Mesoscale modeling of protein-DNA assemblies

University Of Pittsburgh, Pittsburgh PA

Investigators

Abstract

The project will focus on the design of a novel computational procedure for determination and analysis of the structure of protein-DNA assemblies, in which the DNA elastic energy, the electrostatic repulsion of charged residues, and the protein-DNA binding energy are the main components of the assembly energetics. The procedure will include fast new algorithms for calculation of DNA configurations, determination of the free energy of DNA segments and polypeptide tethers, and analysis of protein-DNA binding states. In the project the procedure will be applied to the study of the transcription of the lac operon in E. coli, including the structure of DNA loops induced by the Lac repressor, explanation the effect of interoperator distance on efficiency of repression, determination of the interaction between the loop and RNA polymerase, investigation of the cooperativity of binding of LacR and CAP, and modeling the structure of the upstream promoter region with bound aCTD domains of the RNA polymerase. The methods developed in this project will be applicable to modeling of other complex protein-DNA assemblies that form during DNA replication, recombination, or chromatin remodeling. The goal of this project is to develop a computer program that will provide molecular biologists with a tool they can use to create structural models of intracellular components and hence explore in detail the inner workings of cells. The program will combine modern computer technology with cutting edge knowledge about the physical properties of biological macromolecules, and by allowing the biologists to test hypotheses about cellular functions on the computer the program will save both time and funding on expensive experiments. The program will further reduce the limitations of current experimental techniques by enhancing the interpretation of experimental results. The specific information to be obtained in the course of the project about E. coli will give us an understanding of how genes of E. coli, or any other bacteria, affect its survival in adverse conditions such as those that occur, for example, during bacterial infection.