Simulations of the pressure and temperature unfolding of an alpha-helical peptide.
We study by molecular simulations the reversible folding/unfolding equilibrium as a function of density and temperature of a solvated alpha-helical peptide. We use an extension of the replica exchange molecular dynamics method that allows for density and temperature Monte Carlo exchange moves. We studied 360 thermodynamic states, covering a density range from 0.96 to 1.14 g.cm(-3) and a temperature range from 300 to 547.6 K. We simulated 10 ns per replica for a total simulation time of 3.6 micros. We characterize the structural, thermodynamic, and hydration changes as a function of temperature and pressure. We also calculate the compressibility and expansivity of unfolding. We find that pressure does not affect the helix-coil equilibrium significantly and that the volume change upon pressure unfolding is small and negative (-2.3 ml/mol). However, we find significant changes in the coordination of water molecules to the backbone carbonyls. This finding predicts that changes in the chemical shifts and IR spectra with pressure can be due to changes in coordination and not only changes in the helical content. A simulation of the IR spectrum shows that water coordination effects on frequency shifts are larger than changes due to elastic structural changes in the peptide.
Paschek
Dietmar
D
Department of Physical Chemistry, Otto-Hahn Strasse 6, University of Dortmund, D-44221 Dortmund, Germany.
Gnanakaran
S
S
Garcia
Angel E
AE
D002244:Carbon / Q000737:chemistry; D003198:Computer Simulation; D008239:Lysine / Q000737:chemistry; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry; D011312:Pressure; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012984:Software; D013055:Spectrophotometry, Infrared; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors
D009842:Oligopeptides; D010455:Peptides; D002244:Carbon; D008239:Lysine