Computational approaches to detect allosteric pathways in transmembrane molecular machines

Biochimica Et Biophysica Acta
Sebastian StolzenbergLei Shi

Abstract

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 GPC...Continue Reading

References

Aug 27, 1966·Nature·O Jardetzky
Dec 1, 1993·Proteins·A AmadeiH J Berendsen
May 20, 1994·Journal of Molecular Biology·I K McDonald, J M Thornton
Jan 9, 1996·Proceedings of the National Academy of Sciences of the United States of America·S Jones, J M Thornton
Dec 1, 1995·Proteins·J Janin, F Rodier
Nov 23, 2000·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·H Matsuda
Dec 17, 2002·Nature Structural Biology·Gürol M SüelRama Ranganathan
May 1, 1965·Journal of Molecular Biology·J MONODJ P CHANGEUX
Mar 5, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M E J Newman, M Girvan
May 14, 2004·Annual Review of Biophysics and Biomolecular Structure·Dennis Bray, Thomas Duke
Sep 24, 2004·Proteins·K GunasekaranRuth Nussinov
Nov 17, 2004·Journal of Molecular Biology·Gil AmitaiShmuel Pietrokovski
Dec 16, 2005·Proteins·Oliver F Lange, Helmut Grubmüller
Jan 21, 2006·Current Opinion in Structural Biology·Joanna F Swain, Lila M Gierasch
Jun 2, 2006·Molecular Systems Biology·Antonio del SolRuth Nussinov
Jun 29, 2006·The Journal of Pharmacology and Experimental Therapeutics·Jonathan D UrbanRichard B Mailman
Jul 14, 2006·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Delany Torres-Salazar, Christoph Fahlke
Jul 18, 2006·Nucleic Acids Research·Lee-Wei YangIvet Bahar
Mar 16, 2007·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Hans Peter KochHans Peter Larsson
May 16, 2007·Structure·Yifei Kong, Martin Karplus
May 29, 2007·FEBS Letters·Csaba BödePéter Csermely
Oct 24, 2007·Nature·Søren G F RasmussenBrian K Kobilka
Apr 23, 2008·The Journal of Biological Chemistry·Julie KniazeffUlrik Gether
Dec 17, 2008·Science·Satinder K SinghEric Gouaux
Apr 9, 2009·Proceedings of the National Academy of Sciences of the United States of America·Anurag SethiZaida Luthey-Schulten
May 22, 2009·Nature·Harini KrishnamurthyEric Gouaux
Sep 30, 2009·Chemical Reviews·Ivet BaharIndira H Shrivastava
Feb 18, 2010·Journal of Chemical Theory and Computation·Christopher L McClendonMatthew P Jacobson
Jan 1, 2009·Annual Reports in Computational Chemistry·Alan Grossfield, Daniel M Zuckerman
May 14, 2010·Nature·Yongfang ZhaoJonathan A Javitch
Jun 22, 2010·Nature Structural & Molecular Biology·Derek P ClaxtonHassane S McHaourab
Jul 20, 2010·Neuropharmacology·Peter KeovArthur Christopoulos
Aug 17, 2010·PLoS Computational Biology·Jana SelentGianni De Fabritiis
Aug 18, 2010·Biochimica Et Biophysica Acta·Francesca Fanelli, Angelo Felline

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Citations

Apr 21, 2016·Biochimica Et Biophysica Acta·James C Gumbart, Sergei Noskov
Nov 9, 2016·Nature Communications·Marek WieczorekChristian Freund
Oct 30, 2016·Journal of the American Chemical Society·Sangbae LeeNagarajan Vaidehi
Dec 17, 2016·Journal of Medicinal Chemistry·Mayako MichinoLei Shi
Feb 6, 2020·International Journal of Molecular Sciences·Olivier Sheik AmamuddyOzlem Tastan Bishop
Jul 31, 2016·The Journal of Biological Chemistry·George KhelashviliHarel Weinstein
Jul 3, 2020·The Journal of Chemical Physics·David M LeitnerKorey M Reid
Jul 22, 2019·Proceedings of the National Academy of Sciences of the United States of America·Michael V LeVineHarel Weinstein
Aug 1, 2020·Frontiers in Molecular Biosciences·Gennady M VerkhivkerPeng Tao
Dec 10, 2020·The Journal of Chemical Physics·John W VantAbhishek Singharoy
Apr 5, 2019·The Journal of Physical Chemistry. B·Aria GheeraertIvan Rivalta
Apr 7, 2020·Journal of Chemical Theory and Computation·Peter T LakeMartin McCullagh
May 1, 2019·Journal of Chemical Information and Modeling·Konstantina Karathanou, Ana-Nicoleta Bondar

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