Structure determination using solution-state small angle X-ray scattering (SAXS) data of proteins remains an unsolved problem in structural biology. However, SAXS information can be used for refinement of atomistic models in conjunction with molecular dynamics (MD) simulations. Often, the simulation explores molecular conformations that are close to the initial starting atomistic model and long duration simulations may not sufficiently sample the native conformational space.
This project will develop a comprehensive simulation strategy based on Prof. Essex’s recent accomplishments with antibody-antigen complexes. The sampling of molecular dynamics simulations will be enhanced and combined with experimental SAXS data to generate an ensemble of structures representing the high-resolution solution-state conformations of the protein.
The research project will involve the analysis of SAXS data of selected proteins and their complexes. This project will deliver a simulation toolkit for the analysis of protein systems using atomistic models that are consistent with experimental SAXS data. The project will provide the student with computational experience in enhanced sampling MD simulations, specifically with programs such as GROMACS, HADDOCK, and CNS, experience in ensemble reweighting methods, as well as software development skills. Simulation workflow software, documentation and training materials will be provided to the user community and implemented at the SAXS beamline B21.
Applications for this studentship are now open. Further information is available here.
Closing date is 31 August 2021.
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