Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models.
Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical structure and receptor docking mechanism are still not well understood. The conformational dynamics of this neuron peptide in liquid water are studied here by using all-atom molecular dynamics (MD) and implicit water Langevin dynamics (LD) simulations with AMBER potential functions and the three-site transferable intermolecular potential (TIP3P) model for water. To achieve the same simulation length in physical time, the full MD simulations require 200 times as much CPU time as the implicit water LD simulations. The solvent hydrophobicity and dielectric behavior are treated in the implicit solvent LD simulations by using a macroscopic solvation potential, a single dielectric constant, and atomic friction coefficients computed using the accessible surface area method with the TIP3P model water viscosity as determined here from MD simulations for pure TIP3P water. Both the local and the global dynamics obtained from the implicit solvent LD simulations agree very well with those from the explicit solvent MD simulations. The simulations provide insights into the conformational restrictions that are associated with the bioactivity of the opiate peptide dermorphin for the delta-receptor.
Shen My
Min-yi
MY
James Franck Institute and Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.
Freed
Karl F
KF
D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D004744:Enkephalin, Methionine / Q000737:chemistry*; D008956:Models, Chemical; D009294:Narcotics / Q000737:chemistry; D009842:Oligopeptides / Q000737:chemistry; D018847:Opioid Peptides; D011487:Protein Conformation; D017465:Receptors, Opioid, delta / Q000378:metabolism; D012997:Solvents; D013696:Temperature; D013997:Time Factors; D014867:Water / Q000737:chemistry
D009294:Narcotics; D009842:Oligopeptides; D018847:Opioid Peptides; D017465:Receptors, Opioid, delta; D012997:Solvents; D014867:Water; C030058:dermorphin; D004744:Enkephalin, Methionine