Application of the Theory of Elasticity to Modeling of Protein -Dna Interactions

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biophysics and Computational Biology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2015

Author dc:creator

• Balaeff, Alexander Alexandrovich

Contributors dc:contributor

• Schulten, Klaus J.

• Engineering, Biomedical

Language dc:language

eng

Identifier

(MiAaPQ)AAI3069971

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/85424