Genome-wide membrane protein structure prediction

Current Genomics

Volumn 14, Issue 5, 2013, Pages 324-329

  Piccoli, Stefano ^a   Suku, Eda ^a   Garonzi, Marianna ^a   Giorgetti, Alejandro ^a,b  

^a UNIVERSITY OF VERONA   (Italy)

^b German Research School for Simulation Science   (Germany)

Author keywords

Genome wide scale analysis; Homology modeling; Human membrane proteome; Membrane protein; Multitasking approach; Protein structural bioinformatics

Indexed keywords

G PROTEIN COUPLED RECEPTOR; MEMBRANE ENZYME; MEMBRANE PROTEIN; PROTEOME;

ARTICLE; BIOLOGY; COMPUTER PREDICTION; ENZYME ANALYSIS; GENOME WIDE MEMBRANE PROTEIN MODEL; LIGAND BINDING; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURAL BIOINFORMATICS;

EID: 84882741082     PISSN: 13892029     EISSN: 18755488     Source Type: Journal    
DOI: 10.2174/13892029113149990009     Document Type: Article

References (64)

1. Almén, M.S.; Nordström, K.J.; Fredriksson, R.; Schiöth, H.B. Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. BMC Biol., 2009, 7, 50.
2. Tramontano, A.; Cozzetto, D.; Giorgetti, A.; Raimondo, D. Methods in Molecular Biology, vol. 413: Protein Structure Prediction, 2nd ed.; Humana Press Inc.: Totowa, New York, 2008.
3. Cozzetto, D.; Giorgetti, A.; Raimondo, D.; Tramontano, A. The evaluation of protein structure prediction results. Mol. Biotechnol., 2008, 39, 1-8.
4. Chothia, C.; Lesk, A.M. The relation between the divergence of sequence and structure in proteins. EMBO J., 1986, 5, 823-826.
5. st ed.; Chandrasekaran, A.; Eds.; InTech: Rijeka, Croatia, 2011; pp. 349-364.
6. Pieper, U.; Webb, B.M.; Barkan, D.T.; Schneidman-Duhovny, D.; Schlessinger, A.; Braberg, H.; Yang, Z.; Meng, E.C.; Pettersen, E.F.; Huang, C.C.; Datta, R.S.; Sampathkumar, P.; Madhusudhan, M.S.; Sjölander, K.; Ferrin, T.E.; Burley, S.K.; Sali, A. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res., 2011, 39, 465-474.
7. Pieper, U.; Schlessinger, A.; Kloppmann, E.; Chang, G.A.; Chou, J.J.; Dumont, M.E.; Fox, B.G.; Fromme, P.; Hendrickson, W.A.; Malkowski, M.G.; Rees, D.C.; Stokes, D.L.; Stowell, M.H.; Wiener, M.C.; Rost, B.; Stroud, R.M.; Stevens, R.C.; Sali A. Coordinating the impact of structural genomics on the human a-helical transmembrane proteome. Nat. Struct. Mol. Biol, 2013, 20, 135-138.
8. Johnson, M.; Zaretskaya, I.; Raytselis, Y.; Merezhuk, Y.; McGinnis S.; Madden, TL. NCBI BLAST: a better web interface. Nucleic Acids Res. 2008, 36, 5-9.
9. Finn, R.D.; Clements, J.; Eddy, S.R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Research, 2011, 39, 29-37.
10. Mornon, J.P.; Lehn, P.; Callebaut, I. Molecular models of the open and closed states of the whole human CFTR protein. Cell Mol. Life Sci., 2009, 66, 3469-3486.
11. Shi, Z.; Tiwari, A.K.; Shukla, S.; Robey, R.W.; Singh, S.; Kim, I.W.; Bates, S.E.; Peng, X.; Abraham, I.; Ambudkar, S.V.; Talele, T.T.; Fu, L.W.; Chen, ZS. Sildenafil reverses ABCB1- and ABCG2- mediated chemotherapeutic drug resistance. Cancer Res., 2011, 71, 3029-3041.
12. Yakata, K.; Tani, K.; Fujiyoshi, Y. Water permeability and characterization of aquaporin-11. J. Struct. Biol., 2011, 174, 315-320.
13. Martins, A.P.; Marrone, A.; Ciancetta, A.; Galán Cobo, A.; Echevarría, M.; Moura, TF; Re, N.; Casini, A; Soveral G. Targeting aquaporin function: potent inhibition of aquaglyceroporin-3 by a gold-based compound. PLoS One, 2012: Available from: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0037435.
14. Haeger, S.; Kuzmin, D.; Detro-Dassen, S.; Lang, N.; Kilb, M.; Tsetlin, V.; Betz, H.; Laube, B.; Schmalzing, G. An intramembrane aromatic network determines pentameric assembly of Cys-loop receptors. Nat. Struct. Mol. Biol., 2010, 17, 90-98.
15. Castro, P.A.; Figueroa, M.; Yevenes, G.E.; San Martin, L.S.; Aguayo, LG. The basicproperty of Lys385 is important for potentiation of the human a1 glycine receptor by ethanol. J. Pharmacol. Exp. Ther., 2012, 340, 339-349.
16. Gurba, K.N.; Hernandez, C.C.; Hu, N.; Macdonald, R.L. GABRB3 mutation; G32R, associated with childhood absence epilepsy alters a1p3y2L y-aminobutyric acid type A (GABAA) receptor expression and channel gating. J. Biol. Chem., 2012, 287, 12083-12097.
17. Kulleperuma, K.; Smith, S.M.; Morgan, D.; Musset, B.; Holyoake, J.; Chakrabarti, N.; Cherny, V.V.; DeCoursey, T.E.; Pomès, R. Construction and validation of a homology model of the human voltage-gated proton channel hHV1. J. Gen. Physiol, 2013, 141, 445-465.
18. Durdagi, S.; Deshpande, S.; Duff, H.J.; Noskov, S.Y. Modeling of open; closed; and open-inactivated states of the hERG1 channel: structural mechanisms of the state-dependent drug binding. J. Chem. Inf. Model, 2012, 52, 2760-2774.
19. Depil, K.; Beyl, S.; Stary-Weinzinger, A.; Hohaus, A.; Timin, E.; Hering, S. Timothy mutation disrupts the link between activation and inactivation in Ca(V)1.2 protein. J. Biol. Chem., 2011, 286, 31557-31564.
20. Giorgetti, A.; Nair, A.V.; Codega, P.; Torre, V.; Carloni P. Structural basis of gating of CNG channels. FEBS Lett, 2005, 579, 1968-1972.
21. Mazzolini, M.; Marchesi, A.; Giorgetti, A.; Torre, V. Gating in CNGA1 channels. Pflugers Arch., EJP., 2010, 459, 547-555.
22. Giorgetti, A.; Carloni, P. Molecular modeling of ion channels: structural predictions. Curr Opin Chem Biol, 2003, 7, 150-156.
23. Giorgetti, A.; Carloni, P.; Mistrik, P.; Torre, V. A homology model of the pore region of HCN channels. Biophys J., 2005, 89, 932-944.
24. Bisha, I.; Laio, A.; Magistrato, A.; Giorgetti, A.; Sgrignani, J. A Candidate Ion-Retaining State in the Inward-Facing Conformation of Sodium/Galactose Symporter: Clues from Atomistic Simulations J. Chem. Theory Comput., 2013, 9,1240-1246.
25. Pietra, F. Docking and MD simulations of the interaction of the tarantula peptide psalmotoxin-1 with ASIC 1a channels using a homology model. J Chem. Inf. Model, 2009, 49, 972-977.
26. Kranjc, A.; Grillo, F.W.; Rievaj, J.; Boccaccio, A.; Pietrucci, F.; Menini, A; Carloni, P.; Anselmi, C. Regulation of bestrophins by Ca2+: a theoretical and experimental study. PLoS One, 2009: Available from: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0004672
27. Ravna, A.W.; Sylte, I. Homology modeling of transporter proteins (carriers and ion channels). Methods Mol. Biol., 2012, 857, 281-299.
28. Palmeira, A.; Sousa, E.; Vasconcelos, M.H.; Pinto, M.; Fernandes, M.X. Structure and ligand-based design of P-glycoprotein inhibitors: a historical perspective. Curr. Pharm. Des., 2012, 18, 4197-4214.
29. Terada, T.; Inui, K. Recent advances in structural biology of pep-tide transporters. Curr. Top Membr., 2012, 70, 257-274.
30. Govindaraj, R.G.; Manavalan, B.; Basith, S.; Choi, S. Comparative analysis ofspecies-specific ligand recognition in Toll-like receptor 8 signaling: a hypothesis. PLoS One, 2011: Available from: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025118
31. Sano, M.; Korekane, H.; Ohtsubo, K.; Yamaguchi, Y.; Kato, M.; Shibukawa, Y.; Tajiri, M.; Adachi, H.; Wada, Y.; Asahi, M.; Tani-guchi, N. N-glycans of SREC-I (scavenger receptor expressed b endothelial cells): essential role for ligand binding, trafficking and stability. Glycobiology, 2012, 22, 714-724.
32. Schöneberg, T.; Schulz, A.; Biebermann, H.; Hermsdorf, T.; Röm-pler, H.; Sangkuhl, K. Mutant G-protein-coupled receptors as a cause of human diseases. Pharmacol. Ther., 2004, 104, 173-206.
33. Heilker, R.; Wolff, M.; Tautermann, C.S.; Bieler, M. G-protein-coupled receptor-focused drug discovery using a target class platform approach. Drug. Discov. Today, 2009, 14, 231-240.
34. Rosenbaum, D.M.; Rasmussen, S.G.F.; Kobilka, B.K. The structure and function of G-protein-coupled receptors. Nature, 2009, 459, 356-363.
35. Topiol, S.; Sabio, M. X-ray structure breakthroughs in the GPCR transmembrane region. Biochem. Pharmacol., 2009, 78, 11-20.
36. Sprang, S.R. Cell signalling: binding the receptor at both ends. Nature, 2011,469, 172-173.
37. Xu, F., Wu, H.; Katritch, V.; Han, G.W.; Jacobson, K.A.; Gao, Z.G.; Cherezov, V.; Stevens, R.C. Structure of an agonist-bound human A2A adenosine receptor. Science, 2011, 332, 322-327.
38. Mobarec, J.C.; Sanchez, R.; Filizola, M. Modern homology modeling of G-protein coupled receptors: which structural template to use? J. Med. Chem., 2009, 52, 5207-5216.
39. Yarnitzky, T.; Levit, A.; Niv, M.Y. Homology modeling of G-protein-coupled receptors with X-ray structures on the rise. Curr Opin. Drug. Discov. Devel., 2010, 13, 317-325.
40. Senderowitz, H.; Marantz, Y. G Protein-coupled receptors: target-based in silico screening. Curr. Pharm. Des., 2009, 15, 4049-4068.
41. de Graaf, C.; Rognan, D. Customizing G Protein-coupled receptor models for structure-based virtual screening. Curr. Pharm. Des., 2009, 15, 4026-4048.
42. Cui, M.; Jiang, P.; Maillet, E.; Max, M.; Margolskee, R.F.; Osman, R. The heterodimeric sweet taste receptor has multiple potential ligand binding sites. Curr. Pharm. Des., 2006, 12, 4591-4600.
43. Brockhoff, A.; Behrens, M.; Niv, M.Y.; Meyerhof, W. Structural requirements of bitter taste receptor activation. Proc. Natl. Acad. Sci. U S A., 2010, 107, 11110-11115.
44. Reisert, J.; Restrepo, D. Molecular tuning of odorant receptors and its implication for odor signal processing. Chem. Senses., 2009, 34, 535-545.
45. 2+-sensing receptor interact within overlapping but not identical binding sites in the transmembrane domain. J. Biol. Chem., 2004, 279, 18990-18997.
46. Bhattacharya, S.; Subramanian, G.; Hall, S.; Lin, J.; Laoui, A.; Vaidehi, N. Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1. J. Comput. Aided Mol. Des., 2010, 24, 659-674.
47. Niv, M.Y.; Skrabanek, L.; Filizola, M.; Weinstein, H. Modeling activated states of GPCRs: the rhodopsin template. J. Comput. Aided Mol. Des., 2006, 20, 437-448.
48. Niv, M.Y.; Filizola, M. Influence of oligomerization on the dynamics of G-protein-coupled receptors as assessed by normal mode analysis. Proteins, 2008, 71, 575-586.
49. Ivanov, A.A.; Barak, D.; Jacobson, K.A. Evaluation of homology modeling of G-protein-coupled receptors in light of the A (2A) adenosine receptor crystallographic structure. J. Med. Chem., 2009, 52, 3284-3292.
50. Slack, J.P.; Brockhoff, A.; Batram, C.; Menzel, S.; Sonnabend, C.; Born, S.; Galindo, M.M.; Kohl, S.; Thalmann, S.; Ostopovici-Halip, L.; Simons, C.T.; Ungureanu, I.; Duineveld, K.; Bologa, C.G.; Behrens, M.; Furrer, S.; Oprea, T.I.; Meyerhof, W. Modulation of bitter taste perception by a small molecule hTAS2R antagonist. Curr. Biol., 2010, 20, 1104-1109.
51. Biarnés, X.; Marchiori, A.; Giorgetti, A.; Lanzara, C.; Gasparini, P.; Carloni, P.; Born, S.; Brockhoff, A.; Behrens, M.; Meyerhof, W. Insights into the binding of Phenyltiocarbamide (PTC) agonist to its target human TAS2R38 bitter receptor. PLoS ONE, 2010: Available from: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012394
52. Leguèbe, M.; Nguyen, C.; Capece, L.; Hoang, Z.; Giorgetti, A.; Carloni, P. Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes. PLoS One, 2012: Available from: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047332
53. Marchiori, A.; Capece, L.; Giorgetti, A.; Gasparini, P.; Behrens, M.; Carloni, P.; Meyerhof, W. Coarse-Grained/Molecular Mechanics of the TAS2R38 Bitter Taste Receptor: Experimentally-Validated Detailed Structural Prediction of Agonist Binding. PLoS One., 2013: Available from: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0064675
54. Vaidehi, N.; Pease, J.E.; Horuk, R. Modeling small molecule-compound binding to G-protein-coupled receptors. Methods Enzy-mol., 2009, 460, 263-288.
55. Simms, J.; Hall, N.E.; Lam, P.H.; Miller, L.J.; Christopoulos, A.; Abagyan, R.; Sexton, P.M. Homology modeling of GPCRs. Methods Mol. Biol., 2009, 552, 97-113.
56. st ed.; Vaidehi, N.; Klein-Seetharaman, J.; Eds.; Springer Science Business Media: London, 2012, pp. 179-205.
57. Malo, M.; Persson, R.; Svensson, P.; Luthman, K.; Brive, L. Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the humandopamine D2 receptor. J. Comput. Aided. Mol. Des., 2013, 27, 277-291.
58. Kowalski-Chauvel, A.; Najib, S.; Tikhonova, I.G.; Huc, L.; Lopez, F.; Martinez, L.O.; Cohen-Jonathan-Moyal, E.; Ferrand, A.; Seva, C. Identification of the F1-ATPase at the cell surface of colonic epithelial cells: role in mediating cell proliferation. J. Biol. Chem., 2012, 287, 41458-41468.
59. Siam, A.; Brancale, A.; Simons, C. Comparative modeling of 25-hydroxycholesterol-7a-hydroxylase (CYP7B1): ligand binding and analysis of hereditary spastic paraplegia type 5 CYP7B1 mutations. J. Mol. Model., 2012, 18, 441-453.
60. Floris, M.; Raimondo, D.; Leoni, G.; Orsini, M.; Marcatili, P.; Tramontano, A. MAISTAS: a tool for automatic structural evaluation of alternative splicing products. Bioinformatics. 2011, 27, 1625-1629.
61. McGuffin, L.J.; Street S.A.; Bryson, K.; Sørensen, S.A.; Jones DT. The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucleic Acids Res., 2004, 32, 196-199.
62. McGuffin, L.J.; Smith, R.T.; Bryson, K.; Sørensen, S.A.; Jones DT. High throughput profile-profile based fold recognition for the entire human proteome. BMC Bioinformatics, 2006, 7, 288.
63. Tress, M.L.; Martelli, P.L.; Frankish, A.; Reeves, G.A.; Wesselink, J.J.; Yeats, C; Olason, P.I.; Albrecht, M.; Hegyi, H.; Giorgetti, A.; Raimondo, D.; Lagarde, J.; Laskowski, R.A.; López, G.; Sadowski, M.I.; Watson, J.D.; Fariselli, P.; Rossi, I.; Nagy, A.; Kai, W.; Størling, Z.; Orsini, M.; Assenov, Y.; Blankenburg, H.; Huthmacher, C; Ramírez, F.; Schlicker, A.; Denoeud, F.; Jones, P.; Kerrien, S.; Orchard, S.; Antonarakis, S.E.; Reymond, A.; Birney, E.; Brunak, S.; Casadio, R.; Guigo, R.; Harrow, J.; Hermjakob, H.; Jones, D.T.; Lengauer, T.; Orengo, CA.; Patthy, L.; Thornton, JM.; Tramontano, A.; Valencia A. The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A., 2007, 104, 5495-5500.
64. Piovesan, D.; Martelli, PL.; Fariselli, P.; Zauli, A.; Rossi, I.; Casadio R. BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. Nucleic Acids Res., 2011, 39, 197-202.