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Studying the Stability of a Helical β‐Heptapeptide by Molecular Dynamics Simulations
Author(s) -
Daura Xavier,
van Gunsteren Wilfred F.,
Rigo Dario,
Jaun Bernhard,
Seebach Dieter
Publication year - 1997
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.19970030907
Subject(s) - molecular dynamics , chemistry , methanol , molecule , pyridine , force field (fiction) , peptide , crystallography , molecular model , computational chemistry , stereochemistry , organic chemistry , physics , biochemistry , quantum mechanics
β‐Peptides consisting entirely of homochiral β‐amino acids R‐CH(NH 2 )‐CH 2 CO 2 H form 3 1 ‐helices in solution, as shown previously by NMR analysis of pyridine and methanol solutions. The stability of the helical secondary structure of one such β‐peptide (H‐β‐HVal‐β‐HAla‐β‐HLeu‐( S,S )‐β‐HAla(αMe)‐β‐HVal‐β‐HAla‐β‐HLeu‐OH, 1 ) has been investigated by molecular dynamics simulations using the GROMOS 96 molecular model and force field (962 methanol molecules; T = 298, 350, 400 K; with and without NOE distance restraints). The restraints derived from the NMR studies were equally well satisfied by both the restrained and the unrestrained room‐temperature molecular dynamics simulations. The 3 1 ‐helical conformation of 1 was shown to be so stable that it was restored spontaneously within 400 ps after unfolding had been induced by a sudden increase of the temperature from 298 to 350 K.