Journal
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
Volume 1858, Issue 7, Pages 1652-1662Publisher
ELSEVIER
DOI: 10.1016/j.bbamem.2016.01.010
Keywords
Molecular dynamics; Allosteric interaction network; Transmembrane protein
Categories
Funding
- Intramural Research Program of the NIH, NIDA [ZIA DA000606-01]
- DRS/Marie Curie Post-Doctoral POINT Fellowship [608829]
- Ruth L. Kirschstein National Research Service Award [F31DA035533]
- NIH [P01 DA012408, U54 GM087519, R01 MH054137, R01 DA035263]
- XSEDE (Stampede supercomputer) [TG-MCB090132, TG-MCB120008]
- Office of Science of the U.S. Department of Energy [DE-AC05-00OR22725, DE-AC02-05CH11231]
- [PSCA14026P]
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Many of the functions of transmembrane proteins involved in signal processing and transduction across the cell membrane are determined by allosteric couplings that propagate the functional effects well beyond the original site of activation. Data gathered from breakthroughs in biochemistry, crystallography, and single molecule fluorescence have established a rich basis of information for the study of molecular mechanisms in the allosteric couplings of such transmembrane proteins. The mechanistic details of these couplings, many of which have therapeutic implications, however, have only become accessible in synergy with molecular modeling and simulations. Here, we review some recent computational approaches that analyze allosteric coupling networks (ACNs) in transmembrane proteins, and in particular the recently developed Protein Interaction Analyzer (PIA) designed to study ACNs in the structural ensembles sampled by molecular dynamics simulations. The power of these computational approaches in interrogating the functional mechanisms of transmembrane proteins is illustrated with selected examples of recent experimental and computational studies pursued synergistically in the investigation of secondary active transporters and GPCRs. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Published by Elsevier B.V.
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