Dependence of Interaction Free Energy between Solutes on an External Electrostatic Field

Abstract

To explore the athermal effect of an external electrostatic field on the stabilities of protein conformations and the binding affinities of protein-protein/ligand interactions, the dependences of the polar and hydrophobic interactions on the external electrostatic field, −Eext, were studied using molecular dynamics (MD) simulations. By decomposing Eext into, along, and perpendicular to the direction formed by the two solutes, the effect of Eext on the interactions between these two solutes can be estimated based on the effects from these two components. Eext was applied along the direction of the electric dipole formed by two solutes with opposite charges. The attractive interaction free energy between these two solutes decreased for solutes treated as point charges. In contrast, the attractive interaction free energy between these two solutes increased, as observed by MD simulations, for Eext = 40 or 60 MV/cm. Eext was applied perpendicular to the direction of the electric dipole formed by these two solutes. The attractive interaction free energy was increased for Eext = 100 MV/cm as a result of dielectric saturation. The force on the solutes along the direction of Eext computed from MD simulations was greater than that estimated from a continuum solvent in which the solutes were treated as point charges. To explore the hydrophobic interactions, Eext was applied to a water cluster containing two neutral solutes. The repulsive force between these solutes was decreased/increased for Eext along/perpendicular to the direction of the electric dipole formed by these two solutes.

Resonance-driven ion transport and selectivity in prokaryotic ion channels

“…Here q A and q B are the effective electrical charges of an aqua ion and a bare ion, respectively, and n is the local particle density. This difference quantifies the effect of electrostatic screening on hydrated ions by the envelope dipole water molecules on short-range electrostatic interactions [79,80]. The electrostatic potential is calculated concurrently with Eqs.…”

Effect of external electrostatic field on the stability of β sheet structures

“…The simulation system was built with a parallel or antiparallel β sheet containing two β strands in the water cluster with a radius of 20 Å. or was applied to the water cluster using the modified and verified CHARMM package . The β sheet was positioned near the center of the spherical water cluster.…”

“…The amplitude of the EEF was chosen based on the following results. For the EEF, when E ext was applied to TIP3P water cluster, the electric dipole moment per water molecule was proportional to E ext value in the cases when E ext <40 MV/cm, and the proportionality constant significantly reduced in the cases when E ext >60 MV/cm . For one of the charged atom with charge Q in the water cluster, the electric dipole moment per water molecule in the first coordination shell was proportional to the charge Q in the cases when | Q | <1.0 e .…”

“…However, the solvent molecular density and dielectric polarization computed by the continuum solvent model were different from those computed by the MD simulations . Therefore, the dependence of the interactions between the charged atoms in biomolecules on the EEF has been explored using the MD simulations and an explicit solvent model …”

“…The dependence of the polarization of water molecules, and the interaction mean forces between the charged or neutral atoms in a water cluster on the EEF have been explored using MD simulations . Hydrogen bonds play a significant role in the stability of a protein conformation and binding affinity of the protein–protein/ligand interactions.…”