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Computer simulations of the flexibility of a series of synthetic cyclic peptide analogues
Author(s) -
Thomas Aline,
Roux Benoit,
Smith Jeremy C.
Publication year - 1993
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.360330811
Subject(s) - molecular dynamics , chemistry , molecule , flexibility (engineering) , peptide , normal mode , chemical physics , cyclic peptide , series (stratigraphy) , computational chemistry , statistical physics , biological system , harmonic , physics , quantum mechanics , vibration , organic chemistry , paleontology , biochemistry , statistics , mathematics , biology
Abstract The flexibility of a series of cyclic peptides derived from the epitope of a snake toxin is investigated using computer simulation techniques. Molecular dynamics (MD) simulations and vibrational analyses are performed on chemically constrained peptides modeled on the parent protein loop. In the 50 ps MD simulations, large variations in the atomic fluctuations are seen between the peptides, and can be related to the nature of the chemical constraints present in the molecules. Normal mode analyses are performed on energy‐minimized configurations derived from the dynamics trajectories. The atomic fluctuations calculated from the normal modes are about 30% of those of the molecular dynamics for the more flexible peptides and 70% for the more constrained molecules. The calculated differences in flexibility between the molecules are much less significant in the harmonic approximation. © 1993 John Wiley & Sons, Inc.