title: Evaluation of methods to cap molecular fragments in calculating energies of interaction in avian pancreatic polypeptide.
abstract: The accuracy of the determination of the energy of interaction between Phe20 and the Pro5-Thr6-Tyr7-Pro8 complex inside the hydrophobic core of avian pancreatic polypeptide was investigated using three capping strategies for molecular fractionation with conjugated caps and DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory. The most accurate determination resulted from acetylation of the alpha-amino group combined with methyl amidation of the alpha-carbonyl group with relative deviations less than 10%. Combinations of hydrogenation of the alpha-amino group with the replacement of the alpha-carbonyl group with a hydrogen and the hydrogenation of the alpha-amino group with methylation of the alpha-carbonyl group were less accurate, leading to relative deviations up to 35%. Choice of capping methods depends on the structural features of the polypeptide system, the desired accuracy and the available computational resources.
authors.affiliation: Nebraska Wesleyan University, Lincoln, NE 68504, U.S.A.
authors.forename: Marcus P D
authors.initials: MP
authors.lastname: Hatfield
authors.forename: Nicholas Y
authors.initials: NY
authors.lastname: Palermo
authors.forename: József
authors.initials: J
authors.lastname: Csontos
authors.forename: Richard F
authors.initials: RF
authors.lastname: Murphy
authors.forename: Sándor
authors.initials: S
authors.lastname: Lovas