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(A*STAR) A multiscale approach to modelling the structure and dynamics of large enzymes


Project Description

Much of biochemistry relies on atomic resolution structural information, most commonly determined using X-ray crystallography. However, due to their dynamic nature, it is often not possible to determine the structure of large multi-domain proteins. An alternative hybrid structural biology approach makes use of a range of experimental data to guide computational simulations. Further, with advances in computing power, it is now possible to model (very) large systems, including protein complexes and membrane (associated) proteins and/or explore the dynamics of an enzyme/complex over much longer/physiologically relevant timescales. This project will use state-of-the-art computational simulations in tandem with a range of experimental input and restraints to build and study molecular models of a family of dynamic multi-domain enzymes. The overall objective is to gain insight into a range of medically and biotechnologically important diflavin reductase enzymes through the construction of working (dynamic) molecular models of each enzyme/enzyme complex. Models will be investigated using a range of molecular mechanics simulations and a range of catalytically relevant complexes and conformations will be investigated in order to understand how structure and dynamics are linked to function – i.e. to build ‘molecular movies’ of each enzyme. We aim to construct the first complete models of a number of these enzymes and to show how protein dynamics and conformational sampling allows these enzymes to work efficiency. With a working knowledge of the structure(/dynamics)/function relationship, it becomes possible to re-engineer these proteins as better biocatalysts and to propose novel ways of regulating or inhibiting them (i.e. through novel drug design).

The project will make use of a broad range of computational chemistry and biology techniques in close collaboration with experimentalists. The project will be carried out at both the Manchester Institute of Biotechnology (www.mib.ac.uk) and the Bioinformatics Institute (A*STAR), Singapore (http://www.bii.a-star.edu.sg/). For further information, please contact Sam Hay () or Pete Bond ().

Entry Requirements:
Applications should be submitted online and candidates should make direct contact with the Manchester supervisor to discuss their application directly. Applicants must have obtained, or be about to obtain, at least an upper second class honours degree (or equivalent) in a relevant subject.

Funding Notes

This project is available to UK/EU candidates. Funding covers fees (UK/EU rate) and stipend for four years. Overseas candidates can apply providing they can pay the difference in fees and are from an eligible country. Candidates will be required to split their time between Manchester and Singapore, as outlined on View Website.

As an equal opportunities institution we welcome applicants from all sections of the community regardless of gender, ethnicity, disability, sexual orientation and transgender status. All appointments are made on merit.

References

1] Hay S, Brenner S, Khara B, Quinn AM, Rigby SE, Scrutton NS. (2010) Nature of the energy landscape for gated electron transfer in a dynamic redox protein. J Am Chem Soc. 132, 9738-45
2] Bailey SS, Payne KAP, Saaret A, Marshall SA, Gostimskaya I, Kosov I, Fisher K, Hay S, Leys D. (2019) Enzymatic control of cycloadduct conformation ensures reversible 1,3-dipolar cycloaddition in a prFMN-dependent decarboxylase. Nature Chem. 11, 1049-1057:
3] Czarnota S, Johannissen LO, Baxter NJ, Rummel F, Wilson AL, Cliff MJ, Levy CW, Scrutton NS, Waltho JP, Hay S (2019) Equatorial Active Site Compaction and Electrostatic Reorganization in Catechol-O-methyltransferase. ACS Catal. 9, 4394-4401.
4] Saravanan R, Holdbrook DA, Petrlova J, Singh S, Berglund NA, Choong YK, Kjellström S, Bond PJ, Malmsten M, Schmidtchen A. (2018) Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides. Nature Commun. 9, 2762
5] Wirawan M, Fibriansah G, Marzinek JK, Lim XX, Ng TS, Sim AYL, Zhang Q, Kostyuchenko VA, Shi J, Smith SA, Verma CS, Anand G, Crowe JE Jr, Bond PJ, Lok SM. (2019) Mechanism of Enhanced Immature Dengue Virus Attachment to Endosomal Membrane Induced by prM Antibody. Structure. 27:253-267.e8.

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