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Numerical Simulation of the Effect of Solvent Viscosity on the Motions of a β‐Peptide Heptamer
Author(s) -
Gee Peter J.,
van Gunsteren Wilfred F.
Publication year - 2005
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.200500587
Subject(s) - viscosity , methanol , solvent , folding (dsp implementation) , chemistry , molecular dynamics , thermodynamics , protein folding , peptide , solvent effects , molecule , computational chemistry , organic chemistry , physics , biochemistry , electrical engineering , engineering
This report examines the effect of a decrease in solvent viscosity on the simulated folding behaviour of a β‐peptide heptamer in methanol. Simulations of the molecular dynamics of the heptamer H‐β 3 ‐HVal‐β 3 ‐HAla‐β 3 ‐HLeu‐( S , S )‐β 3 ‐HAla(αMe)‐β 3 ‐HVal‐β 3 ‐HAla‐β 3 ‐HLeu‐OH in methanol, with an explicit representation of the methanol molecules, were performed for 80 ns at various solvent viscosities. The simulations indicate that at a solvent viscosity of one third of that of methanol, only the dynamic aspects of the folding process are altered, and that the rate of folding is increased. At a viscosity of one tenth of that of methanol, insufficient statistics are obtained within the 80 ns period. We suggest that 80 ns is an insufficient time to reach conformational equilibrium at very low viscosity because the dependence of the folding rate of a β‐peptide on solvent viscosity has two regimes; a result that was observed in another computational study for α‐peptides.