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Computer simulations of a tumor surface octapeptide epitope
Author(s) -
Reid Robert H.,
Hooper Charles A.,
Brooks Bernard R.
Publication year - 1989
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.360280146
Subject(s) - chemistry , epitope , molecular dynamics , turn (biochemistry) , glycoprotein , helix (gastropod) , crystallography , linear epitope , stereochemistry , antigen , peptide sequence , biochemistry , computational chemistry , immunology , gene , biology , ecology , snail
Molecular dynamics using CHARMM and GEMM programs with the Star Technologies ST 100 array processor functioning at the speed of super computers was used as a searching algorithm for conformational exploration of the octapeptide Gly‐Asn‐Thr‐Ile‐Val‐Ala‐Glu. This poorly soluble octapeptide is the N‐terminal epitope of an 11 KD glycoprotein antigen residing on human ductal carcinoma (breast) cells. Very long (nanoseconds) simulations were required. Both an α‐helix and the N‐acetyl‐N 1 ‐methylamide derived minimized starting structures gave the same lowest potential energy conformation with simulations at 600 K. The same conformation was found only when using the latter starting conformation with simulations at 300 K. The lowest potential energy conformation was stabilized by 4 hydrophobic contacts and 13 H bonds completing one turn of a left‐handed helix.