ArticleBiophysical journal2023
Influence of electronic polarization on the binding of anions to a chloride-pumping rhodopsin.
Article in Biophysical journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 11 citations in OpenAlex.
- NMR-Derived Salt Bridges in Insulin Analogue: Resolving Artifactual Overbinding in Molecular Dynamics via Charge Scaling.The journal of physical chemistry letters · 2025Article
- Electronic Polarizability Tunes the Function of the Human Bestrophin 1 ClJournal of chemical theory and computation · 2025Article
- Molecular dynamics simulations unveil the aggregation patterns and salting out of polyarginines at zwitterionic POPC bilayers in solutions of various ionic strengths.Computational and structural biotechnology journal · 2024Article
- Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field.Journal of chemical theory and computation · 2024Article
- Molecular mechanism of anion permeation through aquaporin 6.Biophysical journal · 2024Article
- Electronic Polarizability Tunes the Function of the Human Bestrophin 1 ClbioRxiv : the preprint server for biology · 2024Article
- AQcalc: A web server that identifies weak molecular interactions in protein structures.Protein science : a publication of the Protein Society · 2023Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The functional properties of some biological ion channels and membrane transport proteins are proposed to exploit anion-hydrophobic interactions. Here, we investigate a chloride-pumping rhodopsin as an example of a membrane protein known to contain a defined anion binding site composed predominantly of hydrophobic residues. Using molecular dynamics simulations, we explore Cl- binding to this hydrophobic site and compare the dynamics arising when electronic polarization is neglected (CHARMM36 [c36] fixed-charge force field), included implicitly (via the prosECCo force field), or included explicitly (through the polarizable force field, AMOEBA). Free energy landscapes of Cl- moving out of the binding site and into bulk solution demonstrate that the inclusion of polarization results in stronger ion binding and a second metastable binding site in chloride-pumping rhodopsin. Simulations focused on this hydrophobic binding site also indicate longer binding durations and closer ion proximity when polarization is included. Furthermore, simulations reveal that Cl- within this binding site interacts with an adjacent loop to facilitate rebinding events that are not observed when polarization is neglected. These results demonstrate how the inclusion of polarization can influence the behavior of anions within protein binding sites and can yield results comparable with more accurate and computationally demanding methods.
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