Scheduled Seminars on 12/6/2013

Prof. Garegin A. Papoian at 11:00  Edit  Reschedule  Delete
Location: B2 NCBI Library
Affiliation: University of Maryland
Host: Anna Panchenko

The Chromatin Folding Problem: Computer Simulations of Nucleosomes and Histone Tails
DNA undergoes very large compactification in cells of higher organisms, aided by positively charged proteins called histones, which help to fold DNA into dense superstructures known as chromatin. Flexible tails protruding from histones mediate and maintain nucleosomal packaging in chromatin fibers and, thus, significantly contribute to chromosomal remodeling and gene activation processes. How chromatin compaction and dynamics are physically regulated is poorly understood. In our work, we have carried out several microsecond long explicit solvent molecular dynamics simulations of four histone tails, H2A, H2B, H3, and H4, to gain fundamental insights into physics of natively disordered proteins and link our understanding of histone tail dynamics to chromosomal organization. We also investigated how specific post-translational modifications of histone tails, such as the K16 acetylation, may control chromatin compaction. Our extensive atomistic simulations of the nucleosomal core particle revealed counterion condensation patterns near the histone core proteins, pointing to where histone tails are likely to bind. Finally, we have developed a rigorous, yet computationally efficient technique of deriving coarse-grained potentials for ions and biomolecules from corresponding atomistic simulations, based on matching partition functions between two scales. These new force fields allow us to move towards computational modeling of the self-assembly and dynamics of chromatin fibers.

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