Center for Bioinformatics at KU

As part of our public Seminar Series
http://bioinformatics.ku.edu/seminars

August 28, Fri 2009
1:00 pm, MRB 200 Conference Room

Dr. Feng Chen

Kansas State University

Development and testing of protein backbone torsional potentials for the Kirkwood Buff derived force field of peptides and proteins

Recently, we have been developing a force field for biomolecular simulations of peptides and proteins (KBFF) designed to reproduce the experimental Kirkwood-Buff (KB) integrals observed in solution mixtures. This ensures a reasonable balance between solute-solute interactions and solute solvation – usually by water. Here, we describe the development and testing of the backbone torsion potentials, required for accurate modeling of the conformational preferences of amino acids, which are consistent with the corresponding KBFF nonbonded parameters. Molecular dynamics (MD) simulations were performed for dipeptides of glycine, alanine in solutions. Comparisons with crystallographic data and quantum mechanics derived gas phase energy surfaces are also made.