Poster Presentation 2014 International Biophysics Congress

Refinement of the dihedral potential functions for nucleic acids backbone (#528)

Takashi Mitsui 1 , Hideaki Fujitani 1
  1. Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan

 Atomistic simulations have become a major tool for understanding physical bases of structures and functions of biomolecules. The choice of a force field is quite important for energetic description of molecular conformations in such simulations. Among various force field parameters proposed in the last decades, it is recently reported that FUJI force field1 significantly improves conformational populations of proteins, and is one of the most appropriate choices for molecular dynamics. Several efforts have also been made to improve conformational behaviors for nucleic acids in the past decade. However, in order to apply for complex systems of protein and nucleic acids, it is necessary to develop the force field in consistent ways for both proteins and nucleic acids. We re-parameterized dihedral potential functions for nucleic acids backbone in the same manners with FUJI force field. Atomic partial charges for a phosphate are replaced with RESP charges based on quantum mechanical calculations with diffuse functions. All dihedral potential terms of backbone, except for a delta angle, are revised by fitting parameters to reproduce the lowest energies of ab initio molecular orbital calculations at each angle. The new force field is investigated by long-time molecular dynamics simulations for some DNA systems in order to compare with other widely used force field.

  1. H. Fujitani et al., J. Chem. Theory Comput., 5, 1155-1165 (2009)