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Conformational energy calculations with averaged potential functions: Application to the repeat peptides of elastin
Author(s) -
Ralston Evelyn,
Somorjai R. L.
Publication year - 1979
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.1979.360180212
Subject(s) - chemistry , peptide , side chain , elastin , atom (system on chip) , group (periodic table) , computation , center (category theory) , crystallography , computational chemistry , stereochemistry , organic chemistry , algorithm , biochemistry , medicine , pathology , computer science , embedded system , polymer
We present a method that can reduce conformational energy calculations for an arbitrary peptide consisting of n residues ( n ‐peptide) to the complexity of a computation for (Gly) n . This reduction, and the concomitant savings in computer time, is accomplished by replacing all side chains, as well as the backbone C α H α and C α H 2 α groups, by “interaction centers.” The backbone CONH group is left intact in order to preserve its directional character. The interaction centers “see” each other, and the atoms of the CONH group via Boltzmann and space‐averaged effective center‐center and center‐atom potentials, respectively. This averaged‐interaction method is tested on the repeat tetra‐, penta‐, and hexapeptides of elastin, Val‐Pro‐Gly‐Gly (VPGG), Val‐Pro‐Gly‐Val‐Gly (VPGVP), and Ala‐Pro‐Gly‐Val‐Gly‐Val (APGVGV), using the stereoalphabet strategy for the energy calculations. The excellent qualitative and quantitative agreement we obtain with both full atom‐atom calculations and extensive nmr data, coupled with the order‐of‐magnitude reduction in computer time, augurs well for the potential usefulness of the method.