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Title:Application of the Theory of Elasticity to Modeling of Protein -Dna Interactions
Author(s):Balaeff, Alexander Alexandrovich
Doctoral Committee Chair(s):Schulten, Klaus J.
Department / Program:Biophysics and Computational Biology
Discipline:Biophysics and Computational Biology
Degree Granting Institution:University of Illinois at Urbana-Champaign
Subject(s):Engineering, Biomedical
Abstract:A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending anisotropy, and electrostatic properties. All the model parameters are considered to be functions of the loop arclength, so that the DNA sequence-specific properties can be modeled. The developed theory is applied to predict the structure of the DNA loop connecting the protein-bound DNA segments in the crystal structure of the lac repressor-DNA complex. The lac repressor system is used to extensively analyze the parameters and approximations of the model. The capabilities of the model are used to mimic the binding of catabolite gene activator protein (CAP) within the lac repressor loop and to explain the cooperativity in DNA binding between the two proteins. The possibilities for further development of the model and its general applicability in biomolecular modeling are discussed, especially with regard to multi-scale simulations of protein-DNA complexes.
Issue Date:2002
Description:88 p.
Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2002.
Other Identifier(s):(MiAaPQ)AAI3069971
Date Available in IDEALS:2015-09-25
Date Deposited:2002

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