Friday, 16 November 2012 at 11:30am
Room 1400 Biomedical and Physical Sciences Bldg.
Refreshments at 11:15
Speaker: David Case, BioMaPS Institute and Department of Chemistry & Chemical Biology, Rutgers University
Title: Bridging the Divide: All Atom Molecular Dynamics Simulations of Biomolecular Crystals
Abstract:
All-atom molecular dynamics simulations of crystals present an attractive way to connect
crystallography and computational biophysics, We have recently described benchmark
simulations on a variety of small, well-folded proteins whose crystal structures have been
determined at room temperature (J. Phys. Chem. B. 114:12811, 2010). We present here
some newer results on lysozyme, and on a short peptide crystal, refined to a model with
four water molecules per unit cell. We find relatively free movement of water molecules
through channels between unit cells, such that at any given moment a unit cell may
possess as few as 1 and as many as 9 water molecules, yet the average water density
agrees in detail with the reported structure. This system can be used as a test-bed to study
force field accuracy and crystallographic refinement procedures.
These simulations have implications for structural biology in solution as well, and I will discuss some connections to NMR spectroscopy and relaxation measurements in the liquid and solid states.
(Talk based on research by Paweł A. Janoski, David S. Cerutti, and David A. Case)