Funding

Fully funded (UK/EU/International students)

Department

Centre for Enzyme Innovation

Closing date for applications

Monday 4 January 2021 (midnight GMT)

The Centre for Enzyme Innovation is proud to be able to offer two new PhD opportunities through the SoCoBio Doctoral Training Programme (DTP).

Each DTP studentship encompasses a broad, 4-year research training programme which provides students with the skills they need to develop into future bioscience leaders in academia or in industry.

Please note, all applications must be made via the SoCoBio website only. 

Computational predictions of thermostability and binding affinity changes in enzymes

Primary Supervisor

Prof. Paul Cox (University of Portsmouth)

Co-Supervisor(s)

Prof. Jonathan W. Essex (University of Southampton), Dr. Gerhard Koenig (University of Portsmouth)

 


View the project at the South Coast Biosciences Doctoral Training Partnership website >
The use of enzymes for chemical synthesis and recycling is often limited by their low thermostability, as many reactions require high temperature.

Therefore, high performance computing procedures to find mutations that increase protein stability would represent a competitive advantage for the green industry. This project aims at using molecular dynamics simulations to determine the effect of point mutations on the thermostability of different enzymes.

The targets include well-characterized examples from the literature (RNAse SA) for benchmarking, and new mutants of plastic-degrading enzymes that are currently being experimentally evaluated at the CEI (e.g., PETase and cutinases). The mutations are simulated in the folded and the unfolded state to determine the relative free energy changes ΔΔG.

The folded state is modelled based on the crystal structure of the enzyme, and the unfolded state can be modelled by small peptides in water. Ideally, the simulations will provide a scale that ranks all canonical amino acids in terms of their influence on protein stability.

This can be used to train fast bioinformatics approaches. The temperature-dependent data of hydration free energies and conformational entropies of each amino acid type can help to understand the mutation patterns during the evolution of thermophilic organisms.

Another important factor for proper enzyme function is the capability to bind to the substrate at elevated temperatures. Protein-ligand binding is often driven by the hydrophobic effect, which depends on the temperature. Therefore, it is often necessary to optimize the binding pocket to allow substrate binding at high temperatures (e.g., the binding of PET plastics to PETase).

Such calculations are already common in computational drug design, so the required tools already exist in computational chemistry, and only have to be modified to optimize the binding pocket instead of the ligand. Possible applications include the design of thermostable enzymes that can degrade plastics for recycling.

Application deadline:

Monday 4 January 2021 (midnight GMT)

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