Chapter 7: Computational Characterization of Molecular Mechanisms of Membrane Transporter Function

Noah Trebesch, Josh V. Vermaas, Emad Tajkhorshid

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Transport of materials across the cellular membrane is a fundamental process in biology. Active membrane transporters constitute one of the major classes of proteins that mediate this process, and they do so in a highly regulated and selective manner. In order to transport substrates uphill, these molecular machines rely on a diverse spectrum of conformational changes spanning multiple time and size scales, and they couple these motions to various sources of energy, including transmembrane electrochemical gradients and ATP hydrolysis. Computational techniques such as molecular dynamics simulations and free energy calculations provide us with a powerful repertoire of biophysical tools offering unparalleled spatial and temporal resolutions that complement experimental methodologies and help us understand the molecular basis of function in membrane transporters. In this chapter, we present an overview of a number of examples of recent studies performed in our own lab in which computational methods and simulation techniques have been successfully employed to investigate and to characterize the microscopic molecular events that underlie membrane transporter function. While highlighting a number of recent approaches developed specifically to tackle challenging problems in membrane transporters, e.g., characterizing the nature of large-scale conformational changes, the presented studies also provide examples of a variety of mechanistically interesting and biologically important transporter systems.

Original languageEnglish (US)
Title of host publicationComputational Biophysics of Membrane Proteins
EditorsJonathan Hirst, Carmen Domene
PublisherRoyal Society of Chemistry
Pages197-236
Number of pages40
Edition10
DOIs
StatePublished - Jan 1 2017

Publication series

NameRSC Theoretical and Computational Chemistry Series
Number10
Volume2017-January
ISSN (Print)2041-3181
ISSN (Electronic)2041-319X

Fingerprint

Membrane Transport Proteins
Membranes
Computational methods
Free energy
Adenosinetriphosphate
Molecular dynamics
Hydrolysis
Adenosine Triphosphate
Computer simulation
Proteins
Substrates

ASJC Scopus subject areas

  • Chemistry(all)
  • Computer Science Applications

Cite this

Trebesch, N., Vermaas, J. V., & Tajkhorshid, E. (2017). Chapter 7: Computational Characterization of Molecular Mechanisms of Membrane Transporter Function. In J. Hirst, & C. Domene (Eds.), Computational Biophysics of Membrane Proteins (10 ed., pp. 197-236). (RSC Theoretical and Computational Chemistry Series; Vol. 2017-January, No. 10). Royal Society of Chemistry. https://doi.org/10.1039/9781782626695-00197

Chapter 7 : Computational Characterization of Molecular Mechanisms of Membrane Transporter Function. / Trebesch, Noah; Vermaas, Josh V.; Tajkhorshid, Emad.

Computational Biophysics of Membrane Proteins. ed. / Jonathan Hirst; Carmen Domene. 10. ed. Royal Society of Chemistry, 2017. p. 197-236 (RSC Theoretical and Computational Chemistry Series; Vol. 2017-January, No. 10).

Research output: Chapter in Book/Report/Conference proceedingChapter

Trebesch, N, Vermaas, JV & Tajkhorshid, E 2017, Chapter 7: Computational Characterization of Molecular Mechanisms of Membrane Transporter Function. in J Hirst & C Domene (eds), Computational Biophysics of Membrane Proteins. 10 edn, RSC Theoretical and Computational Chemistry Series, no. 10, vol. 2017-January, Royal Society of Chemistry, pp. 197-236. https://doi.org/10.1039/9781782626695-00197
Trebesch N, Vermaas JV, Tajkhorshid E. Chapter 7: Computational Characterization of Molecular Mechanisms of Membrane Transporter Function. In Hirst J, Domene C, editors, Computational Biophysics of Membrane Proteins. 10 ed. Royal Society of Chemistry. 2017. p. 197-236. (RSC Theoretical and Computational Chemistry Series; 10). https://doi.org/10.1039/9781782626695-00197
Trebesch, Noah ; Vermaas, Josh V. ; Tajkhorshid, Emad. / Chapter 7 : Computational Characterization of Molecular Mechanisms of Membrane Transporter Function. Computational Biophysics of Membrane Proteins. editor / Jonathan Hirst ; Carmen Domene. 10. ed. Royal Society of Chemistry, 2017. pp. 197-236 (RSC Theoretical and Computational Chemistry Series; 10).
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