Influence of electronic polarization in a chloride-pumping rhodopsin binding site.

Abstract

Biological ion channels and membrane transport proteins are suggested to utilize anion-hydrophobic interactions to achieve selective anion transport. Here, we investigate a chloride-pumping rhodopsin (ClR) as an example of a Clˉ-selective protein known to contain a defined binding site composed predominantly of hydrophobic residues. Using molecular dynamics (MD) simulations, we explore Clˉ binding to this hydrophobic binding site and compare the dynamics arising when electronic polarization is either (i) neglected (CHARMM36 (c36) fixed-charge force field), (ii) included implicitly (via the prosECCo force field based on the electronic-continuum-correction method), or (iii) included explicitly (through the polarizable force field, AMOEBA). Free energy landscapes of a Clˉ moving out of the binding site and into bulk solution demonstrate stronger ion binding and exhibit a second metastable site with the inclusion of polarization effects. Simulations of a small protein fragment containing the binding site indicate longer binding durations and closer ion proximity with the inclusion of polarization. Finally, examination of larger protein fragment simulations consisting of the binding site and a neighboring loop reveal a mechanism that facilitates Clˉ rebinding events which are not observed with the non-polarizable force field. These results demonstrate the importance of modelling polarization (effects) which can influence the behavior of anions within real protein binding sites and suggest important mechanistic insights.