Quantitative Biology / Gene Expression in Development & Disease Seminar

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

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)