis..etc) because of their roles in virulence and subversion of the host signalling pathways. To understand their diverse functional roles it is essential that we learn the molecular basis for their specific substrate recognition and targeting, which can then be exploited in the design and development of specific inhibitory compounds. Our pioneering work on the characterization of PTPs from parasites and bacterial pathogens has resulted in significant publications and lead to collaborative links with laboratories worldwide to develop specific inhibitors against infectious diseases.

My laboratory offers training and expertise in a number of techniques including biochemical/biophysical techniques: (enzyme kinetics, CD, LS, Analytical AUC, ITC), structural techniques (SAXS, X-ray crystallography) and computational/postgenomic science (Fingerprinting, BioOntologies). We also provide excellent research environment with international collaborations and we host a training node for Bioinformatics and Structural Biology of the EU-FP6 funded Marie Curie Training network of protein tyrosine phosphatases (PTPNET).
 

• Beresford NJ, Mulhearn D, Szczepankiewicz B, Liu G, Johnson ME, Fordham-Skelton A, Abad-Zapatero C, Cavet JS, Tabernero L. Inhibition of MptpB phosphatase from Mycobacterium tuberculosis impairs mycobacterial survival in macrophages. J Antimicrob Chemother. 2009 Feb 24.
• Chu ML, Chavas LM, Douglas KT, Eyers PA, Tabernero L. Crystal structure of the catalytic domain of the mitotic checkpoint kinase Mps1 in complex with SP600125. J Biol Chem. 2008, 283, 21495-500.
• Tabernero, L., Aricescu, A. R., Jones, E. Y., Szedlacsek, S. The Structure-Function Relationship in Protein Tyrosine Phosphatases. (2008) FEBS Journal, 275, 867-82, Review.
• R. Brenchley, H. Tariq, H. McElhinney, B. Szoor, J. Huxley-Jones, R. Stevens, K. Matthews, L. Tabernero. The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains. (2007) BMC Genomics 8:434.
• N. Beresford, S. Patel, J. Armstrong, Balázs Szöor, T. Fordham-Skelton and Tabernero, L. MptpB, a virulence factor from Mycobacterium tuberculosis exhibits triple specificity phosphatase activity. (2007) Biochem J 406, 13-18.

• Biochemistry
• Bioinformatics
• Molecular Cancer Studies
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Tendons link muscle to bone and are therefore essential for normal skeletal function. Damage to tendons leads to severe disability, and is a huge socio-economic burden. There is an urgent need to develop therapies to treat and repair tendon injuries. We have shown that human marrow stromal cells/mesenchymal stem cells (hMSCs) generate tendon tissue in culture. During tendon formation in vitro, the cells transcriptionally upregulate integrin ß5, 6 and 8, as well as TGF?3, in response to uniaxial tension in a 3D matrix environment [1,2]. Importantly, inhibition of TGFß3 binding to its cognate receptor, TGFBR2, results in the absence of phosphorylated Smad2 and the absence of a tendon tissue. It is important to understand the mechanism of hMSC-tendon induction so that we can induce endogenous cells to effect repair and to build ex vivo tendons for regenerative medicine. The aims of the project are:
1. To identify which integrin is important in activating TGFß3? Our candidates are integrin ß5, 6 or 8. We aim to knockdown each integrin using siRNA and assay TGFß3 signalling and tendon formation.
2. To identify the levels of tension needed for TGFß3 signalling and integrin engagement. We have developed an inline tensiometer that works in cell culture to measure tissue tension. We will measure TGFß3 signalling over a range of tissue tensions.

Techniques that will be learned include: molecular biology, stem cell biology, immunofluorescence, cell culture and biochemistry.
 

1. Kapacee Z, Yeung CY, Lu Y, Crabtree D, Holmes DF, et al. (2010) Synthesis of embryonic tendon-like tissue by human marrow stromal/mesenchymal stem cells requires a three-dimensional environment and transforming growth factor beta3. Matrix Biol in press.

2. Kapacee Z, Richardson SH, Lu Y, Starborg T, Holmes DF, et al. (2008) Tension is required for fibripositor formation. Matrix Biol 27: 371-375.

• Biochemistry
• Cell Biology
• Cell Matrix Research
• Stem Cell Research
• Structural Biology
• Developmental Biology
   

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Salinization of soils is a growing problem worldwide, with large areas of previously productive agricultural land being lost every year. We urgently need to develop crops with increased salt tolerance. By examining processes in natural salt tolerant species, we will be able to identify traits that give rise to salt stress tolerance

Recently, we examined the salt tolerant species Thellungiella halophila and identified a protein in the chloroplast that we believe confers tolerance not only to salt conditions but to environmental stress in general. The protein is called the plastid terminal oxidase (Ptox) and catalyses the reduction of oxygen to produce water. It is thought that this allows it to act as a “safety valve” for photosynthesis under stress conditions, protecting plants from environmental stress by preventing the formation of highly damaging reactive oxygen species.

In this project you will isolate and characterise this previously poorly described protein. You will receive training in biochemical approaches to protein purification and identify novel subunits of the Ptox. Depending on your interests and the progress in the project, you will then seek to characterise the protein structurally and functionally using different spectroscopic techniques and to use molecular biology approaches to alter expression of the protein to determine more clearly its function in stress tolerance.
 

Stepien P. and Johnson G.N. (2009) Contrasting responses of photosynthesis to salt stress in the glycophyte Arabidopsis thaliana and the halophyte Thellungiella halophila. Role of the plastid terminal oxidase as an alternative electron sink. Plant Physiology 149, 1154-1165

• Adaptive Organismal Biology
• Biochemistry
• Biotechnology
• Cell Biology
• Environmental Biology
• Gene Expression
• Plant Sciences

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Structural studies greatly enhance our understanding of molecular function and mechanisms. We have been studying the molecular mechanisms of protein synthesis and its control in eukaryotic cells. Protein synthesis is a multistep process that relies on a dynamic series of protein-protein and protein-RNA interactions necessary to assemble ribosomes, factors, tRNAs and mRNA. This project will use recombinant protein expression systems to purify specific protein complexes and then use electron microscopy techniques to obtain images to gain insight into the structures of these molecules that are critical for protein synthesis and its control and which are important for human health and disease. For example, mutations in eIF2B cause a genetically inherited brain disease, while regulation of eIF2B activity is critical for a wide variety of cues, including: nutritional responses, stress, fighting viral infections, and long-term memory.

Protein complexes and co-complexes will be generated by purification from yeast cells engineered to overexpress the target proteins. Samples will be prepared by a combination of the negative stain and cryo techniques, and images collected on the transmission electron microscope. Structures of the complexes will be reconstructed in three dimensions.

Analysis of the complex and co-complexes will provide new information to assign the positions of subunits and build a 3D model. Where possible, models of individual subunits/domains generated from Xray crystallography and/or homology modelling will be fitted by density docking into the three dimensional EM maps. Known disease state mutations will then be mapped onto the structures. These experiments will allow deeper understanding and provide insight into the structure/functions of these factors and guide future functional experimentation.
 

• Martin D. Jennings and Graham D. Pavitt. (2010). eIF5 has GDI activity necessary for translational control by eIF2 phosphorylation. Nature, 465(7296), 378-381.
• Pavitt GD, Proud CG. (2009). Protein synthesis and its control in neuronal cells with a focus on vanishing white matter disease. Biochem Society Transactions, 37, 1298-1310.
• Mohammad-Qureshi SS, Haddad R, Hemingway EJ, Richardson JP, and Pavitt GD (2007) Critical contacts between the eukaryotic initiation factor 2B (eIF2B) catalytic domain and both eIF2beta and 2gamma mediate guanine nucleotide exchange. Molecular and Cellular Biology 27(14): 5225-34.
• Roseman, A.M., Berriman, J.A., Wynne, S.A., Butler, P.J.G. & Crowther R.A. (2005). A structural model for hepatitis B virus core maturation. Proc. Natl. Acad. Sci. USA 44, 15821-15826.
• Roseman, A.M., Chen, S., White, H., Braig, K. & Saibil, H.R. (1996). The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL. Cell 87, 241-251.

• Biochemistry
• Biomolecular Sciences
• Gene Expression
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Ribonucleic acids (RNA) perform a wide range of functions in living systems and are the focus of intense research around the world. As with proteins, the most direct approach to determining how RNAs function is to solve the structure-function paradigm; how does RNA structure regulate RNA function? However, far fewer RNA structures have been reported than for proteins as X-ray crystallography and NMR spectroscopy are often difficult to apply to RNAs. There is an urgent requirement for new techniques to probe both RNA structure and the conformational changes that govern their roles in transcription, signalling, structural roles etc. The student working on this biotechnology project will help to develop several laser-based techniques for structural analysis of RNAs in solution; Raman spectroscopy, Raman optical activity (ROA) and surface enhanced Raman (SERS).

Initial studies will involve spectral analysis of RNA bases to establish spectral marker bands for common RNA components and cancer-linked modifications, with following studies focusing on physiologically related structural changes of the dsRNA-regulated protein kinase, a key drug target for cellular and viral proteins and non-coding RNAs. The project involves collaboration with Dr Graeme Conn at Emory Medical School in Atlanta, USA, and the student will be expected to spend some time there to learn RNA preparation and handling techniques.
 

• Hobro, A.J., Rouhi, M., Blanch, E.W. and G.L. Conn, “Raman and Raman Optical Activity (ROA) Analysis of RNA Structural Motifs in Domain I of the EMCV IRES”, Nucleic Acids Research (2007) 35, 1169-1177.

• Biochemistry
• Biomolecular Sciences
• Microbiology
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

PhD projects on a number of classes of prokaryotic membrane proteins are available. These include (i) Ligand and Glutamate gated ion channels – homologues of ionotrophic synaptic receptors; (ii) Adenosine tri-phosphate binding cassette transporters involved in ion uptake or export in bacteria; (iii) Mechano-sensitive channels from Gram negative bacteria, and (iv) Structural studies on a Magnesium ion channel from archaeobacteria.
Up to 30% of the genome of any given organism codes for integral membrane proteins, and over 50% of pharmacological targets are membrane proteins. Recent developments in the use of protein over-expression systems have overcome the restrictions imposed by membrane protein scarcity. Recombinant technology can therefore be combined with structural biology to address membrane protein biology, revealing functionally relevant information on this important class of proteins.In addition to training in structural biology, membrane protein production and functional assays, these projects will provide opportunities for work relevant to comparative computational biology (i and iv) and novel antibiotic targeting of disease causing opportunistic pathogens (ii and iii).
 

• Biochemistry
• Bioinformatics
• Biomolecular Sciences
• Biotechnology
• Channels & Transports
• Microbiology
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

This project will be jointly supervised by Philip Woodman (Lead Supervisor), Lydia Tabernero and Stuart Pickering-Brown

Many neurodegenerative diseases are linked to defects in ubiquitin homeostasis/protein folding and/or endosomal trafficking. We have recently identified that UBAP1, a novel risk factor for frontotemporal lobar degeneration (FTLD) (1), is a component of the Endosomal Sorting Complex Required for Transport (ESCRT) pathway (2). This pathway is a series of ubiquitin-recognising protein complexes (ESCRTs 0-III) that orchestrate the sorting of endocytosed signalling receptors to the multivesicular body (MVB), a key transport stage on the lysosomal, degradative pathway (3).

We have shown that UBAP1 is a component of the ESCRT-I complex. ESCRT-I has been shown to perform several cellular roles in addition to endosomal sorting, and this diversity may be linked to the existence of isoforms for several ESCRT-I components. Importantly, we have found that UBAP1 is an isoform of one of these ESCRT-I subunits, and defines the population of ESCRT-I that acts at the endosome (2). UBAP1 is a multidomain protein. It has a tandem C-terminal UBA domain that binds ubiquitin, and a central domain that binds His Domain Protein Tyrosine Phosphatase (HDPTP), a regulator of ESCRT-dependent MVB sorting that we have recently identified (4). It also has an N-terminal region responsible for incorporating UBAP1 into the endosome-specific ESCRT-I complex. Hence, UBAP1 has a central position in organising the MVB sorting of ubiquitinated receptors. Although UBAP1 mutations are linked to FTLD, UBAP1 itself is ubiquitously expressed, and we have shown it is essential for EGF receptor trafficking to the MVB and lysosome (2). We will therefore be able to undertake a detailed structure-function analysis of UBAP1 and understand how it interacts with ESCRT-I and HDPTP. These studies will bring insight into the mechanism of action of UBAP1 and provide clues about how FTLD-associated mutations affect UBAP1 function.

1. Rollinson, S., Rizzu, P., Sikkink, S., Baker, M., Halliwell, N., Snowden, J., Traynor, B.J., Ruano, D., Cairns, N., Rohrer, J.D., et al. (2009). Ubiquitin associated protein 1 is a risk factor for frontotemporal lobar degeneration. Neurobiol Aging 30, 656-665.
2. Stefani, F., Zhang, L., Taylor, S., Donovan, J., Rollinson, S., Doyotte, A., Brownhill, K., Bennion, J., Pickering-Brown, S., and Woodman, P. (2011). UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting. Current Biology 21, 1245–1250.
3. Woodman, P. G., and Futter, C. E. (2008). Multivesicular bodies: co-ordinated progression to maturity. Curr. Opin. Cell Biol. 20, 408–414.
4. Doyotte, A., Mironov, A., McKenzie, E., and Woodman, P. (2008). The Bro1-related protein HD-PTP/PTPN23 is required for endosomal cargo sorting and multivesicular body morphogenesis. Proceedings of the National Academy of Sciences 105, 6308-6313.

Biochemistry
Biomolecular Sciences
Cell Biology
Membrane Trafficking
Molecular & Cellular Neuroscience
Molecular Biology
Organelle Function

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Neisseria meningitidis is the causative agent of meningococcal meningitis and a serious public health problem in developed and developing countries. The outer membrane proteins from N. meningitidis carry out a variety of functions for the bacterium, including transport of small molecule solutes and adhesion to host cell surfaces. They are also important to public health because they are potential vaccine components. This project seeks to determine the structures of these proteins by X-ray crystallography and/or NMR, and to understand how their functions are delivered at the molecular level. It will also examine how the outer membrane proteins interact with immune system molecules, such as antibodies, and how they recognize host cell surface receptors. The work will involve protein expression, purification, structural analysis by X-ray crystallography or NMR and analysis of ligand or protein binding. The studentship would suit a graduate in Biochemistry, Chemistry or a related discipline who wishes to apply their skills to the study of bacterial pathogenicity.

• Prince, S.M., Achtman, M. & Derrick, J.P. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 3417-3421. Crystal structure of the OpcA integral membrane adhesin from Neisseria meningitidis.
• Bond, P.J., Derrick, J.P. & Sansom, M.S.P. (2007) Biophys. J. 92, 23-25. Membrane Simulations of OpcA: Gating in the Loops?
• Bennett, J. S., Callaghan, M. J., Derrick, J. P. and Maiden, M. C. J. (2008) Microbiology 154, 1525-1534. Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.
• Cherezov, V., Liu, W., Derrick, J. P., Luan, B., Aksimentiev, A., Katritch, V. and Caffrey, M. (2008) Proteins 71, 24-34. In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin.

• Biochemistry
• Biomolecular Sciences
• Microbiology
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Whilst ~2% of the human genome encodes protein, >40% encodes RNA, of which the bulk are functional non-coding RNAs. New functions for ncRNA are continually emerging. Here, we study ncRNAs that are actually catalytic (ribozymes) and are also interesting form an evolutionary perspective. Eukaryotic RNase P and RNase MRP are two very similar ribonucleoprotein endonucleases involved in gene expression. Both catalyse RNA processing events; processing pre-tRNA and pre-rRNA, respectively, via cleavage at precise sites. In yeast, RNase P has one RNA subunit (369 nts) and 9 proteins. RNase MRP has one RNA (340 nts) and 10 protein subunits. The RNA subunit is responsible for catalysis by both endonucleases. The MRP RNA is only present in eukaryotes and nature appears to have adapted the P RNA through evolution to perform distinct functions. The catalytic role for the RNA raises the question: what do all the proteins do? In bacteria, only one protein assists the RNase P ribozyme. Why the increased complexity of the eukaryotic system? The proteins could adopt a number of roles including acting as cofactors in catalysis, aiding substrate recognition, directing nuclear localisation or interacting with other RNP particles involved in RNA processing. Eight of the protein subunits are present in both enzymes. Presumably the proteins unique to each enzyme are directly involved in directing the different activities of the two enzymes. The work will involve assembly of RNA-protein complexes, together with subunit mutagenesis and substrate RNA cleavage assays in order to attribute function to the protein assistants of these catalytic non-coding RNAs. The work is performed in vitro with recombinant subunits.

• Walker, S.C & Engelke, D,R. (2006) Ribonuclease P: the evolution of an ancient RNA enzyme. Crit Rev Biochem Mol Biol. 41: 77-102.
• Aspinall, T.V., Gordon, J.M.B., Bennett, H.J., Karahalios, P., Bukowski, J.-P, Walker, S.C. Engelke, D.R. & Avis, J.M. (2007) Interactions between subunits of Saccharomyces cerevisiae RNase MRP support a conserved eukaryotic RNase P/MRP architecture. Nucleic Acids Res. 35, 6439-50.
• Esakova O and Krasilnikov A (2010) Of proteins and RNA: The RNase P/MRP family.
• RNA Journal. Epub ahead of print. Access the most recent version at doi:10.1261/rna.2214510

• Biochemistry
• Biomolecular Sciences
• Gene Expression
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

We are developing novel experimental and theoretical methods to study the role of quantum mechanical entanglement and coherence during enzyme catalysis. It is well established that these phenomena play a key role during electronic energy transfer. We aim to identify and characterise other enzyme-catalysed reactions that exploit entanglement. Our current area of study is DNA replication, but other biological processes can be investigated as part of a PhD project. The work is interdisciplinary and students will have the option of using experimental and/or theoretical approaches during the project. Training in a broad range of experimental (biophysical, molecular biology and biochemical) and/or computational (numerical modelling, computational chemistry) methods will be offered. The research group is located in the Manchester Interdisciplinary Biocentre and is part of the Molecular Enzymology section.

Students with backgrounds in biophysics, chemistry, (bio)physical chemistry, biochemistry, or related areas are welcome to apply. For more information please contact Dr Sam Hay.
 

V. Vedral Quantifying entanglement in macroscopic systems. Nature 2008, 453, 1004

G. D. Scholes Quantum-coherent electronic energy transfer: Did nature think of it first? J. Phys. Chem. B. 2010, 1, 2.

A. Patel. Quantum algorithms and the genetic code. arXiv: quant-ph/0002037v3

• Biochemistry
• Bioinformatics
• Biomolecular Sciences
• Molecular Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

A common polymorphism (Y402H) in the gene encoding human complement factor H (CFH) has been identified as a major risk factor for Age-related Macular Degeneration (AMD), which is the main cause of blindness in the industrialised world. Loss of central vision results from the destruction of the macula (the central part of the retina). AMD is preceded by formation and accumulation of particulate matter (called drusen) within the macula, which is made up of cellular debris. This is believed to arise due to a dysregulation of the complement system (i.e. innate immunity), leading to inflammation and tissue damage. CFH is an important regulator of the complement system where it is thought to localise on host tissues (and thus suppress complement activation) via its binding to negatively charged molecular patterns. In our recent work we have found that the Y402H polymorphism associated with AMD, which causes an amino acid coding change at residue 402 in the CFH protein, has a profound affect on the ligand-binding specificity of CFH [1-5], e.g. for negatively charged sugar molecules (called glycosaminoglycans or GAGs for short). This change in specificity in GAG recognition may affect the localisation of the disease-associated form of CFH in the human eye [1,2] and thus contribute directly to the pathogenesis of AMD (i.e. due to impaired immunoregulation). This project will form part of an ongoing programme of work in Professor Day’s lab (in collaboration with Professor Paul Bishop in the Faculty of Medicine and Human Sciences, University of Manchester), aimed at understanding the molecular basis of AMD to facilitate the design of novel treatments for this devastating disease. A wide variety of techniques are being employed in this research including fluorescent microscopy, cell biology, molecular biology, interaction analysis and structural biology.

1. Clark, S.J., Perveen, R., Hakobyan, S., Morgan, B.P., Sim, R.B., Bishop, P.N. & Day A.J. AMD-associated factor H polymorphism (Y402H) affects binding-site recognition in human macula. J. Biol. Chem., in press. Published as a “Paper in Press” online on 26th July 2010.

2. Clark, S.J., Bishop, P.N. & Day, A.J. Complement factor H and age-related macular degeneration: the role of glycosaminoglycans in disease pathology. (2010) Biochem. Soc. Trans., in press. REVIEW ARTICLE.

3. Prosser, B.E., Johnson, S., Roversi, P., Herbert, A.P., Blaum, B.S., Tyrrell, J., Jowitt, T.A., Clark, S.J., Tarelli, E., Uhrin, D., Barlow, P.N., Sim, R.B., Day, A.J. & Lea, S.M. Structural basis for complement factor H linked age-related macular degeneration. (2007) J. Exp. Med. 204, 2277-2283.
4. Sjöberg, A.P., Clark, S.J., Trouw, L., Heinegård, D., Sim, R.B., Day, A.J. & Blom, A.M. Factor H variant associated with age-related macular degeneration (H384) and non-disease-associated form bind differentially to C reactive protein, fibromodulin, DNA and necrotic cells. (2007) J. Biol. Chem. 282, 10894-10900.

5. Clark, S.J., Higman, V.A., Mulloy, B., Perkins, S.J., Lea, S.M., Sim, R.B. & Day, A.J. H384 allotypic variant of factor H associated with age-related macular degeneration has different heparin-binding properties from the non-disease associated form. (2006) J. Biol. Chem. 281, 24713-24720.
 

• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Cell Matrix Research
• Genetics
• Immunology
• Molecular and Cellular Neuroscience
• Molecular Biology
• Neuroscience
• Ophthalmology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

In normal physiology, the polymeric mucins MUC5AC and MUC5B provide the organizing framework of the airways mucus gel and are major contributors to its properties. However, much of our knowledge of mucins has been gained after isolation under conditions that have disrupted their native interactions in mucus. Thus, we have no adequate description of their 3D-organisation within mucus and how this changes in obstructive airway diseases such as asthma, cystic fibrosis and chronic obstructive pulmonary disease. Such interactions are key to understanding the architecture of mucins, their rheological and transport properties.

This studentship will address the hypothesis that organisation of the mucus gel is defective in obstructive airways disease, resulting in mucus with sub-optimal transport properties and leading to tethering (adhesion) to the epithelial surface. We will focus on this fundamentally important problem to address the following questions:

• How are mucins organized within mucus?
• Is this altered in disease?
• What is the nature of mucin/mucus adhesion to the epithelial surface?

To answer these questions we are working together with clinical colleagues and Faculty members and we will apply a number of state-of-the-art methodologies; these include airway epithelial cell culture, advanced polymer imaging using electron microscopy, mass spectrometry and mucin characterization and quantification. This work is a vital first step in understanding the nature of mucin organization and interactions within mucus. It is anticipated that greater understanding of these processes will lead to better application of current mucus-altering therapies to treat obstructive lung disease and ultimately development of novel agents.

Kirkham, S., Kolsum, U., Rousseau, K., Singh, D., Vestbo, J. & Thornton, D.J. (2008) MUC5B is the major mucin in the gel-phase of sputum in chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 178, 1033-1039.

Thornton, D.J., Rousseau, K. & McGuckin, M. (2008) Structure and function of the polymeric mucins in airways mucus. Annu. Rev. Physiol. 70, 5.1-5.28.

Rosenberg MF, O'Ryan LP, Hughes G, Zhao Z, Aleksandrov LA, Riordan JR, Ford RC. The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR): Three-dimensional structure and localization of a channel gate. J Biol Chem. (2011) 286(49), 42647-54.

• Biochemistry
• Cell Matrix Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Enzymes have the potential to contribute extensively in white biotechnology, for example in industrial biocatalysis and the generation of novel biofuels. We are developing deep understanding of the structures and mechanisms of enzyme systems with a view to targeting enzymes for applications in novel biocatalysis and biofuels applications. Work in the group involves high throughput evolution and structure-based rational design of enzyme systems across a broad spectrum of disciplines involving enzyme biophysics (spectroscopy and structure determination), chemical biology, kinetics, robotic screening of enzyme variants and library construction, rational design through modelling and mutagenesis. We have state-of-the-art facilities for high throughput laboratory based enzyme evolution and infrastructure for mechanistic analysis of enzyme systems. The PhD programme is interdisciplinary and would suit a student with interests in chemistry or biochemistry. The project will provide excellent training in modern mechanistic and structural enzymology in a large and well-funded research group working generally in the area of biological catalysis.

Biocatalysis with thermostable enzymes: structure and properties of a thermophilic ‘ene’-reductase related to Old Yellow Enzyme (2009). Adalbjörnsson, B. V., Toogood, H.S., Fryszkowska, A., Pudney, C. R., Jowitt, T. A., Leys, D. & Scrutton, N. S. ChemBioChem. 11, 197-207

Asymmetric reduction of activated alkenes by pentaerythritol tetranitrate reductase: specificity and control of stereochemical outcome by reaction optimisation (2009). Fryszkowska, A., Toogood, H., Sakuma, M., Gardiner, J. M., Stephens, G. M. & Scrutton, N. S. Adv. Synth. Catal. 351, 2976-2990

Structure-based insight into the asymmetric bioreduction of the C=C double bond of a-b-unsaturated nitroalkenes by pentaerythritol tetranitrate reductase (2008). Toogood, H. S., Fryszkowska, A., Hare, V., Fisher, K., Roujeinikova, A., Leys, D., Gardiner, J. M., Stephens, G. M. & Scrutton, N. S. Adv. Synth. Catal. 350, 2789-2803.
 

Biomolecular Sciences

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Worldwide crop production is under increasing pressure to meet the needs of a growing populations food and industrial requirements. Plants unlike animals have the ability to produce their own food via photosynthesis. Photosynthesis produces carbohydrates, such as starch, and other important food products such as amino acids, proteins and fats. The major site of these biosynthetic processes is within the family of organelles known as plastids. This PhD will focus on understanding the role and regulation of specific processes within the plastid using a combination of molecular and proteomic approaches. Such studies will provide a clear insight into how different aspects of plastid metabolism contribute to, for example, crop yield. Such information can be combined with biotechnological methods to develop crops able to cope with changing environmental conditions. For example, photosynthetic ferredoxin NADP+ oxidoreductase (pFNR) is an enzymes involved in photosynthesis. pFNR helps the plant cope with environmental conditions such as drought, salinity and temperature stress. Depending on environmental conditions, there are different forms of this enzyme present in the plant. This variation in pFNR forms and the way they function affects the overall ability of the leaf to produce carbohydrates, fats and proteins and therefore crop yield. A PhD undertaken to study this enzyme would provide an understanding of how pFNR forms vary within the plant. This is important because it will help us to understand how photosynthesis is regulated and may lead to an increase in overall yield of the plant.

.

• Moolna A and CG Bowsher (2010). The physiological importance of photosynthetic NADP+ oxidoreductase (FNR) isoforms in wheat. J Exp Bot (in Press).
• Tickle P, MM Burrell, SA Coates, MJ Emes, IJ Tetlow and CG Bowsher (2009). Characterisation of plastidial starch phosphorylase in Triticum aestivum L. endosperm. J Pl Phys 166, 1465-1478.
• Bowsher CG (2008). Chloroplast – the biosynthetic powerhouse?. Biological Sciences Review 21.
• Bowsher CG, M Steer, AK Tobin (2008). Plant Biochemistry. Garland Science 500pp
• Bowsher CG, AE Lacey, GT Hanke, DT Clarkson, LR Saker, I Stulen and MJ Emes (2007). The effect of Glc6P uptake and its subsequent oxidation within pea root plastids on nitrite reduction and glutamate synthesis. J Exp Bot 58, 1109-1118.

• Biochemistry
• Biomolecular Science
• Environmental Biology
• Gene Expression
• Membrane Trafficking
• Molecular Biology
• Organelle Function
• Plant Sciences

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Notch receptors are transmembrane glycoproteins that are of fundamental importance in multiple cell-fate decisions, such as occur during stem cell maintenance and cell differentiation. Notch receptors interact with membrane-tethered ligands (Delta and Jagged) presented on neighbouring cells, resulting in downstream events that lead to control over the receiving cell’s differentiation programme. Dysregulation of Notch has been implicated in a myriad of disease states, including cancers. To achieve a signal, the Notch receptor must undergo three proteolytic cleavage events that enable release of the Notch intracellular domain into the cytosol, whereupon it translocates to the nucleus to act as a transcription factor. The second proteolytic cleavage, at a site ‘S2’, is key to Notch activation, triggered by ligand binding. The crystal structure of the Notch heterodimerisation (HD) domain, together with the adjacent LNR domain reveals that this S2 site is normally buried and that Notch is thus autoinhibited. This S2 site needs to be unmasked to activate Notch. We will explore the hypothesis that ligand binds to the extracellular domain of Notch and then exerts sufficient force (upon its endocytosis) to cause exposure of the S2 site through conformational change. Together with physical scientists, we will thus conduct an investigation into the mechanical stability of the Notch LNR and HD domains. We have already produced recombinant Notch LNR and HD domains and subjected single molecules to mechanical force, observing unfolding of individual domains. This PhD will continue the single molecule work, using atomic force microscopy to establish whether mechanical unfolding can expose the S2 site. The work can extend to analysis of Notch mechanical unfolding and activation on live cells, ideally subsequently tracking the translocation of the intracellular domain to the nucleus (new method development). The work can also include a computational analysis for modelling of structural changes to the Notch receptor.

• Hansson EM, Lendahl U, Chapman G (2004) Notch signaling in development and disease . Semin Cancer Biol. 14, 320-8.
• Louvi A, Arboleda-Velasquez JF, Artavanis-Tsakonas S. (2006) CADASIL: A critical look at a Notch disease. Dev Neurosci. 28, 5-12
• Gordon WR, Vardar-Ulu D, Histen G, Sanchez-Irizarry C, Aster JC, Blacklow SC. (2007) Structural basis for autoinhibition of Notch . Nat Struct Mol Biol. 14, 295-300.
• Malecki MJ, Sanchez-Irizarry C, Mitchell JL, Histen G, Xu ML, Aster JC, Blacklow SC. (2006) Leukemia-associated mutations within the NOTCH1 heterodimerization domain fall into at least two distinct mechanistic classes. Mol Cell Biol. 26, 4642-51.
• Vogel V (2006) Mechanotransduction involving multimodular proteins: converting force into biochemical signals. Annu. Rev Biophys Biomol Struct 35, 459-488.

• Biochemistry
• Bioinformatics
• Biomolecular Sciences
• Developmental Biology
• Gene Expression
• Molecular Biology
• Molecular Cancer Studies
• Stem Cell Research
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Gram-negative pathogenic bacteria, such as Neisseria, Pseudomonas and Vibrio, produce long, thin protein fibres, or pili, from their surfaces. Pili have been shown to be major virulence determinants. They have a number of functions, including binding to specific receptors on the surfaces of the cells of the infected host. In addition, type IV pili also exhibit dynamic behaviour: they are capable of rapid retraction, generating a powerful motor force in the process. The process of retraction has been linked to the ability of bacteria to spread out on certain types of surfaces, a property which influences their ability to cause infection. At least a dozen different proteins are known to be involved in the assembly and disassembly of the pilus fibre, but the way in which they act together as a molecular motor is poorly understood. The overall aim of this project is to understand this process at the molecular level; to do so, we aim to introduce a systems-based approach to the study of pilus biogenesis, developing a quantitative model for the way the retractile machine works. Such work could ultimately help in the development of inhibitors of the process. The studentship would suit a graduate in Microbiology, Biochemistry, Chemistry or a related discipline.

• Collins, R.F., Frye, S.A., Kitmitto, A., Ford, R.C., Tønjum, T. & Derrick J.P. (2004) J. Biol. Chem. 279, 39750-39756. Structure of the Neisseria meningitidis outer membrane PilQ secretin complex at 12 Ångstrom resolution.
• Collins, R.F., Frye, S.A., Balasingham, S., Ford, R.C., Tønjum, T. & Derrick J.P. (2005) J. Biol. Chem. 280, 18923-18930. Interaction with type IV pili induces structural changes in the bacterial outer membrane secretin PilQ.
• Golovanov, A.P., Balasingham, S., Tzitzilonis, C., Goult, B.T., Lian, L.Y., Homberset, H., Tønjum, T. & Derrick J.P. (2006) J. Mol. Biol. 364, 186-195. The Solution Structure of a Domain from the Neisseria meningitidis Lipoprotein PilP Reveals a New Beta-Sandwich Fold.
• Derrick JP. (2008) Structure 16, 1441-1442. A pilot sheds light on secretin assembly.
• Karuppiah, V., Hassan, D., Saleem, M. and Derrick, J.P. (2010) Proteins 78, 2049-2057. Structure and oligomerization of the PilC type IV pilus biogenesis protein from Thermus thermophilus.

• Biochemistry
• Biomolecular Sciences
• Microbiology
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Some fifty years after the three dimensional structures of globular proteins were first determined, biochemistry has now moved beyond static protein structures. The movements of proteins and the energies that power these motions are now recognised as key elements in our understanding of protein function. This multidisciplinary project operates at the interface between physics and biochemistry, applying advanced electron magnetic resonance (EMR) techniques to the study of protein motion and the link between such motion and function. The objective of the research is to optimize the experimental approach while providing real data on proteins of biological significance. The techniques employed include electron paramagnetic resonance (EPR) spectroscopy, electron nuclear double resonance (ENDOR) spectroscopy, electron spin echo envelope modulation (ESEEM) spectroscopy and electron electron double resonance (ELDOR) spectroscopy. These techniques rely on the use of unpaired electrons, either artificially introduced or present as part of the protein’s biological function, as probes of protein structure and function. Furthermore, the fusion of these EMR techniques with kinetic approaches, such as freeze quench and laser initiation, is available in the laboratory. This allows protein motions to be followed over timescales varying from hundreds of nanoseconds to tens of seconds. Training in the implementation and application of all the above techniques will be provided and no prior knowledge of the techniques will be assumed. However, a willingness to understand the physical basis of the techniques and to become involved in the operation of computer-driven spectrometers is essential

Hay, S. Brenner, S., Khara, B., Quin, A-M, Rigby, S. E J. and Scrutton, N. S. (2010) Nature of the energy landscape for gated electron transfer in a dynamic redox protein. J. Am. Chem. Soc. 132, 9728-9735.

• Biochemistry
• Biomolecular Science
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Bacterial halorespiration is an microbial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors (1,2). This leads to effective dehalogenation of these toxic, recalcitrant and xenobiotic compounds. The bacterial species, their enzymes and other components responsible for this unusual metabolism have only recently been identified. Unlocking the full potential of this process for bioremediation of persistent organohalides (such as polychlorinated biphenyls and tetrachloroethene) requires detailed understanding of the underpinning biochemistry. However, the regulation, mechanism and structure of the reductive dehalogenase (=the key enzyme) are little understood.
Our group seeks to study representatives of the distinct reductive dehalogenases classes as well as key elements of the associated regulatory systems. Our group has been at the fore of studying the biochemistry underpinning transcriptional regulation of halorespiration, by providing atomic level detail insights for the protein CprK (3,4). However, only a subset of reductive dehalogenases are regulated by CprK homologues with little known about the other regulators. On the other hand, studies on the reductive dehalogenases themselves have been hampered by the inability to purify sufficient amounts. Using an interdisciplinary, biophysical approach focused around X-ray crystallography, enzymology and molecular biology, and funded by a 5-year ERC 1.2 million € grant, we aim to provide a detailed understanding and identification of the structural elements crucial to reductive dehalogenase mechanism and regulation. In conjunction, we aim to study the feasibility of generating improved (de)halorespiratory components for biosensing or bioremediation applications.
PhD projects are available to elucidate the structure and function of selected components of this intriguing pathway. These projects will use a mixture of structural biology and biochemistry techniques. The research group is located in the newly build Manchester Interdisciplinary Biocentre and is part of the Molecular Enzymology section. For more information please contact Dr David Leys or see Current Research.
 

• [1] Stringer R. & Johnston P. 2001 Chlorine and the Environment: An Overview of the Chlorine Industry. Kluwer
• [2] Smidt et al. (2004) Annu. Rev. Microbiol. 58:43
• [3] Joyce et al. 2006 J. Biol. Chem. 281: 28318
• [4] Levy et al. 2008 Microbiology 70:151

• Biochemistry
• Biomolecular Sciences
• Biotechnology
• Environmental Biology
• Microbiology
• Molecular Biology
• Structural Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.