College of Liberal Arts & Sciences

Role of explicit polarization in the conformational heterogeneity of peptides and DNA studied using the classical Drude oscillator force field

Thursday, October 29, 2015

Thursday, October 29, 2015
4:00 pm, MRB 202

Dr. Alexander D. MacKerell, Jr.

Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland

Role of explicit polarization in the conformational heterogeneity of peptides and DNA studied using the classical Drude oscillator force field

Explicit treatment of electronic polarizability in empirical force fields offers the potential to significantly improve the accuracy of molecular simulations of macromolecules in condensed phases. Towards achieving this we have developed a polarizable force field based on the classical Drude oscillator model. An overview of the model and the parameter optimization approach will be presented. Results will then be presented on MD simulations of macromolecules with emphasis on proteins and nucleic acids. Results include microsecond molecular dynamics (MD) simulations of multiple proteins in explicit solvent. In addition, the polarizable model more accurately treats cooperative helix formation of the (AAQAA)3 peptide, yields improved agreement with experiment for base flipping in DNA and more accurately treats the interactions of ions with DNA. Data obtained to date indicate that the inclusion of explicit electronic polarizability leads to significant differences in the physical forces affecting the structure and dynamics of macromolecules, which can be investigated in a computationally tractable fashion in the context of the Drude model.



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