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Computer building of β‐helical polypeptide models
Author(s) -
Koeppe Roger E.,
Kimura Michio
Publication year - 1984
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.360230104
Subject(s) - turn (biochemistry) , chemistry , helix (gastropod) , dipeptide , unit (ring theory) , hydrogen bond , crystallography , peptide , molecule , mathematics , organic chemistry , ecology , biochemistry , mathematics education , snail , biology
A general method is presented for computing the atomic coordinates of helices in which a dipeptide is the repeating unit. The method will generate both single‐ and double‐stranded model helices having idealized bond lengths and angles, and any arbitrary, user‐specified, pitch and number of residues per turn. The variation of inter‐ and intrastrand hydrogen bonds with pitch and number of residues per turn can thus be examined. An application of the method is the construction of a β‐helix having pitch of 6.3 Å per turn and 4.85 residues per turn, a model which can pack nicely into the unit cell of crystals of cation‐bound gramicidin A.