Capturing functional motions of membrane channels and transporters with molecular dynamics simulation

Saher Afshan Shaikh, Po Chao Wen, Giray Enkavi, Zhijian Huang, Emad Tajkhorshid

Research output: Contribution to journalReview article

Abstract

Conformational changes of proteins are involved in all aspects of protein function in biology. Almost all classes of proteins respond to changes in their environment, ligand binding, and interaction with other proteins and regulatory agents through undergoing conformational changes of various degrees and magnitudes. Membrane channels and transporters are the major classes of proteins that are responsible for mediating efficient and selective transport of materials across the cellular membrane. Similar to other proteins, they take advantage of conformational changes to make transitions between various functional states. In channels, large-scale conformational changes are mostly involved in the process of "gating," i.e., opening and closing of the pore of the channel protein in response to various signals. In transporters, conformational changes constitute various steps of the conduction process, and, thus, are more closely integrated in the transport process. Owing to significant progress in developing highly efficient parallel algorithms in molecular dynamics simulations and increased computational resources, and combined with the availability of high-resolution, atomic structures of membrane proteins, we are in an unprecedented position to use computer simulation and modeling methodologies to investigate the mechanism of function of membrane channels and transporters. While the entire transport cycle is still out of reach of current methodologies, many steps involved in the function of transport proteins have been characterized with molecular dynamics simulations. Here, we present several examples of such studies from our laboratory, in which functionally relevant conformational changes of membrane channels and transporters have been characterized using extended simulations.

Original languageEnglish (US)
Pages (from-to)2481-2500
Number of pages20
JournalJournal of Computational and Theoretical Nanoscience
Volume7
Issue number12
DOIs
StatePublished - Dec 1 2010

Fingerprint

transporter
Membrane Transport Proteins
Ion Channels
Molecular Dynamics Simulation
Molecular dynamics
Membrane
molecular dynamics
membranes
proteins
Proteins
Membranes
Protein
Motion
Computer simulation
simulation
methodology
Membrane Protein
Computer Modeling
Methodology
Transport Processes

Keywords

  • Biological membranes
  • Membrane channels
  • Membrane transporters
  • Molecular dynamics simulation
  • Protein conformational changes

ASJC Scopus subject areas

  • Chemistry(all)
  • Materials Science(all)
  • Condensed Matter Physics
  • Computational Mathematics
  • Electrical and Electronic Engineering

Cite this

Capturing functional motions of membrane channels and transporters with molecular dynamics simulation. / Shaikh, Saher Afshan; Wen, Po Chao; Enkavi, Giray; Huang, Zhijian; Tajkhorshid, Emad.

In: Journal of Computational and Theoretical Nanoscience, Vol. 7, No. 12, 01.12.2010, p. 2481-2500.

Research output: Contribution to journalReview article

Shaikh, Saher Afshan ; Wen, Po Chao ; Enkavi, Giray ; Huang, Zhijian ; Tajkhorshid, Emad. / Capturing functional motions of membrane channels and transporters with molecular dynamics simulation. In: Journal of Computational and Theoretical Nanoscience. 2010 ; Vol. 7, No. 12. pp. 2481-2500.
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