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Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP

Mechanistic understanding of dynamic membrane proteins such as transporters, receptors, and channels requires accurate depictions of conformational ensembles, and the manner in which they interchange as a function of environmental factors including substrates, lipids, and inhibitors. Spectroscopic t...

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Autores principales: Leone, Vanessa, Waclawska, Izabela, Kossmann, Katharina, Koshy, Caroline, Sharma, Monika, Prisner, Thomas F., Ziegler, Christine, Endeward, Burkhard, Forrest, Lucy R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Rockefeller University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400524/
https://www.ncbi.nlm.nih.gov/pubmed/30728216
http://dx.doi.org/10.1085/jgp.201812111
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author Leone, Vanessa
Waclawska, Izabela
Kossmann, Katharina
Koshy, Caroline
Sharma, Monika
Prisner, Thomas F.
Ziegler, Christine
Endeward, Burkhard
Forrest, Lucy R.
author_facet Leone, Vanessa
Waclawska, Izabela
Kossmann, Katharina
Koshy, Caroline
Sharma, Monika
Prisner, Thomas F.
Ziegler, Christine
Endeward, Burkhard
Forrest, Lucy R.
author_sort Leone, Vanessa
collection PubMed
description Mechanistic understanding of dynamic membrane proteins such as transporters, receptors, and channels requires accurate depictions of conformational ensembles, and the manner in which they interchange as a function of environmental factors including substrates, lipids, and inhibitors. Spectroscopic techniques such as electron spin resonance (ESR) pulsed electron–electron double resonance (PELDOR), also known as double electron–electron resonance (DEER), provide a complement to atomistic structures obtained from x-ray crystallography or cryo-EM, since spectroscopic data reflect an ensemble and can be measured in more native solvents, unperturbed by a crystal lattice. However, attempts to interpret DEER data are frequently stymied by discrepancies with the structural data, which may arise due to differences in conditions, the dynamics of the protein, or the flexibility of the attached paramagnetic spin labels. Recently, molecular simulation techniques such as EBMetaD have been developed that create a conformational ensemble matching an experimental distance distribution while applying the minimal possible bias. Moreover, it has been proposed that the work required during an EBMetaD simulation to match an experimentally determined distribution could be used as a metric with which to assign conformational states to a given measurement. Here, we demonstrate the application of this concept for a sodium-coupled transport protein, BetP. Because the probe, protein, and lipid bilayer are all represented in atomic detail, the different contributions to the work, such as the extent of protein backbone movements, can be separated. This work therefore illustrates how ranking simulations based on EBMetaD can help to bridge the gap between structural and biophysical data and thereby enhance our understanding of membrane protein conformational mechanisms.
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spelling pubmed-64005242019-03-07 Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP Leone, Vanessa Waclawska, Izabela Kossmann, Katharina Koshy, Caroline Sharma, Monika Prisner, Thomas F. Ziegler, Christine Endeward, Burkhard Forrest, Lucy R. J Gen Physiol Research Articles Mechanistic understanding of dynamic membrane proteins such as transporters, receptors, and channels requires accurate depictions of conformational ensembles, and the manner in which they interchange as a function of environmental factors including substrates, lipids, and inhibitors. Spectroscopic techniques such as electron spin resonance (ESR) pulsed electron–electron double resonance (PELDOR), also known as double electron–electron resonance (DEER), provide a complement to atomistic structures obtained from x-ray crystallography or cryo-EM, since spectroscopic data reflect an ensemble and can be measured in more native solvents, unperturbed by a crystal lattice. However, attempts to interpret DEER data are frequently stymied by discrepancies with the structural data, which may arise due to differences in conditions, the dynamics of the protein, or the flexibility of the attached paramagnetic spin labels. Recently, molecular simulation techniques such as EBMetaD have been developed that create a conformational ensemble matching an experimental distance distribution while applying the minimal possible bias. Moreover, it has been proposed that the work required during an EBMetaD simulation to match an experimentally determined distribution could be used as a metric with which to assign conformational states to a given measurement. Here, we demonstrate the application of this concept for a sodium-coupled transport protein, BetP. Because the probe, protein, and lipid bilayer are all represented in atomic detail, the different contributions to the work, such as the extent of protein backbone movements, can be separated. This work therefore illustrates how ranking simulations based on EBMetaD can help to bridge the gap between structural and biophysical data and thereby enhance our understanding of membrane protein conformational mechanisms. Rockefeller University Press 2019-03-04 /pmc/articles/PMC6400524/ /pubmed/30728216 http://dx.doi.org/10.1085/jgp.201812111 Text en © 2019 Leone et al. https://creativecommons.org/licenses/by/4.0/This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).
spellingShingle Research Articles
Leone, Vanessa
Waclawska, Izabela
Kossmann, Katharina
Koshy, Caroline
Sharma, Monika
Prisner, Thomas F.
Ziegler, Christine
Endeward, Burkhard
Forrest, Lucy R.
Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP
title Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP
title_full Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP
title_fullStr Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP
title_full_unstemmed Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP
title_short Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP
title_sort interpretation of spectroscopic data using molecular simulations for the secondary active transporter betp
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400524/
https://www.ncbi.nlm.nih.gov/pubmed/30728216
http://dx.doi.org/10.1085/jgp.201812111
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