Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics.
Replica exchange molecular dynamics (MD) simulations of Met-enkephalin in explicit solvent reveal helical and nonhelical structures. Four predominant structures of Met-enkephalin are sampled with comparable probabilities (two helical and two nonhelical). The energy barriers between these configurations are low, suggesting that Met-enkephalin switches easily between configurations. This is consistent with the requirement that Met-enkephalin be sufficiently flexible to bind to several different receptors. Replica exchange simulations of 32 ns are shown to sample approximately five times more configurational space than constant temperature MD simulations of the same duration. The energy landscape for the replica exchange simulation is presented. A detailed study of replica trajectories demonstrates that the significant increases in temperature provided by the replica exchange technique enable transitions from nonhelical to helical structures that would otherwise be prevented by kinetic trapping. Met-enkephalin (Type Entrez Proteins; Value A61445; Service Entrez Proteins).
Sanbonmatsu
K Y
KY
Los Alamos National Laboratory, Los Alamos, New Mexico, USA. kys@lanl.gov
García
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AE
D000465:Algorithms; D004744:Enkephalin, Methionine / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D012996:Solutions; D013696:Temperature; D014867:Water
D012996:Solutions; D014867:Water; D004744:Enkephalin, Methionine