Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation

J. V. Vermaas, N. Trebesch, C. G. Mayne, S. Thangapandian, M. Shekhar, P. Mahinthichaichan, J. L. Baylon, T. Jiang, Y. Wang, M. P. Muller, E. Shinn, Z. Zhao, P. C. Wen, E. Tajkhorshid

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Membrane transporters mediate one of the most fundamental processes in biology. They are the main gatekeepers controlling active traffic of materials in a highly selective and regulated manner between different cellular compartments demarcated by biological membranes. At the heart of the mechanism of membrane transporters lie protein conformational changes of diverse forms and magnitudes, which closely mediate critical aspects of the transport process, most importantly the coordinated motions of remotely located gating elements and their tight coupling to chemical processes such as binding, unbinding and translocation of transported substrate and cotransported ions, ATP binding and hydrolysis, and other molecular events fueling uphill transport of the cargo. An increasing number of functional studies have established the active participation of lipids and other components of biological membranes in the function of transporters and other membrane proteins, often acting as major signaling and regulating elements. Understanding the mechanistic details of these molecular processes require methods that offer high spatial and temporal resolutions. Computational modeling and simulations technologies empowered by advanced sampling and free energy calculations have reached a sufficiently mature state to become an indispensable component of mechanistic studies of membrane transporters in their natural environment of the membrane. In this article, we provide an overview of a number of major computational protocols and techniques commonly used in membrane transporter modeling and simulation studies. The article also includes practical hints on effective use of these methods, critical perspectives on their strengths and weak points, and examples of their successful applications to membrane transporters, selected from the research performed in our own laboratory.

Original languageEnglish (US)
Title of host publicationMethods in Enzymology
PublisherAcademic Press Inc.
Pages373-428
Number of pages56
DOIs
StatePublished - 2016

Publication series

NameMethods in Enzymology
Volume578
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

Fingerprint

Membrane Transport Proteins
Computer Simulation
Biological membranes
Membranes
Chemical Phenomena
Fueling
Active Biological Transport
Chemical elements
Free energy
Hydrolysis
Membrane Proteins
Adenosine Triphosphate
Ions
Sampling
Technology
Lipids
Substrates
Research
Proteins

Keywords

  • Active transport
  • Biological systems modeling
  • Conformational change
  • Free energy calculations
  • Lipid bilayers
  • Membrane transporter
  • Molecular dynamics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Vermaas, J. V., Trebesch, N., Mayne, C. G., Thangapandian, S., Shekhar, M., Mahinthichaichan, P., ... Tajkhorshid, E. (2016). Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. In Methods in Enzymology (pp. 373-428). (Methods in Enzymology; Vol. 578). Academic Press Inc.. https://doi.org/10.1016/bs.mie.2016.05.042

Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. / Vermaas, J. V.; Trebesch, N.; Mayne, C. G.; Thangapandian, S.; Shekhar, M.; Mahinthichaichan, P.; Baylon, J. L.; Jiang, T.; Wang, Y.; Muller, M. P.; Shinn, E.; Zhao, Z.; Wen, P. C.; Tajkhorshid, E.

Methods in Enzymology. Academic Press Inc., 2016. p. 373-428 (Methods in Enzymology; Vol. 578).

Research output: Chapter in Book/Report/Conference proceedingChapter

Vermaas, JV, Trebesch, N, Mayne, CG, Thangapandian, S, Shekhar, M, Mahinthichaichan, P, Baylon, JL, Jiang, T, Wang, Y, Muller, MP, Shinn, E, Zhao, Z, Wen, PC & Tajkhorshid, E 2016, Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. in Methods in Enzymology. Methods in Enzymology, vol. 578, Academic Press Inc., pp. 373-428. https://doi.org/10.1016/bs.mie.2016.05.042
Vermaas JV, Trebesch N, Mayne CG, Thangapandian S, Shekhar M, Mahinthichaichan P et al. Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. In Methods in Enzymology. Academic Press Inc. 2016. p. 373-428. (Methods in Enzymology). https://doi.org/10.1016/bs.mie.2016.05.042
Vermaas, J. V. ; Trebesch, N. ; Mayne, C. G. ; Thangapandian, S. ; Shekhar, M. ; Mahinthichaichan, P. ; Baylon, J. L. ; Jiang, T. ; Wang, Y. ; Muller, M. P. ; Shinn, E. ; Zhao, Z. ; Wen, P. C. ; Tajkhorshid, E. / Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. Methods in Enzymology. Academic Press Inc., 2016. pp. 373-428 (Methods in Enzymology).
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