Structure and dynamics of end-to-end loop formation of the penta-peptide Cys-Ala-Gly-Gln-Trp in implicit solvents.
To investigate the effects of implicit solvents on peptide structure and dynamics, we performed extensive molecular dynamics simulations on the penta-peptide Cys-Ala-Gly-Gln-Trp. Two different implicit solvent models based on the CHARMM22 all-atom force field were used. Structural properties of the peptide such as distributions of end-to-end distances and dihedral angles obtained from molecular dynamics simulations with implicit solvent models were in a good agreement with those obtained from a previous explicit solvent simulation using the same force field. Representative structures observed in explicit solvent were sampled by implicit solvent models but with different relative probabilities. However, we observed significant differences in dynamical properties in explicit and implicit solvent models when we used traditional methods for the temperature control, such as Nose-Hoover or Berendsen thermostats. The explicitly solvated peptide displayed the slowest dynamics in both end-to-end contact formation and intrinsic diffusive motion of end-to-end distances. A closer agreement between implicit and explicit solvated peptide dynamics was observed when Langevin dynamics with a friction coefficient of 10 ps(-1) was used to maintain the temperature of the systems.
Yeh
In-Chul
IC
Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702-5012, USA. icy@bioanalysis.org
Wallqvist
Anders
A
D000595:Amino Acid Sequence; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*
D010455:Peptides; D012997:Solvents