We will perform a computational study of selected properties of the membrane bound part of ATP synthase, the protein responsible for the synthesis of ATP. The objective of this proposal is to achieve training in the interdisciplinary field of molecular dynamics simulations of proteins through research in a project that is of both fundamental and practical importance. The research plan includes the study of:
a) the conformational change of the subunit c;
b) the rotation of the subunit c ring;
c) the pathway for the proton translocation in the ATP synthase;
d) the interaction of the Fo complex with the F1 complex;
e) the rotation of subunit gamma driven by Fo.
We will use the CHARMM computational framework for the study of biomolecules together with tools developed at the host laboratory and related visualisation programs. We will build models using the published NMR structures of two subunit c conformations and the low-resolution X-ray structure of the subunit c ring, so as to be able to insert the ring into a model membrane. We will analyse the conformational change of the subunit c by means of reaction path techniques and molecular dynamics approaches. We will perform normal mode, electrostatic, and free energy analysis of selected conformations of the individual subunits and the entire ring. We will model the combined Fo F1 complex based on the known structure ofF1 and the model of Fo.
The computational study of biomolecules is a new direction of study for the researcher. His background in computational materials science methodologies will need to be complemented with the concepts and methods of protein dynamics. He will become fully engaged in the progress of this multidisciplinary field and will use the latest information from structure determination, mutation, and cross-linking experiments to perform his simulations.
Call for proposal
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