July 14, 201412:00-13:00

Yuko OKAMOTO, Nagoya University, Nagoya, Japan*

OPTIMIZATION OF PROTEIN FORCE-FIELD PARAMETERS

Conventional Monte Carlo (MC) and molecular dynamics (MD) simulations of protein folding use effective potential energy, or force field. In order to succeed in folding into correct native three-dimensional structures of proteins, one has to use accurate parameters for the force field functions. In this talk I will present the results of our attempts in optimizing force-field parameters (for a review, see Ref. [1]). The first method minimizes the sum of forces acting on each atom of proteins with native structures in the Protein Data Bank [2]. We then introduced a double-Fourierseries for the torsion-energy term [3,4]. We have also introduced an amino-acid-dependentforce-field function [4]. Using the optimized force fields, we performed folding simulations of small proteins, and the results will also be presented.

[1] Y. Sakae and Y. Okamoto, in Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes - from Bioinformatics to Molecular Quantum Mechanics, A. Liwo (ed.) (Springer-Verlag, Berlin Heidelberg, 2014) pp. 195-247.[2] Y. Sakae and Y. Okamoto, Chemical Physics Letters 382, 626-636 (2003).[3] Y. Sakae and Y. Okamoto, Journal of the Physical Society of Japan 75, 054802 (9 pages) (2006).[4] Y. Sakae and Y. Okamoto, Molecular Simulation 39, 85-93 (2013).

[5] Y. Sakae and Y. Okamoto, Journal of Chemical Physics 138, 064103 (8 pages) (2013).

*1 Department of Physics, Graduate School of Science, 2 Structural Biology Research Center, Graduate School of Science, 3 Center for Computational Science, Graduate School of Engineering, 4 Information Technology Center

Mazarredo14,48009Bilbao,BasqueCountry,Spain www.bcamath.org

Scientific Seminar