Molecular Dynamics Simulations and Cross-Link Analysis of the Rotary Molecular Motor F(o) of ATP Synthase
Kanchanawarin, Chalermpol
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https://hdl.handle.net/2142/80521
Description
Title
Molecular Dynamics Simulations and Cross-Link Analysis of the Rotary Molecular Motor F(o) of ATP Synthase
Author(s)
Kanchanawarin, Chalermpol
Issue Date
2005
Doctoral Committee Chair(s)
Schulten, Klaus
Department of Study
Physics
Discipline
Physics
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Physics, Molecular
Language
eng
Abstract
The protein F1Fo ATP synthase is responsible for the generation of the molecule adenosine tri-phosphate (ATP). It consists of two coupled rotary motors, F1 and Fo. ATP is generated via a rotary mechanism that couples the synthesis of ATP in F1 to the proton translocation across Fo which is driven by the electrochemical proton gradient across the membrane. F1 consists of three different subunits in the stoichiometry a1b2c10. So far, only the structure of the c-subunit and a partial structure of the b-subunit have been solved at atomic level detail. However, enough biochemical and structural information is available to construct an atomic model of Fo. There are still many open questions about Fo operation ranging from the subunit arrangement to the proton pathway and proton conduction mechanism to the rotary mechanism that couples the proton conduction to the rotation of its rotor. In this thesis study, I investigated the following four aspects of Fo: the proton pathway in Fo; the motion of F o subunits during its rotation; the rotation of the C-terminal helix of the c-subunit induced by a pH change; the forced rotation of a c10 ring in a membrane. Using molecular dynamics (MD) simulations, I was able to identify a proton pathway formed as two half proton channels in F o, i.e., a proton entrance channel and a proton exit channel. This is in good agreement with experiment. Furthermore, based on the diagramatic cross-link analysis, I propose a new Fo rotary mechanism which shows the cooperative movement of helices in Fo during proton transport and can explain experimental results which could not be explained by previous models. The investigation of the C-terminal helix rotation by NM simulations showed no pH induced rotation of the helix of the c-subunit. Finally, using steered MD simulations, I found that the c10 ring is mechanically robust against forced rotation in vacuum but not in a membrane on the MD time scale. Overall, structural information combined with my cross-link analysis of F o and with MD simulations provided insight into the connection between the proton conduction and the rotary mechanism of Fo.
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