Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl−/H+ Antiporter

Intracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl− anion and a proton (H+), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at n...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Ekaterina Kots, Derek M. Shore, Harel Weinstein
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	CLC transporters pH-dependent activity molecular dynamics (MD) simulations high-resolution atomic force microscopy (HR-AFM) protonation state representations net charge conservation protocol Organic chemistry QD241-441
Acceso en línea:	https://doaj.org/article/3fcb8aab014141448b78da10c6219dc3
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:3fcb8aab014141448b78da10c6219dc3
record_format	dspace
spelling	oai:doaj.org-article:3fcb8aab014141448b78da10c6219dc32021-11-25T18:28:42ZSimulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter10.3390/molecules262269561420-3049https://doaj.org/article/3fcb8aab014141448b78da10c6219dc32021-11-01T00:00:00Zhttps://www.mdpi.com/1420-3049/26/22/6956https://doaj.org/toc/1420-3049Intracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl<sup>−</sup> anion and a proton (H<sup>+</sup>), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at neutral pH. However, a structure of the WT protein at acidic pH is not available, making it difficult to assess the global conformational rearrangements that support a pH-dependent gating mechanism. To enable modeling of the CLC-ec1 dimer at acidic pH, we have applied molecular dynamics simulations (MD) featuring a new force field modification scheme—termed an Equilibrium constant pH approach (ECpH). The ECpH method utilizes linear interpolation between the force field parameters of protonated and deprotonated states of titratable residues to achieve a representation of pH-dependence in a narrow range of physiological pH values. Simulations of the CLC-ec1 dimer at neutral and acidic pH comparing ECpH-MD to canonical MD, in which the pH-dependent protonation is represented by a binary scheme, substantiates the better agreement of the conformational changes and the final model with experimental data from NMR, cross-link and AFM studies, and reveals structural elements that support the gate-opening at pH 4.5, including the key glutamates Glu<sub>in</sub> and Glu<sub>ex</sub>.Ekaterina KotsDerek M. ShoreHarel WeinsteinMDPI AGarticleCLC transporterspH-dependent activitymolecular dynamics (MD) simulationshigh-resolution atomic force microscopy (HR-AFM)protonation state representationsnet charge conservation protocolOrganic chemistryQD241-441ENMolecules, Vol 26, Iss 6956, p 6956 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	CLC transporters pH-dependent activity molecular dynamics (MD) simulations high-resolution atomic force microscopy (HR-AFM) protonation state representations net charge conservation protocol Organic chemistry QD241-441
spellingShingle	CLC transporters pH-dependent activity molecular dynamics (MD) simulations high-resolution atomic force microscopy (HR-AFM) protonation state representations net charge conservation protocol Organic chemistry QD241-441 Ekaterina Kots Derek M. Shore Harel Weinstein Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter
description	Intracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl<sup>−</sup> anion and a proton (H<sup>+</sup>), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at neutral pH. However, a structure of the WT protein at acidic pH is not available, making it difficult to assess the global conformational rearrangements that support a pH-dependent gating mechanism. To enable modeling of the CLC-ec1 dimer at acidic pH, we have applied molecular dynamics simulations (MD) featuring a new force field modification scheme—termed an Equilibrium constant pH approach (ECpH). The ECpH method utilizes linear interpolation between the force field parameters of protonated and deprotonated states of titratable residues to achieve a representation of pH-dependence in a narrow range of physiological pH values. Simulations of the CLC-ec1 dimer at neutral and acidic pH comparing ECpH-MD to canonical MD, in which the pH-dependent protonation is represented by a binary scheme, substantiates the better agreement of the conformational changes and the final model with experimental data from NMR, cross-link and AFM studies, and reveals structural elements that support the gate-opening at pH 4.5, including the key glutamates Glu<sub>in</sub> and Glu<sub>ex</sub>.
format	article
author	Ekaterina Kots Derek M. Shore Harel Weinstein
author_facet	Ekaterina Kots Derek M. Shore Harel Weinstein
author_sort	Ekaterina Kots
title	Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter
title_short	Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter
title_full	Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter
title_fullStr	Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter
title_full_unstemmed	Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter
title_sort	simulation of ph-dependent conformational transitions in membrane proteins: the clc-ec1 cl<sup>−</sup>/h<sup>+</sup> antiporter
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/3fcb8aab014141448b78da10c6219dc3
work_keys_str_mv	AT ekaterinakots simulationofphdependentconformationaltransitionsinmembraneproteinstheclcec1clsupsuphsupsupantiporter AT derekmshore simulationofphdependentconformationaltransitionsinmembraneproteinstheclcec1clsupsuphsupsupantiporter AT harelweinstein simulationofphdependentconformationaltransitionsinmembraneproteinstheclcec1clsupsuphsupsupantiporter
_version_	1718411069618126848

Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter

Ejemplares similares