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Title:Biochemically realistic MD and kinetic models of the Rhodobacter sphaeroides bc1 complex
Author(s):Rose, Stuart Wallace
Director of Research:Corfts, Antony R
Doctoral Committee Chair(s):Corfts, Antony R
Doctoral Committee Member(s):Gennis, Robert; Gruebele, Martin; Pogorelov, Taras
Department / Program:School of Molecular & Cell Bio
Discipline:Biophysics & Computnl Biology
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):bc1 complex, mechanism, kinetics, membrane
Abstract:This work seeks to duplicate a realistic membrane for a more natural model of the Rb. sphaeroides bc1 complex which in past studies has lacked several details in composition of the fatty acids and relative quantities of each lipid. Past studies have shown some distortion on MD relaxation relating to a large void volume in the protein structures. In this model we have set up the membrane with the complement of lipids reported for the chromatophore membrane, and have taken steps to ameliorate the structural distortions on relaxation of the protein by populating the void with a complement of lipids. The MD model is used to determine diffusion constants and motions of the system in preparation for calculating potentials of mean force for wild type and ISP tether mutants. The current kinetic model provides a kinetic and thermodynamic understanding of the rate-limiting reaction, and associated partial processes that lead to successive turnovers. Since both bacterial and mitochondrial complexes have essentially the same catalytic core, their mechanisms are essentially similar, and a better understanding of the bacterial system can be extrapolated to the context of mitochondrial function, and medically important roles in cellular physiology, cardiovascular disease, apoptosis, and diseases associated with aging.
Issue Date:2017-04-21
Type:Thesis
URI:http://hdl.handle.net/2142/97431
Rights Information:Copyright 2017 Stuart Rose
Date Available in IDEALS:2017-08-10
Date Deposited:2017-05


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