Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors
Corresponding Author
Gregory V. Nikiforovich
MolLife Design LLC, St. Louis, Missouri 63141
MolLife Design LLC, 751 Aramis Drive, St. Louis, MO 63141===Search for more papers by this authorChristina M. Taylor
Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri 63110
Search for more papers by this authorGarland R. Marshall
Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri 63110
Search for more papers by this authorThomas J. Baranski
Department of Internal Medicine, Washington University Medical School, St. Louis, Missouri 63110
Search for more papers by this authorCorresponding Author
Gregory V. Nikiforovich
MolLife Design LLC, St. Louis, Missouri 63141
MolLife Design LLC, 751 Aramis Drive, St. Louis, MO 63141===Search for more papers by this authorChristina M. Taylor
Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri 63110
Search for more papers by this authorGarland R. Marshall
Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri 63110
Search for more papers by this authorThomas J. Baranski
Department of Internal Medicine, Washington University Medical School, St. Louis, Missouri 63110
Search for more papers by this authorAbstract
This study presents the results of a de novo approach modeling possible conformational dynamics of the extracellular (EC) loops in G-protein-coupled receptors (GPCRs), specifically in bovine rhodopsin (bRh), squid rhodopsin (sRh), human β-2 adrenergic receptor (β2AR), turkey β-1 adrenergic receptor (β1AR), and human A2 adenosine receptor (A2AR). The approach deliberately sacrificed a detailed description of any particular 3D structure of the loops in GPCRs in favor of a less precise description of many possible structures. Despite this, the approach found ensembles of the low-energy conformers of the EC loops that contained structures close to the available X-ray snapshots. For the smaller EC1 and EC3 loops (6–11 residues), our results were comparable with the best recent results obtained by other authors using much more sophisticated techniques. For the larger EC2 loops (25–34 residues), our results consistently yielded structures significantly closer to the X-ray snapshots than the results of the other authors for loops of similar size. The results suggested possible large-scale movements of the EC loops in GPCRs that might determine their conformational dynamics. The approach was also validated by accurately reproducing the docking poses for low-molecular-weight ligands in β2AR, β1AR, and A2AR, demonstrating the possible influence of the conformations of the EC loops on the binding sites of ligands. The approach correctly predicted the system of disulfide bridges between the EC loops in A2AR and elucidated the probable pathways for forming this system. Proteins 2010. © 2009 Wiley-Liss, Inc.
REFERENCES
- 1 Kroeze WK,Sheffler DJ,Roth BL. G-protein-coupled receptors at a glance. J Cell Sci 2003; 116: 4867–4869.
- 2 Drews J. Drug discovery: a historical perspective. Science 2000; 287: 1960–1964.
- 3 Avlani VA,Gregory KJ,Morton CJ,Parker MW,Sexton PM,Christopoulos A. Critical role for the second extracellular loop in the binding of both orthosteric and allosteric G protein-coupled receptor ligands. J Biol Chem 2007; 282: 25677–25686.
- 4 Wacker JL,Feller DB,Tang XB,Defino MC,Namkung Y,Lyssand JS,Mhyre AJ,Tan X,Jensen JB,Hague C. Disease-causing mutation in GPR54 reveals the importance of the second intracellular loop for class A G-protein-coupled receptor function. J Biol Chem 2008; 283: 31068–31078.
- 5 De Graaf C,Foata N,Engkvist O,Rognan D. Molecular modeling of the second extracellular loop of G-protein coupled receptors and its implication on structure-based virtual screening. Proteins 2008; 71: 599–620.
- 6 Gkountelias K,Tselios T,Venihaki M,Deraos G,Lazaridis I,Rassouli O,Gravanis A,Liapakis G. Alanine scanning mutagenesis of the second extracellular loop of type 1 corticotropin releasing factor receptor revealed residues critical for peptide binding. Mol Pharmacol 2009; 75: 793–800.
- 7 Sura-Trueba S,Aumas C,Carre A,Durif S,Leger J,Polak M,De Roux N. An inactivating mutation within the first extracellular loop of the thyrotropin receptor impedes normal posttranslational maturation of the extracellular domain. Endocrinology 2009; 150: 1043–1050.
- 8 Chee MJ,Morl K,Lindner D,Merten N,Zamponi GW,Light PE,Beck-Sickinger AG,Colmers WF. The third intracellular loop stabilizes the inactive state of the neuropeptide Y1 receptor. J Biol Chem 2008; 283: 33337–33346.
- 9 Storjohann L,Holst B,Schwartz TW. A second disulfide bridge from the N-terminal domain to extracellular loop 2 dampens receptor activity in GPR39. Biochemistry 2008; 47: 9198–9207.
- 10 Klco JM,Wiegand CB,Narzinski K,Baranski TJ. Essential role for the second extracellular loop in C5a receptor activation. Nat Struct Mol Biol 2005; 12: 320–326.
- 11 Samson M,Larosa G,Libert F,Paindavoine P,Detheux M,Vassart G,Parmentier M. The second extracellular loop of CCR5 is the major determinant of ligand specificity. J Biol Chem 1997; 272: 24934–24941.
- 12 Shi L,Javitch JA. The second extracellular loop of the dopamine D2 receptor lines the binding-site crevice. Proc Natl Acad Sci USA 2004; 101: 440–445.
- 13 Scarselli M,Li B,Kim SK,Wess J. Multiple residues in the second extracellular loop are critical for M3 muscarinic acetylcholine receptor activation. J Biol Chem 2007; 282: 7385–7396.
- 14 Ahuja S,Hornak V,Yan EC,Syrett N,Goncalves JA,Hirshfeld A,Ziliox M,Sakmar TP,Sheves M,Reeves PJ,Smith SO,Eilers M. Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation. Nat Struct Mol Biol 2009; 16: 168–175.
- 15 Mustafi D,Palczewski K. Topology of class A G protein-coupled receptors: insights gained from crystal structures of rhodopsins, adrenergic and adenosine receptors. Mol Pharmacol 2009; 75: 1–12.
- 16 Palczewski K,Kumasaka T,Hori T,Behnke CA,Motoshima H,Fox BA,Le Trong I,Teller DC,Okada T,Stenkamp RE,Yamamoto M,Miyano M. Crystal structure of rhodopsin: a G protein-coupled receptor. Science 2000; 289: 739–745.
- 17 Murakami M,Kouyama T. Crystal structure of squid rhodopsin. Nature 2008; 453: 363–367.
- 18 Cherezov V,Rosenbaum DM,Hanson MA,Rasmussen SG,Thian FS,Kobilka TS,Choi HJ,Kuhn P,Weis WI,Kobilka BK,Stevens RC. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor [see comment]. Science 2007; 318: 1258–1265.
- 19 Warne T,Serrano-Vega MJ,Baker JG,Moukhametzianov R,Edwards PC,Henderson R,Leslie AG,Tate CG,Schertler GF. Structure of a beta1-adrenergic G-protein-coupled receptor. Nature 2008; 454: 486–491.
- 20 Jaakola VP,Griffith MT,Hanson MA,Cherezov V,Chien EY,Lane JR,Ijzerman AP,Stevens RC. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 2008; 322: 1211–1217.
- 21 Cozzini P,Kellogg GE,Spyrakis F,Abraham DJ,Costantino G,Emerson A,Fanelli F,Gohlke H,Kuhn LA,Morris GM,Orozco M,Pertinhez TA,Rizzi M,Sotriffer CA. Target flexibility: an emerging consideration in drug discovery and design. J Med Chem 2008; 51: 6237–6255.
- 22 Sellers BD,Zhu K,Zhao S,Friesner RA,Jacobson MP. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins 2008; 72: 959–971.
- 23 Groban ES,Narayanan A,Jacobson MP. Conformational changes in protein loops and helices induced by post-translational phosphorylation. PLoS Comput Biol 2006; 2: e32.
- 24 Nikiforovich GV,Marshall GR,Baranski TJ. Modeling Molecular Mechanisms of Binding of the Anaphylotoxin C5a to the C5a Receptor. Biochemistry 2008; 47: 3117–3130.
- 25 Rossi KA,Weigelt CA,Nayeem A,Krystek SR. Loopholes and missing links in protein modeling. Protein Sci 2007; 16: 1999–2012.
- 26 Olson MA,Feig M,Brooks CL. Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J Comput Chem 2008; 29: 820–831.
- 27 Mehler EL,Hassan SA,Kortagere S,Weinstein H. Ab initio computational modeling of loops in G-protein-coupled receptors: lessons from the crystal structure of rhodopsin. Proteins 2006; 64: 673–690.
- 28 Spassov VZ,Flook PK,Yan L. LOOPER: a molecular mechanics-based algorithm for protein loop prediction. Protein Eng Des Selection 2008; 21: 91–100.
- 29 Lee D-S,Seok C. Protein loop modeling using fragment assembly. J Korean Phys Soc 2008; 52: 1137–1142.
- 30 Lin MS,Head-Gordon T. Improved energy selection of nativelike protein loops from loop decoys. J Chem Theory Comput 2008; 4: 515–521.
- 31 Cui M,Mezei M,Osman R. Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field. Protein Eng Des Selection 2008; 21: 729–735.
- 32 Hu X,Wang H,Ke H,Kuhlman B. High-resolution design of a protein loop. Proc Natl Acad Sci USA 2007; 104: 17668–17673.
- 33 Nikiforovich GV,Marshall GR. Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor. Biophys J 2005; 89: 3780–3789.
- 34 Soto CS,Fasnacht M,Zhu J,Forrest L,Honig B. Loop modeling: sampling, filtering, and scoring. Proteins 2008; 70: 834–843.
- 35 Felts AK,Gallicchio E,Chekmarev D,Paris KA,Friesner RA,Levy RM. Predictiion of protein loop conformations using the AGBNP implicit solvent model and torsional angle sampling. J Chem Theory Comput 2008; 4: 855–868.
- 36 Fernandez-Fuentes N,Oliva B,Fiser A. A supersecondary structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Res 2006; 34: 2085–2097.
- 37 Mirzadegan T,Benko G,Filipek S,Palczewski K. Sequence analyses of G-protein coupled receptors: similarities to rhodopsin. Biochemistry 2003; 42: 2759–2767.
- 38 Rohl CA,Strauss CE,Chivian D,Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins 2004; 55: 656–677.
- 39 Wang C,Bradley P,Baker D. Proten-protein docking with backbone flexibility. J Mol Biol 2007; 373: 503–519.
- 40 Kortagere S,Roy A,Mehler EL. Ab initio computational modeling of long loops in G-protein coupled receptors. J Comput Aided Mol Des 2006; 20: 427–436.
- 41 Ballesteros JA,Shi L,Javitch JA. Structural mimicry in G protein-coupled receptors: implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors. Mol Pharmacol 2001; 60: 1–19.
- 42 Dunfield LG,Burgess AW,Scheraga HA. Energy parameters in polypeptides. VIII. Empirical potential energy algorithm for the conformational analysis of large molecules. J Phys Chem 1978; 82: 2609–2616.
- 43 Nemethy G,Pottle MS,Scheraga HA. Energy parameters in polypeptides. IX. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occuring amino acids. J Phys Chem 1983; 87: 1883–1887.
- 44 Nikiforovich GV,Hruby VJ,Prakash O,Gehrig CA. Topographical requirements for delta-selective opioid peptides. Biopolymers 1991; 31: 941–955.
- 45 Nikiforovich GV. Computational molecular modeling in peptide design. Int J Pept Protein Res 1994; 44: 513–531.
- 46 Meiler J,Baker D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 2006; 65: 538–548.
- 47 Tastan O,Klein-Seetharaman J,Meirovitch H. The effect of loops on the structural organization of α-helical membrane proteins. Biophys J 2009; 96: 2299–2312.
- 48 Michino M,Abola E, GPCR Dock 2008 Participants, Brooks CL,Dixon JS,Moult J,Stevens RC. Community-wide blind assessment of methods for GPCR structure modeling and docking. Nat Rev Drug Discovery 2009; 8: 455–463.
- 49 Zhu K,Pincus DL,Zhao S,Friesner RA. Long loop prediction using the protein local optimization program. Proteins 2006; 65: 438–452.
- 50 Zhang G,Liu S,Zhou Y. Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. Protein Sci 2004; 13: 391–399.
- 51 Dror RO,Arlow DH,Borhani DW,Jensen MO,Piana S,Shaw DE. Identification of two distinct inactive conformations of the β2-adrenergic receptor reconciles structural and biochemical observations. Proc Natl Acad Sci USA 2009; 106: 4689–4694.
Citing Literature
