Structural genomics plucks high-hanging membrane proteins

Current Opinion in Structural Biology

Volumn 22, Issue 3, 2012, Pages 326-332

  Kloppmann, Edda ^a,b   Punta, Marco ^c   Rost, Burkhard ^a,b  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b NEW YORK STRUCTURAL BIOLOGY CENTER   (United States)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRAL MEMBRANE PROTEIN; MEMBRANE PROTEIN; UNCLASSIFIED DRUG;

ALPHA HELIX; HIGH THROUGHPUT SEQUENCING; HUMAN; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN STABILITY; REVIEW; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; STRUCTURAL GENOMICS; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

COMPUTATIONAL BIOLOGY; GENOMICS; HUMANS; MEMBRANE PROTEINS; PROTEIN CONFORMATION;

EID: 84862601592     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2012.05.002     Document Type: Review

References (51)

1. von Heijne G. The membrane protein universe: what's out there and why bother?. J Intern Med 2007, 261:543-557.
2. von Heijne G. Membrane-protein topology. Nat Rev Mol Cell Biol 2006, 7:909-918.
3. Liu J., Rost B. Comparing function and structure between entire proteomes. Protein Sci 2001, 10:1970-1979.
4. Fagerberg L., Jonasson K., von Heijne G., Uhlen M., Berglund L. Prediction of the human membrane proteome. Proteomics 2010, 10:1141-1149.
5. Overington J.P., Al-Lazikani B., Hopkins A.L. How many drug targets are there?. Nat Rev Drug Discov 2006, 5:993-996.
6. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res 2000, 28:235-242.
7. Tusnady G.E., Dosztanyi Z., Simon I. PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res 2005, 33:D275-D278.
8. White S.H. Biophysical dissection of membrane proteins. Nature 2009, 459:344-346.
9. Punta M., Love J., Handelman S., Hunt J.F., Shapiro L., Hendrickson W.A., Rost B. Structural genomics target selection for the New York consortium on membrane protein structure. J Struct Funct Genomics 2009, 10:255-268.
10. Rost B. Marrying structure and genomics. Structure 1998, 6:259-263.
11. Montelione G.T., Anderson S. Structural genomics: keystone for a Human Proteome Project. Nat Struct Biol 1999, 6:11-12.
12. Levitt M. Growth of novel protein structural data. Proc Natl Acad Sci U S A 2007, 104:3183-3188.
13. Liu J., Montelione G.T., Rost B. Novel leverage of structural genomics. Nat Biotechnol 2007, 25:849-851.
14. Uversky V.N., Dunker A.K. Understanding protein non-folding. Biochim Biophys Acta 2010, 1804:1231-1264.
15. 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.
16. Shimamura T., Shiroishi M., Weyand S., Tsujimoto H., Winter G., Katritch V., Abagyan R., Cherezov V., Liu W., Han G.W., et al. Structure of the human histamine H1 receptor complex with doxepin. Nature 2011, 475:65-70.
17. Punta M., Coggill P.C., Eberhardt R.Y., Mistry J., Tate J., Boursnell C., Pang N., Forslund K., Ceric G., Clements J., et al. The Pfam protein families database. Nucleic Acids Res 2012, 40:D290-D301.
18. Nair R., Liu J., Soong T.-t., Acton T.B., Everett J., Kouranov A., Fiser A., Godzik A., Jaroszewski L., Orengo C., et al. Structural genomics is the largest contributor of novel structural leverage. J Struct Funct Genomics 2009, 10:181-191.
19. Burley S.K., Joachimiak A., Montelione G.T., Wilson I.A. Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI production centers. Structure 2008, 16:5-11.
20. 2+ transporter. Nature 2006, 440:833-837.
21. Waight A.B., Love J., Wang D.N. Structure and mechanism of a pentameric formate channel. Nat Struct Mol Biol 2010, 17:31-37.
22. Levin E.J., Quick M., Zhou M. Crystal structure of a bacterial homologue of the kidney urea transporter. Nature 2009, 462:757-761.
23. +-independent amino acid transporter. Science 2009, 325:1010-1014.
24. Chen Y.H., Hu L., Punta M., Bruni R., Hillerich B., Kloss B., Rost B., Love J., Siegelbaum S.A., Hendrickson W.A. Homologue structure of the SLAC1 anion channel for closing stomata in leaves. Nature 2010, 467:1074-1080.
25. Cao Y., Jin X., Levin E.J., Huang H., Zong Y., Quick M., Weng J., Pan Y., Love J., Punta M., et al. Crystal structure of a phosphorylation-coupled saccharide transporter. Nature 2011, 473:50-54.
26. Cao Y., Jin X., Huang H., Derebe M.G., Levin E.J., Kabaleeswaran V., Pan Y., Punta M., Love J., Weng J., et al. Crystal structure of a potassium ion transporter, TrkH. Nature 2011, 471:336-340.
27. Arnold K., Kiefer F., Kopp J., Battey J.N., Podvinec M., Westbrook J.D., Berman H.M., Bordoli L., Schwede T. The Protein Model Portal. J Struct Funct Genomics 2009, 10:1-8.
28. 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., et al. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 2011, 39:D465-D474.
29. Faraldo-Gomez J.D., Forrest L.R. Modeling and simulation of ion-coupled and ATP-driven membrane proteins. Curr Opin Struct Biol 2011, 21:173-179.
30. Thomine S., Barbier-Brygoo H. Structural biology: a peep through anion channels. Nature 2010, 467:1058-1059.
31. Zhou P., Lugovskoy A.A., McCarty J.S., Li P., Wagner G. Solution structure of DFF40 and DFF45 N-terminal domain complex and mutual chaperone activity of DFF40 and DFF45. Proc Natl Acad Sci U S A 2001, 98:6051-6055.
32. Dessailly B.H., Nair R., Jaroszewski L., Fajardo J.E., Kouranov A., Lee D., Fiser A., Godzik A., Rost B., Orengo C. PSI-2: structural genomics to cover protein domain family space. Structure 2009, 17:869-881.
33. Mancia F., Love J. High throughput platforms for structural genomics of integral membrane proteins. Curr Opin Struct Biol 2011, 21:517-522.
34. Punta M., Forrest L.R., Bigelow H., Kernytsky A., Liu J., Rost B. Membrane protein prediction methods. Methods 2007, 41:460-474.
35. Love J., Mancia F., Shapiro L., Punta M., Rost B., Girvin M., Wang D.N., Zhou M., Hunt J.F., Szyperski T., et al. The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins. J Struct Funct Genomics 2010, 11:191-199.
36. Li M., Hays F.A., Roe-Zurz Z., Vuong L., Kelly L., Ho C.M., Robbins R.M., Pieper U., O'Connell J.D., Miercke L.J., et al. Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. J Mol Biol 2009, 385:820-830.
37. Kelly L., Pieper U., Eswar N., Hays F.A., Li M., Roe-Zurz Z., Kroetz D.L., Giacomini K.M., Stroud R.M., Sali A. A survey of integral alpha-helical membrane proteins. J Struct Funct Genomics 2009, 10:269-280.
38. Viklund H., Granseth E., Elofsson A. Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. J Mol Biol 2006, 361:591-603.
39. Kauko A., Illergard K., Elofsson A. Coils in the membrane core are conserved and functionally important. J Mol Biol 2008, 380:170-180.
40. Forrest L.R., Tang C.L., Honig B. On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys J 2006, 91:508-517.
41. Park Y., Elsner M., Staritzbichler R., Helms V. Novel scoring function for modeling structures of oligomers of transmembrane alpha-helices. Proteins 2004, 57:577-585.
42. Pirovano W., Feenstra K.A., Heringa J. PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. Bioinformatics 2008, 24:492-497.
43. Hill J.R., Kelm S., Shi J., Deane C.M. Environment specific substitution tables improve membrane protein alignment. Bioinformatics 2011, 27:i15-i23.
44. Price W.N., Chen Y., Handelman S.K., Neely H., Manor P., Karlin R., Nair R., Liu J., Baran M., Everett J., et al. Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data. Nat Biotechnol 2009, 27:51-57.
45. Kandaswamy K.K., Pugalenthi G., Suganthan P.N., Gangal R. SVMCRYS: an SVM approach for the prediction of protein crystallization propensity from protein sequence. Protein Pept Lett 2010, 17:423-430.
46. Mizianty M.J., Kurgan L. Sequence-based prediction of protein crystallization, purification and production propensity. Bioinformatics 2011, 27:i24-i33.
47. Lomize M.A., Lomize A.L., Pogozheva I.D., Mosberg H.I. OPM: orientations of proteins in membranes database. Bioinformatics 2006, 22:623-625.
48. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012, 40:D71-D75.
49. Kall L., Krogh A., Sonnhammer E.L. An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics 2005, 21(Suppl 1):i251-i257.
50. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 2004, 25:1605-1612.
51. Chen L., Oughtred R., Berman H.M., Westbrook J. TargetDB: a target registration database for structural genomics projects. Bioinformatics 2004, 20:2860-2862.