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Peptide models XVI. The identification of selected HCO—L—SER—NH 2 conformers via a systematic grid search using ab initio potential energy surfaces
Author(s) -
Perczel András,
Farkas Ödön,
Csizmadia Imre G.
Publication year - 1996
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(199605)17:7<821::aid-jcc6>3.0.co;2-u
Subject(s) - ramachandran plot , conformational isomerism , chemistry , ab initio , side chain , crystallography , stereochemistry , computational chemistry , molecule , protein structure , polymer , organic chemistry , biochemistry
Abstract Multidimensional conformational analysis (MDCA) predicted the existence of ninestable backbone conformations (α L , α D , β L ,γ L , γ D , δ L , δ D , ϵ L , and ϵ D ) on the 2D‐Ramachandran map, E = E (ϕ, ψ), for a single amino acid diamide (HCONH‐CHR‐CONH 2 ).The potential energy hypersurfaces (E = E[ϕ, ψ, χ 1 ,χ 2 ]) of For‐L‐Ser‐NH 2 associated with theα L ‐, bgr; L ‐, γ L ‐, δ L ‐, andϵ L ‐type stable backbone orientations are investigated in this article.An appropriate number of side‐chain rotamers is associated with each of the backboneconformers. In the case of serine, where R = −CH 2 OH, the twosidechain torsional angles (χ 1 , χ 2 ) should lead to 3 *3 = 9 different sidechain orientations according to MDCA. For certain backbonestructures, some of the sidechain conformations were nonexistent. © 1996 by JohnWiley & Sons, Inc.