Notice Board

The Department of Chemistry & Biochemistry Presents:

Dr. Alexey Savelyev
Department of Chemistry & Biochemistry
University of Montana

Multi-Scale Computational Modeling of DNA and Applications to Biophysical Problems

November 15, 2018
11:00 a.m. 
C674
University Hall

All are welcome to attend

Abstract:
Computational modeling by means of Molecular Dynamics (MD) simulations is an integral part of many biophysical studies. MD represents a powerful approach to explore energetics and structural transitions at different levels of detail representation in complex biological molecules such as DNA, proteins, membranes and their complexes. It is an invaluable tool complementing or sometimes substituting such traditional experimental biophysical techniques as X-ray crystallography and solution NMR which are plagued by a number of problems associated with the object’s crystallization and resolution issues, as well as accessibility to short lived high energy states and time domain information. I will briefly cover basics of MD and ideas of the force-field development for biomolecules modeled at different resolutions. As an example, I will discuss two DNA models developed during my past research which are very distant from each other on the detail scale: (1) the CHARMM polarizable model based on the Drude oscillator formalism where each heavy atom is supplemented by auxiliary Drude particle(s) to mimic induced polarization, and (2) the 2-beads-per-base-pair coarse-grained (CG) model where an entire nucleotide is reduced to a single particle. On a practical side, I will discuss predictions of these two MD simulated models for a range of biophysical problems including counterion condensation theory, competitive ionic binding to DNA, conformational DNA properties in solutions of different ionic buffers as seen from numerically computed SAXS profiles and Principal Component Analysis performed on MD trajectory, structural transitions in torsionally stressed DNA nanocircles, dependence of the DNA persistence length on ionic strength of solution, and more. Finally, I will mention implications of these MD simulations results to such vitally important questions as protein-DNA recognition and chromatin folding.