Energetics of infinite homopolypeptide chains: a new look at commonly used force fields.
We present a novel method for comparing the long-range part of force fields in the presence of a maximally cooperative network of nonbonded interactions. The method is based on mapping the potential energy surface of an infinite polypeptide chain in the gas phase by using cylindrical coordinates (the twist and pitch) as geometry descriptors. We apply our method to an infinite polyalanine chain and consider the AMBER99, AMBER99SB, CHARMM27, and OPLS-AA/L fixed partial-charge force fields and the protein-specific version of the AMOEBA polarizable force field. Results from our analysis are compared to those obtained from high-level density-functional theory (DFT) calculations. We find that all force fields produce stronger stabilization of the helical conformations as compared to DFT, with only AMBER99/AMBER99SB satisfactorily reproducing all three helical conformations (pi, alpha, and 3(10)).
Penev
Evgeni
E
Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA.
Ireta
Joel
J
Shea
Joan-Emma
JE
D003198:Computer Simulation; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory
D010455:Peptides; C019529:polyalanine