Dynamical fine structure of proteins and nucleic acids via molecular simulation

Chemistry Department, Wesleyan University, Middletown, CT 06457, USA.

Abstract

We have recently been investigating the dynamical fine structure of DNA oligonucleotides and protein structures based on molecular dynamics simulation. Recent results via d(CGCGAATTCGCG) and HIV-1 protease will be presented with an emphasis on new methods for tire analysis of aspects of structure which originate uniquely in dynamical motions. The results are compared with corresponding crystal structures and NMR data. A dynamical definition of persistence length is proposed for the analysis of oligonucleotide structures, and used to analyze the extent of axis bending in simulations as compared with crystal structures. In the protease, molecular dynamics results provide evidence for domain-domain interactions that are possibly significant in the functional energetics. Analysis of domain correlations via dynamical cross correlation maps will be discussed.