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

Leone, V., Waclawska, I., Kossmann, K., Koshy, C., Sharma, M., Prisner, T. F., et al. (2019). Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP. Journal of General Physiology, 151(3), 381-394. doi:10.1085/jgp.201812111.

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 Creators:
Leone, Vanessa1, Author
Waclawska, Izabela2, Author              
Kossmann, Katharina3, Author
Koshy, Caroline2, Author              
Sharma, Monika1, Author
Prisner, Thomas F.4, Author
Ziegler, Christine3, Author
Endeward, Burkhard4, Author
Forrest, Lucy R.1, Author
Affiliations:
1Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, ou_persistent22              
2Department of Structural Biology, Max Planck Institute of Biophysics, Max Planck Society, ou_2068291              
3Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Regensburg, Germany, ou_persistent22              
4Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany, ou_persistent22              

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 Abstract: 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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Language(s): eng - English
 Dates: 2018-11-262018-04-272019-01-112019-02-062019-03-04
 Publication Status: Published in print
 Pages: 14
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1085/jgp.201812111
 Degree: -

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Title: Journal of General Physiology
  Other : J. Gen. Physiol.
  Abbreviation : JGP
Source Genre: Journal
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Publ. Info: Rockefeller University Press
Pages: 14 Volume / Issue: 151 (3) Sequence Number: - Start / End Page: 381 - 394 Identifier: ISSN: 0022-1295
CoNE: https://pure.mpg.de/cone/journals/resource/954925413895