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Comprehensive conformational analysis of (Gly‐Pro‐Pro) n and (Gly‐Pro‐Hyp) n related to collagen
Author(s) -
Tumanyan Vladimir G.,
Esipova Natalia G.
Publication year - 1982
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360210302
Subject(s) - chemistry , dihedral angle , pyrrolidine , crystallography , hydrogen bond , molecule , helix (gastropod) , diffraction , computational chemistry , stereochemistry , physics , ecology , organic chemistry , snail , optics , biology
A complete analysis of all possible conformations with correct hydrogen bonds of the collagen II type was performed on the basis of developed simultaneous equations. Using a unimodal search (by varying Ψ 3 ), the energetically favorable structure was obtained. No other energetically satisfactory structural solutions are possible. The next aim was to obtain a precise model of the molecule. The program used includes a subroutine for continual deformation of the pyrrolidine rings. The set of parameters determining the structure consists of 14 independent variables (8 dihedral and 6 bond angles). As starting points for the energy optimization, conformations produced by scanning and some structures from previous work were used. The final structures (practically the same for both polymers) have helix parameters h = 0.285 nm and t = 52°, which are in excellent agreement with the 7/2 symmetry of diffraction data. The conformations of the pyrrolidine rings are of the B type, i.e., C 2 ‐C β ‐ exo ‐C γ ‐ endo . For both polypeptides, the conformations of imino acids in position 3 of the triplet are the same; in position 2, however, they are slightly different. The difference in diffraction patterns for the 7/2 and 10/3 helices is discussed.