Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.

The leucine transporter (LeuT) has recently commanded exceptional attention due mainly to two distinctions; it provides the only crystal structures available for a protein homologous to the pharmacologically relevant neurotransmitter: sodium symporters (NSS), and, it exhibits a hallmark 5-TM inverte...

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Autores principales:	Saher Afshan Shaikh, Emad Tajkhorshid
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/0730c8c591574c7da34dfbbf460cc1e3
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spelling	oai:doaj.org-article:0730c8c591574c7da34dfbbf460cc1e32021-11-18T05:49:22ZModeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.1553-734X1553-735810.1371/journal.pcbi.1000905https://doaj.org/article/0730c8c591574c7da34dfbbf460cc1e32010-08-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20865057/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The leucine transporter (LeuT) has recently commanded exceptional attention due mainly to two distinctions; it provides the only crystal structures available for a protein homologous to the pharmacologically relevant neurotransmitter: sodium symporters (NSS), and, it exhibits a hallmark 5-TM inverted repeat ("LeuT-fold"), a fold recently discovered to also exist in several secondary transporter families, underscoring its general role in transporter function. Constructing the transport cycle of "LeuT-fold" transporters requires detailed structural and dynamic descriptions of the outward-facing (OF) and inward-facing (IF) states, as well as the intermediate states. To this end, we have modeled the structurally unknown IF state of LeuT, based on the known crystal structures of the OF state of LeuT and the IF state of vSGLT, a "LeuT-fold" transporter. The detailed methodology developed for the study combines structure-based alignment, threading, targeted MD and equilibrium MD, and can be applied to other proteins. The resulting IF-state models maintain the secondary structural features of LeuT. Water penetration and solvent accessibility calculations show that TM1, TM3, TM6 and TM8 line the substrate binding/unbinding pathway with TM10 and its pseudosymmetric partner, TM5, participating in the extracellular and intracellular halves of the lumen, respectively. We report conformational hotspots where notable changes in interactions occur between the IF and OF states. We observe Na2 exiting the LeuT-substrate- complex in the IF state, mainly due to TM1 bending. Inducing a transition in only one of the two pseudosymmetric domains, while allowing the second to respond dynamically, is found to be sufficient to induce the formation of the IF state. We also propose that TM2 and TM7 may be facilitators of TM1 and TM6 motion. Thus, this study not only presents a novel modeling methodology applied to obtain the IF state of LeuT, but also describes structural elements involved in a possibly general transport mechanism in transporters adopting the "LeuT-fold".Saher Afshan ShaikhEmad TajkhorshidPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 6, Iss 8 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Saher Afshan Shaikh Emad Tajkhorshid Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.
description	The leucine transporter (LeuT) has recently commanded exceptional attention due mainly to two distinctions; it provides the only crystal structures available for a protein homologous to the pharmacologically relevant neurotransmitter: sodium symporters (NSS), and, it exhibits a hallmark 5-TM inverted repeat ("LeuT-fold"), a fold recently discovered to also exist in several secondary transporter families, underscoring its general role in transporter function. Constructing the transport cycle of "LeuT-fold" transporters requires detailed structural and dynamic descriptions of the outward-facing (OF) and inward-facing (IF) states, as well as the intermediate states. To this end, we have modeled the structurally unknown IF state of LeuT, based on the known crystal structures of the OF state of LeuT and the IF state of vSGLT, a "LeuT-fold" transporter. The detailed methodology developed for the study combines structure-based alignment, threading, targeted MD and equilibrium MD, and can be applied to other proteins. The resulting IF-state models maintain the secondary structural features of LeuT. Water penetration and solvent accessibility calculations show that TM1, TM3, TM6 and TM8 line the substrate binding/unbinding pathway with TM10 and its pseudosymmetric partner, TM5, participating in the extracellular and intracellular halves of the lumen, respectively. We report conformational hotspots where notable changes in interactions occur between the IF and OF states. We observe Na2 exiting the LeuT-substrate- complex in the IF state, mainly due to TM1 bending. Inducing a transition in only one of the two pseudosymmetric domains, while allowing the second to respond dynamically, is found to be sufficient to induce the formation of the IF state. We also propose that TM2 and TM7 may be facilitators of TM1 and TM6 motion. Thus, this study not only presents a novel modeling methodology applied to obtain the IF state of LeuT, but also describes structural elements involved in a possibly general transport mechanism in transporters adopting the "LeuT-fold".
format	article
author	Saher Afshan Shaikh Emad Tajkhorshid
author_facet	Saher Afshan Shaikh Emad Tajkhorshid
author_sort	Saher Afshan Shaikh
title	Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.
title_short	Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.
title_full	Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.
title_fullStr	Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.
title_full_unstemmed	Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.
title_sort	modeling and dynamics of the inward-facing state of a na+/cl- dependent neurotransmitter transporter homologue.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/0730c8c591574c7da34dfbbf460cc1e3
work_keys_str_mv	AT saherafshanshaikh modelinganddynamicsoftheinwardfacingstateofanacldependentneurotransmittertransporterhomologue AT emadtajkhorshid modelinganddynamicsoftheinwardfacingstateofanacldependentneurotransmittertransporterhomologue
_version_	1718424769732280320

Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.

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