Polarization Effects on Peptide Conformations at Water]Membrane Interface by Molecular Dynamics Simulation

Abstract

The electrostatic image method was applied to investigate the conformation of peptides characterized by different hydrophobicities in a water]membrane interface model. The interface was represented by a surface of discontinuity between two media with different dielectric constants, taking into account the difference between the polarizabilities of the aqueous medium and the hydrocarbon one. The method consists of a substitution of the real problem, which involves the charges and the induced polarization at the surface of discontinuity, by a simpler problem formed with charges and their images. The electric field due to the polarization induced at the surface by charge q was calculated using a hypothetical charge q9 image of q., symmetrically located on the opposite side of the surface. The value of q9 was determined using the appropriate electrostatic boundary conditions at the surface. By means of this procedure, the effect of the interface can be introduced easily in the usual force field. We included this extension in the computational package that we are developing for molecular dynamics simulations THOR.. The peptides studied included hydrophilic tetraaspartic acid Asp]Asp]Asp]Asp., tetralysine Lys]Lys]Lys]Lys., hydrophobic tetrapeptide His]Phe]Arg]Trp., an amphiphilic fragment of b-endorphin, and the signal sequence of the E. coli l-receptor. The simulation results are in agreement with known experimental data regarding the behavior of peptides at the water]membrane interface. An analysis of the conformational dynamics of the signal sequence peptide at the interface was performed over the course of a few nanoseconds.