Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP. J Gen Physiol 2019 Mar 04;151(3):381-394
Date
02/08/2019Pubmed ID
30728216Pubmed Central ID
PMC6400524DOI
10.1085/jgp.201812111Scopus ID
2-s2.0-85062413313 (requires institutional sign-in at Scopus site) 10 CitationsAbstract
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.
Author List
Leone V, Waclawska I, Kossmann K, Koshy C, Sharma M, Prisner TF, Ziegler C, Endeward B, Forrest LRAuthor
Vanessa Leone PhD Assistant Professor in the Biophysics department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
Bacterial ProteinsElectron Spin Resonance Spectroscopy
Molecular Dynamics Simulation
Symporters
