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Studies on the conformation of amino acids. IX. Conformations of butyl, seryl, threonyl, cysteinyl, and valyl residues in a dipeptide unit
Author(s) -
Ponnuswamy P. K.,
Sasisekharan V.
Publication year - 1971
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.360100311
Subject(s) - chemistry , dipeptide , intramolecular force , molecule , myoglobin , crystallography , residue (chemistry) , heteroatom , stereochemistry , hydrogen bond , lysozyme , conformational isomerism , side chain , sulfur , amino acid , ring (chemistry) , organic chemistry , biochemistry , polymer
Potential energies of conformation of a dipeptide unit with butyl, seryl, threonyl, eysteinyl, and valyl side groups have been computed by using classical energy expressions. The presence of a γ‐atom introduces characteristic restrictions on the backbone rotational angles ϕ and ψ the γ‐atom itself is restricted to three staggered positions about the C α —C β bond. The important results are that a γ‐carbon in position I (χ 1 ≃ 60°) cannot be accommodated in the standard right‐and left‐handed α‐helices, whereas a γ‐oxygen or sulfur could easily be accommodated in the right‐handed α‐helix. Further, a γ‐carbon or a heteroatom in position II (χ 1 ≃ 180°) does not favor a conformation ψ ≃ 180°, compared to two other positions. The valyl side group significantly reduces the allowed ϕ and ψ values and energetically prefers a β‐conformation compared to right‐or left‐handed α‐helical conformations. The less favorable α‐helical conformation is possible only for γ (III, II) combination of the valyl residue. The observed ϕ, ψ, and χ 1 values of all the amino acid residues in the three protein molecules, lysozyme, myoglobin, and chymotrypsin are compared with the theoretical predictions and the agreement is excellent. The results bring out the important fact that even in large molecules, the conformation of local segments are predominantly governed by the short‐range intramolecular interactions.