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Simulation-led enzyme engineering and design of antibiotic drugs

  • Full or part time
  • Application Deadline
    Monday, November 25, 2019
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

The use of enzymes as biocatalysts is attractive for industry, but natural enzymes often need modification to efficiently produce the desired products. On the other hand, microbial enzymes have become increasingly efficient in breaking down antibiotic drugs, which has to be circumvented to avoid an ’antibiotic apocalypse’. Depending on the candidate, the project will focus on one of these aspects. For both, we will employ state-of-the-art biomolecular simulation to study the dynamics of the enzyme-substrate complexes, as well as the reactions catalyzed by the enzymes (using multi-scale QM/MM simulations). The environment and resources for computational biochemistry in Bristol are excellent (see http://www.bristol.ac.uk/bcompb). Close collaboration with leading experimental groups in structural biology and enzyme kinetics will ensure that a combined computational-experimental approach can be applied.

Website: http://www.vanderkampgroup.wordpress.com

Funding Notes

Link to project: View Website

DEADLINE: 5.00 pm on Friday 25th NOVEMBER 2019
Please complete application to the GW4 BioMed MRC DTP for an ‘offer of funding’. You also need to make an 'offer to study' to your chosen institution(s) – details are on the website. View Website
A 3.5 year funded studentship by the GW4BioMed MRC Doctoral Training Partnership. Full UK/EU tuition fees, a stipend matching UK Research Council Minimum (£15,009 p.a. for 2019/20, updated each year).
Additional research training and support funding of up to £5,000 per annum is also available.

References

1. SA Serapian, MW van der Kamp (2019) Unpicking the cause of stereoselectivity in actinorhodin ketoreductase variants with atomistic simulations. ACS Catalysis 9 (3), 2381-2394. DOI: 10.1021/acscatal.8b04846
2. RA Fritz, JH Alzate-Morales, J Spencer, AJ Mulholland, MW van der Kamp (2018) Multiscale Simulations of Clavulanate Inhibition Identify the Reactive Complex in Class A β-Lactamases and Predict the Efficiency of Inhibition. Biochemistry 57 (26), 3560-3563. DOI: 10.1021/acs.biochem.8b00480
3. MJ Byrne, NR Lees, LC Han, MW van der Kamp, AJ Mulholland, JEM Stach, CL Willis, PR Race (2016) The catalytic mechanism of a natural Diels–Alderase revealed in molecular detail. Journal of the American Chemical Society 138 (19), 6095-6098. DOI: 10.1021/jacs.6b00232

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