alanyl-alanyl-alanine and sodium-bromide

The electric field effects on conformational properties of trialanine in different halide solutions were explored with long-scale molecular dynamics simulations. NaF, NaCl, NaBr and NaI solutions of low (0.2 M) and high (2 M) concentrations were exposed to a constant electric field of 1000 V/m. Generally, the electric field does not disturb trialanine's structure. Large structural changes appear only in the case of the supersaturated 2.0 M NaF solution containing NaF crystals. Although the electric field affects in a complex way, all the ions-water-peptide interactions, it predominantly affects the electroselectivity effect, which describes specific interactions such as the ion-pair formation.

Topics: Bromides; Electromagnetic Fields; Halogens; Ions; Molecular Dynamics Simulation; Oligopeptides; Sodium Chloride; Sodium Compounds; Sodium Fluoride; Sodium Iodide; Software; Solutions; Water

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.

Topics: Bromides; Computer Simulation; Electrochemistry; Iodates; Ions; Oligopeptides; Protein Conformation; Quantum Theory; Sodium Chloride; Sodium Compounds; Sodium Fluoride; Solutions; Solvents; Water