Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.

ABSTRACT: Coarse-grained force fields for protein simulations are usually designed and parameterized to treat proteins composed of natural L-amino-acid residues. However, D-amino-acid residues occur in bacterial, fungal (e.g., gramicidins), as well as human-designed proteins. For this reason, we have extended the UNRES coarse-grained force field developed in our laboratory to treat systems with D-amino-acid residues. We developed the respective virtual-bond-torsional and double-torsional potentials for rotation about the C ^α · · · C ^α virtual-bond axis and two consecutive C ^α · · · C ^α virtual-bond axes, respectively, as functions of virtual-bond-dihedral angles γ. In turn, these were calculated as potentials of mean forc

SUBMITTER: Sieradzan AK 

PROVIDER: S-EPMC3982868 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature