Literature DB >> 20074514

Concerted interconversion between ionic lock substates of the beta(2) adrenergic receptor revealed by microsecond timescale molecular dynamics.

Tod D Romo1, Alan Grossfield, Michael C Pitman.   

Abstract

The recently solved crystallographic structures for the A(2A) adenosine receptor and the beta(1) and beta(2) adrenergic receptors have shown important differences between members of the class-A G-protein-coupled receptors and their archetypal model, rhodopsin, such as the apparent breaking of the ionic lock that stabilizes the inactive structure. Here, we characterize a 1.02 mus all-atom simulation of an apo-beta(2) adrenergic receptor that is missing the third intracellular loop to better understand the inactive structure. Although we find that the structure is remarkably rigid, there is a rapid influx of water into the core of the protein, as well as a slight expansion of the molecule relative to the crystal structure. In contrast to the x-ray crystal structures, the ionic lock rapidly reforms, although we see an activation-precursor-like event wherein the ionic lock opens for approximately 200 ns, accompanied by movements in the transmembrane helices associated with activation. When the lock reforms, we see the structure return to its inactive conformation. We also find that the ionic lock exists in three states: closed (or locked), semi-open with a bridging water molecule, and open. The interconversion of these states involves the concerted motion of the entire protein. We characterize these states and the concerted motion underlying their interconversion. These findings may help elucidate the connection between key local events and the associated global structural changes during activation. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Entities:  

Mesh:

Substances:

Year:  2010        PMID: 20074514      PMCID: PMC2800975          DOI: 10.1016/j.bpj.2009.09.046

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  42 in total

Review 1.  Sequence analyses of G-protein-coupled receptors: similarities to rhodopsin.

Authors:  Tara Mirzadegan; Gil Benkö; Sławomir Filipek; Krzysztof Palczewski
Journal:  Biochemistry       Date:  2003-03-18       Impact factor: 3.162

2.  An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.

Authors:  Jeffery B Klauda; Bernard R Brooks; Alexander D MacKerell; Richard M Venable; Richard W Pastor
Journal:  J Phys Chem B       Date:  2005-03-24       Impact factor: 2.991

Review 3.  Conformational complexity of G-protein-coupled receptors.

Authors:  Brian K Kobilka; Xavier Deupi
Journal:  Trends Pharmacol Sci       Date:  2007-07-13       Impact factor: 14.819

4.  Crystal structure of the ligand-free G-protein-coupled receptor opsin.

Authors:  Jung Hee Park; Patrick Scheerer; Klaus Peter Hofmann; Hui-Woog Choe; Oliver Peter Ernst
Journal:  Nature       Date:  2008-06-18       Impact factor: 49.962

5.  Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin.

Authors:  Alan Grossfield; Michael C Pitman; Scott E Feller; Olivier Soubias; Klaus Gawrisch
Journal:  J Mol Biol       Date:  2008-05-22       Impact factor: 5.469

Review 6.  The structure and function of G-protein-coupled receptors.

Authors:  Daniel M Rosenbaum; Søren G F Rasmussen; Brian K Kobilka
Journal:  Nature       Date:  2009-05-21       Impact factor: 49.962

7.  A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids.

Authors:  Alan Grossfield; Scott E Feller; Michael C Pitman
Journal:  Proc Natl Acad Sci U S A       Date:  2006-03-17       Impact factor: 11.205

8.  Structure of a beta1-adrenergic G-protein-coupled receptor.

Authors:  Tony Warne; Maria J Serrano-Vega; Jillian G Baker; Rouslan Moukhametzianov; Patricia C Edwards; Richard Henderson; Andrew G W Leslie; Christopher G Tate; Gebhard F X Schertler
Journal:  Nature       Date:  2008-06-25       Impact factor: 49.962

9.  Observation of "ionic lock" formation in molecular dynamics simulations of wild-type beta 1 and beta 2 adrenergic receptors.

Authors:  Stefano Vanni; Marilisa Neri; Ivano Tavernelli; Ursula Rothlisberger
Journal:  Biochemistry       Date:  2009-06-09       Impact factor: 3.162

10.  The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist.

Authors:  Veli-Pekka Jaakola; Mark T Griffith; Michael A Hanson; Vadim Cherezov; Ellen Y T Chien; J Robert Lane; Adriaan P Ijzerman; Raymond C Stevens
Journal:  Science       Date:  2008-10-02       Impact factor: 47.728

View more
  32 in total

1.  Structural insights into human GPCR protein OA1: a computational perspective.

Authors:  Anirban Ghosh; Uddhavesh Sonavane; Sai Krishna Andhirka; Gopala Krishna Aradhyam; Rajendra Joshi
Journal:  J Mol Model       Date:  2011-09-22       Impact factor: 1.810

Review 2.  The significance of G protein-coupled receptor crystallography for drug discovery.

Authors:  John A Salon; David T Lodowski; Krzysztof Palczewski
Journal:  Pharmacol Rev       Date:  2011-12       Impact factor: 25.468

3.  Putative active states of a prototypic g-protein-coupled receptor from biased molecular dynamics.

Authors:  Davide Provasi; Marta Filizola
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

4.  Identification of motions in membrane proteins by elastic network models and their experimental validation.

Authors:  Basak Isin; Kalyan C Tirupula; Zoltán N Oltvai; Judith Klein-Seetharaman; Ivet Bahar
Journal:  Methods Mol Biol       Date:  2012

5.  Agonist dynamics and conformational selection during microsecond simulations of the A(2A) adenosine receptor.

Authors:  Ji Young Lee; Edward Lyman
Journal:  Biophys J       Date:  2012-05-02       Impact factor: 4.033

6.  Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor?

Authors:  Chris Neale; Henry D Herce; Régis Pomès; Angel E García
Journal:  Biophys J       Date:  2015-10-20       Impact factor: 4.033

7.  Molecular Dynamics Methodologies for Probing Cannabinoid Ligand/Receptor Interaction.

Authors:  Diane L Lynch; Dow P Hurst; Derek M Shore; Mike C Pitman; Patricia H Reggio
Journal:  Methods Enzymol       Date:  2017-07-04       Impact factor: 1.600

8.  Structural basis of ligand recognition and self-activation of orphan GPR52.

Authors:  Xi Lin; Mingyue Li; Niandong Wang; Yiran Wu; Zhipu Luo; Shimeng Guo; Gye-Won Han; Shaobai Li; Yang Yue; Xiaohu Wei; Xin Xie; Yong Chen; Suwen Zhao; Jian Wu; Ming Lei; Fei Xu
Journal:  Nature       Date:  2020-02-19       Impact factor: 49.962

Review 9.  Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins.

Authors:  Mikhail N Ryazantsev; Dmitrii M Nikolaev; Andrey V Struts; Michael F Brown
Journal:  J Membr Biol       Date:  2019-09-30       Impact factor: 1.843

Review 10.  Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors.

Authors:  Jennifer M Johnston; Marta Filizola
Journal:  Curr Opin Struct Biol       Date:  2011-07-19       Impact factor: 6.809

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.