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PMID: 20074514 Published · ppublish English Journal Article

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

Biophysical journal ·Vol. 98 ·No. 1 ·2010-01-06 ·Pages 76-84

Romo TD, Grossfield A, Pitman MC

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.

MeSH Terms
Computer Simulation Ions Kinetics Models, Chemical Models, Molecular Protein Conformation Receptors, Adrenergic, beta-2/chemistry,ultrastructure
Chemicals
Ions Receptors, Adrenergic, beta-2
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Romo Tod D
Department of Biochemistry and Biophysics, University of Rochester Medical School, Rochester, New York, USA.
Grossfield Alan
Pitman Michael C
References (42)
42 references, click to expand
  1. Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations.
    Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4689-94 PMID: 19258456
  2. The superfamily of heptahelical receptors.
    Nat Cell Biol. 2000 Jul;2(7):E133-6 PMID: 10878827
  3. A sampling problem in molecular dynamics simulations of macromolecules.
    Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3288-92 PMID: 7724554
  4. A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids.
    Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4888-93 PMID: 16547139
  5. All-atom empirical potential for molecular modeling and dynamics studies of proteins.
    J Phys Chem B. 1998 Apr 30;102(18):3586-616 PMID: 24889800
  6. GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function.
    Science. 2007 Nov 23;318(5854):1266-73 PMID: 17962519
  7. Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin.
    J Mol Biol. 2008 Aug 29;381(2):478-86 PMID: 18585736
  8. Structure of a beta1-adrenergic G-protein-coupled receptor.
    Nature. 2008 Jul 24;454(7203):486-91 PMID: 18594507
  9. The structure and function of G-protein-coupled receptors.
    Nature. 2009 May 21;459(7245):356-63 PMID: 19458711
  10. Structure and function in rhodopsin: mapping light-dependent changes in distance between residue 316 in helix 8 and residues in the sequence 60-75, covering the cytoplasmic end of helices TM1 and TM2 and their connection loop CL1.
    Biochemistry. 2001 Dec 25;40(51):15493-500 PMID: 11747424
  11. G protein coupled receptor structure and activation.
    Biochim Biophys Acta. 2007 Apr;1768(4):794-807 PMID: 17188232
  12. Quantifying uncertainty and sampling quality in biomolecular simulations.
    Annu Rep Comput Chem. 2009 Jan 1;5:23-48 PMID: 20454547
  13. Conformational complexity of G-protein-coupled receptors.
    Trends Pharmacol Sci. 2007 Aug;28(8):397-406 PMID: 17629961
  14. Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties.
    J Am Chem Soc. 2002 Jan 16;124(2):318-26 PMID: 11782184
  15. Dynamics of the internal water molecules in squid rhodopsin.
    Biophys J. 2009 Apr 8;96(7):2572-6 PMID: 19348742
  16. Crystal structure of the ligand-free G-protein-coupled receptor opsin.
    Nature. 2008 Jul 10;454(7201):183-7 PMID: 18563085
  17. The role of internal water molecules in the structure and function of the rhodopsin family of G protein-coupled receptors.
    Chembiochem. 2007 Jan 2;8(1):19-24 PMID: 17173267
  18. Similarities between principal components of protein dynamics and random diffusion
    Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Dec;62(6 Pt B):8438-48 PMID: 11138145
  19. The repertoire of G-protein-coupled receptors in fully sequenced genomes.
    Mol Pharmacol. 2005 May;67(5):1414-25 PMID: 15687224
  20. Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography.
    Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5982-7 PMID: 11972040
  21. Crystal structure of the human beta2 adrenergic G-protein-coupled receptor.
    Nature. 2007 Nov 15;450(7168):383-7 PMID: 17952055
  22. Convergence of sampling in protein simulations.
    Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Mar;65(3 Pt 1):031910 PMID: 11909112
  23. Dynamic behavior of fully solvated beta2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist.
    Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4882-7 PMID: 16551744
  24. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist.
    Science. 2008 Nov 21;322(5905):1211-7 PMID: 18832607
  25. Scalable molecular dynamics with NAMD.
    J Comput Chem. 2005 Dec;26(16):1781-802 PMID: 16222654
  26. An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.
    J Phys Chem B. 2005 Mar 24;109(11):5300-11 PMID: 16863197
  27. Crystal structure of rhodopsin: A G protein-coupled receptor.
    Science. 2000 Aug 4;289(5480):739-45 PMID: 10926528
  28. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor.
    Science. 2007 Nov 23;318(5854):1258-65 PMID: 17962520
  29. High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation.
    Proc Natl Acad Sci U S A. 2008 May 27;105(21):7439-44 PMID: 18490656
  30. Molecular mechanism of 7TM receptor activation--a global toggle switch model.
    Annu Rev Pharmacol Toxicol. 2006;46:481-519 PMID: 16402913
  31. Large-amplitude nonlinear motions in proteins.
    Phys Rev Lett. 1992 Apr 27;68(17):2696-2699 PMID: 10045464
  32. Convergence of molecular dynamics simulations of membrane proteins.
    Proteins. 2007 Apr 1;67(1):31-40 PMID: 17243153
  33. Structure and function in rhodopsin: mapping light-dependent changes in distance between residue 65 in helix TM1 and residues in the sequence 306-319 at the cytoplasmic end of helix TM7 and in helix H8.
    Biochemistry. 2001 Dec 25;40(51):15483-92 PMID: 11747423
  34. Discovery of new GPCR biology: one receptor structure at a time.
    Structure. 2009 Jan 14;17(1):8-14 PMID: 19141277
  35. Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin.
    Science. 1996 Nov 1;274(5288):768-70 PMID: 8864113
  36. Observation of "ionic lock" formation in molecular dynamics simulations of wild-type beta 1 and beta 2 adrenergic receptors.
    Biochemistry. 2009 Jun 9;48(22):4789-97 PMID: 19378975
  37. The hydrophobic tryptic core of the beta-adrenergic receptor retains Gs regulatory activity in response to agonists and thiols.
    J Biol Chem. 1987 Dec 5;262(34):16655-62 PMID: 2890639
  38. Sequence analyses of G-protein-coupled receptors: similarities to rhodopsin.
    Biochemistry. 2003 Mar 18;42(10):2759-67 PMID: 12627940
  39. Functional role of the "ionic lock"--an interhelical hydrogen-bond network in family A heptahelical receptors.
    J Mol Biol. 2008 Jul 18;380(4):648-55 PMID: 18554610
  40. Structural basis for ligand binding and specificity in adrenergic receptors: implications for GPCR-targeted drug discovery.
    Biochemistry. 2008 Oct 21;47(42):11013-23 PMID: 18821775
  41. Activation of the beta 2-adrenergic receptor involves disruption of an ionic lock between the cytoplasmic ends of transmembrane segments 3 and 6.
    J Biol Chem. 2001 Aug 3;276(31):29171-7 PMID: 11375997
  42. LOOS: an extensible platform for the structural analysis of simulations.
    Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:2332-5 PMID: 19965179
Article Info
Journal
Biophysical journal
Abbr.
Biophys J
ISSN
1542-0086
Published
2010-01-06
Pages
76-84
Language
English
Region
United States
NLM ID
0370626
PMCID
PMC2800975
Subset
IM
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