Solvent effects and hydration of a tripeptide in sodium halide aqueous solutions: an in silico study.
In this work we are trying to gain insight into the mechanisms of ion-protein interactions in aqueous media at the molecular scale through fully atomistic molecular dynamics simulations. We present a systematic molecular simulation study of interactions of sodium and halide ions with a trialanine peptide in aqueous sodium halide solutions with different salts concentrations (0.20, 0.50, 1.0 and 2.0 M). Each simulation covers more than fifty nanoseconds to ensure the convergence of the results and to enable a proper determination of the tripeptide-ion interactions through the potentials of mean force. Changes in ion densities in the vicinity of different peptide groups are analysed and implications for the tripeptide conformations are discussed.
Fedorov
Maxim V
MV
Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UKCB2 1EW.
Goodman
Jonathan M
JM
Schumm
Stephan
S
D001965:Bromides / Q000737:chemistry*; D003198:Computer Simulation; D004563:Electrochemistry; D007452:Iodates / Q000737:chemistry*; D007477:Ions; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory; D012965:Sodium Chloride / Q000737:chemistry*; D017670:Sodium Compounds / Q000737:chemistry*; D012969:Sodium Fluoride / Q000737:chemistry*; D012996:Solutions; D012997:Solvents / Q000737:chemistry; D014867:Water / Q000737:chemistry*
D001965:Bromides; D007452:Iodates; D007477:Ions; D009842:Oligopeptides; D017670:Sodium Compounds; D012996:Solutions; D012997:Solvents; D014867:Water; D012965:Sodium Chloride; C039944:alanyl-alanyl-alanine; D012969:Sodium Fluoride; C027938:sodium bromide; C032285:sodium iodate