Influence of electronic polarization on the binding of anions to a chloride-pumping rhodopsin

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F23%3A00571004" target="_blank" >RIV/61388963:_____/23:00571004 - isvavai.cz</a>

Result on the web

<a href="https://doi.org/10.1016/j.bpj.2023.03.026" target="_blank" >https://doi.org/10.1016/j.bpj.2023.03.026</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.bpj.2023.03.026" target="_blank" >10.1016/j.bpj.2023.03.026</a>

Result language

angličtina

Original language name

Influence of electronic polarization on the binding of anions to a chloride-pumping rhodopsin

Original language description

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 Clˉ 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 Clˉ 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 Clˉ 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.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10403 - Physical chemistry

Project

—

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Biophysical Journal

ISSN

0006-3495

e-ISSN

1542-0086

Volume of the periodical

122

Issue of the periodical within the volume

8

Country of publishing house

US - UNITED STATES

Number of pages

9

Pages from-to

1548-1556

UT code for WoS article

000986127700001

EID of the result in the Scopus database

2-s2.0-85151559989