Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide.
The rate constant for the transition between the equatorial and axial conformations of N-acetylalanyl-N'-methylamide has been determined from Langevin dynamics (LD) simulations with no explicit solvent. The isomerization rate is maximum at collision frequency gamma = 2 ps-1, shows diffusive character for gamma greater than or equal to 10 ps-1, but does not approach zero even at gamma = 0.01 ps-1. This behavior differs from that found for a one-dimensional bistable potential and indicates that both collisional energy transfer with solvent and vibrational energy transfer between internal modes are important in the dynamics of barrier crossing for this system. It is suggested that conformational searches of peptides be carried out using LD with a collision frequency that maximizes the isomerization rate (i.e., gamma approximately 2 ps-1). This method is expected to be more efficient than either molecular dynamics in vacuo (which corresponds to LD with gamma = 0) or molecular dynamics in solvent (where dynamics is largely diffusive).
Loncharich
R J
RJ
Division of Computer Research and Technology, National Institutes of Health, Bethesda, Maryland 20892.
Brooks
B R
BR
Pastor
R W
RW
D000409:Alanine / Q000031:analogs & derivatives* / Q000737:chemistry; D003198:Computer Simulation; D007536:Isomerism; D007700:Kinetics; D008433:Mathematics; D008962:Models, Theoretical
C024314:N-acetylalanyl-N-methylamide; D000409:Alanine