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https://hdl.handle.net/2142/85445
Description
Title
Protonation and Membrane Protein Function
Author(s)
Varma, Sameer
Issue Date
2005
Doctoral Committee Chair(s)
Erik Jakobsson
Department of Study
Biophysics and Computational Biology
Discipline
Biophysics and Computational Biology
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Chemistry, Biochemistry
Language
eng
Abstract
Many biochemical reactions are electrostatically driven. Titratable amino acids significantly contribute to the electrical forces that drive these reactions. The protonation state of a titratable residue embedded in a protein environment can differ from its default value in bulk water at neutral pH. It is thus necessary to correctly evaluate its protonation state in order to generate meaningful reaction models in in-silico experiments. Such evaluations are non-trivial in situations where titratable amino acids interact electrostatically with each other, or interact with ions. In this work, a comprehensive approach towards evaluating protonation states of such interacting titratable residues is described. It is then shown, that this approach is essential to correctly describing the structural and functional properties of two biological systems: (a) a bacterial ion channel, outer membrane protein F (OmpF) and, (b) the Ca2+-activated membrane docking module (C2 domain) of human cytosolic phospholipase A2. Both of these biological systems were investigated using a multiscale approach, in which the results of the electrostatics calculations to determine protonation states are used to parameterize molecular dynamics simulations, which in turn reveal significant insights into the structural and the functional properties of these proteins. Finally, the development of a grid-based scientific computing environment is described, specifically for the study of pore forming membrane proteins.
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