title: High-Level ab Initio Calculations To Improve Protein Backbone Dihedral Parameters.
abstract: We present new molecular mechanical dihedral parameters for the Ramachandran angles ϕ and ψ of a protein backbone based on high-level ab initio molecular orbital calculations for hydrogen-blocked or methyl-blocked glycine and alanine dipeptides. Fully relaxed 15° (ϕ, ψ) contour maps were calculated at the MP2/6-31G(d) level of theory. Finding out the lowest energy path for ϕ (or ψ) to change from -180° to 180° in the contour map, we performed a DF-LCCSD(T0)/Aug-cc-pVTZ//DF-LMP2/Aug-cc-pVTZ level calculation to get the torsional energy profiles of ϕ (or ψ). Molecular mechanical torsion profiles with AMBER force field variants significantly differed from the ab initio profiles, so we derived new molecular mechanical dihedral parameters of a protein backbone to fit the ab initio profiles.
authors.affiliation: Fujitsu Laboratories Ltd., 10-1 Morinosato-Wakamiya, Atsugi 243-0197, Japan.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Fujitani
authors.affiliation: Fujitsu Laboratories Ltd., 10-1 Morinosato-Wakamiya, Atsugi 243-0197, Japan.
authors.forename: Azuma
authors.initials: A
authors.lastname: Matsuura
authors.affiliation: Fujitsu Laboratories Ltd., 10-1 Morinosato-Wakamiya, Atsugi 243-0197, Japan.
authors.forename: Sino
authors.initials: S
authors.lastname: Sakai
authors.affiliation: Fujitsu Laboratories Ltd., 10-1 Morinosato-Wakamiya, Atsugi 243-0197, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Sato
authors.affiliation: Fujitsu Laboratories Ltd., 10-1 Morinosato-Wakamiya, Atsugi 243-0197, Japan.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Tanida