Protein-DNA interactions : molecular modeling and energetics

Citation

Plaxco, Kevin W. (1994) Protein-DNA interactions : molecular modeling and energetics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/fdk3-5402. https://resolver.caltech.edu/CaltechTHESIS:11112009-144801757

Abstract

The thesis deals with the structural elements involved in and the energetics of sequence specific recognition of DNA. Chapter 1 of the thesis provides a brief overview on the mechanics and applicability of molecular dynamics based methods for studying the structure and function of molecules of proteins, DNA and other macromolecules of biological relevance. Chapter 2 presents a constrained molecular dynamics derived model we have developed for the DNA binding domain of the protein Hin Recombinase. Based on a combination of homology modeling and experimentally derived placement constraints we used molecular dynamics to conduct a search of conformation space constrained to remain consistent with the then known experimental characterizations of the protein. The model generated by this approach allowed us to correctly predict the sequence selectivity of the Hin, and lead to a number of insights into the nature of its sequence selectivity. Chapter 3 discusses a variety of experimental results that have been obtained on the structure of the Hin-hix complex. While these results primarily conform with model based predictions, others have pointed towards further refinements that are possible. Chapter 4 of the thesis provides a brief overview of the methods and applicability of perturbation thermodynamic analysis as applied to the molecular dynamics based simulation of proteins and DNA in general and some specific issues of concern with regard to the simulations reported in this thesis. In chapter 5 we report on our perturbation thermodynamic molecular dynamics analysis of the relative free energy of solvation of thymine and uricil. This work provides important insights into the role solvation plays in the formation of sequence specific protein-DNA complexes. Finally, chapter 6 is a report on our investigations into the mechanisms of sequence specific binding for the minor groove binding peptide Netropsin. Steric, electrostatic and solvation effects are all investigated using a perturbation thermodynamic approach to elucidate the mechanisms involved in complex formation for this important class of DNA binding ligands.

Thesis Files