Conformational regions of Boc-Ala-Aib-Ala-OMe. Sampling with molecular dynamics simulations using time averaging of distance restraints.
The method of time averaging of distance restraints in molecular dynamics simulations is applied to Boc-Ala-Aib-Ala-OMe in order to demonstrate the improved sampling properties of this method compared to conventional distance restraining. Two conformational regions, beta-turn type II and gamma-turn, are seen during MD runs at a simulation temperature of 500 K, while in simulations with conventional distance restraining, no conformational transitions could be observed for temperatures up to 1000 K.
Brunne
R M
RM
Institute of Organic Chemistry, University of Bremen, Federal Republic of Germany.
Leibfritz
D
D
D000595:Amino Acid Sequence; D003198:Computer Simulation; D008432:Mathematical Computing; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry*; D017433:Protein Structure, Secondary
D009842:Oligopeptides; C079226:tert-butyloxycarbonyl-alanyl-aminoisobutyryl-alanyl methyl ester