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Conformational study of dipeptides: A sensitivity analysis approach
Author(s) -
Susnow Roberta,
Schutt Clarence,
Rabitz Herschel,
Subramaniam Shankar
Publication year - 1994
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/jcc.540150905
Subject(s) - ramachandran plot , dipeptide , side chain , chemistry , stereochemistry , van der waals force , computational chemistry , crystallography , protein structure , amino acid , molecule , organic chemistry , biochemistry , polymer
This article studies the backbone influence on the side chains of N ‐methyl N ′‐acetyl amides (dipeptides) of alanine, valine, phenylalanine, leucine, isoleucine, glutamine, and lysine. Several local minima corresponding to protein ϕ, ψ, and χ values for each dipeptide are determined through optimization in the MM2 force field. These local minima are located in various regions on the Ramachandran map related to particular protein secondary structures. The dipeptide backbone influence on the side chain is explored via the sensitivity of the side chain torsion angles χ with respect to the backbone ϕ and ψ angles. Sensitivity coefficients are calculated, describing the χ response to an externally imposed change in ϕ or ψ. The χ response, which depends on the backbone conformation in a particular region, is induced primarily by the van der Waals and dipole interactions between the backbone and the side chain, which change with a deviation in ϕ or ψ. Various sensitivity trends are observed in the particular Ramachandran regions, revealing the subtle relationships between the dipeptide backbone and the side chain. © 1994 by John Wiley & Sons, Inc.