Structural genomics of membrane proteins

Genome Biology

Volumn 5, Issue 4, 2004, Pages

  Walian, Peter ^a   Cross, Timothy A ^b   Jap, Bing K ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

BIOCHEMISTRY; CELL FREE SYSTEM; ELECTRON MICROSCOPY; GENE CONSTRUCT; GENE OVEREXPRESSION; GENE SEQUENCE; GENE TARGETING; GENETIC SELECTION; HOST CELL; HUMAN; MOLECULAR BIOLOGY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PROCESSING; PROTEIN PURIFICATION; PROTEIN STRUCTURE; REVIEW; STRUCTURAL GENE; X RAY CRYSTALLOGRAPHY;

ANIMALS; GENOMICS; HUMANS; MEMBRANE PROTEINS; PROTEIN STRUCTURE, TERTIARY;

EID: 2442619448     PISSN: 14656906     EISSN: None     Source Type: Journal    
DOI: 10.1186/gb-2004-5-4-215     Document Type: Review

References (54)

1. Protein Data Bank [http://www.rcsb.org/pdb]
2. Membrane Proteins of Known 3D Structure [http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html]
3. Wallin E, von Heijne G: Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 1998, 7:1029-1038.
4. Russell RB, Eggleston DS: New roles for structure in biology and drug discovery. Nat Struct Biol 2000, 7 Suppl:928-930.
5. Heinemann U: Structural genomics in Europe: slow start, strong finish? Nat Struct Biol 2000, 7 Suppl:940-942.
6. Terwilliger T: Structural genomics in North America. Nat Struct Biol 2000, 7 Suppl:935-939.
7. Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, et al: Structural genomics projects in Japan. Nat Struct Biol 2000, 7 Suppl:943-945.
8. Mycobacterium tuberculosis Membrane Protein Collaboratory [http://magnet.fsu.edu/~rhudy/grant/tb-start.html]
9. Edwards AM, Arrowsmith CH, Christendat D, Dharamsi A, Friesen JD, Greenblatt JF, Vedadi M: Protein production: feeding the crystallographers and NMR spectroscopists. Nat Struct Biol 2000, 7 Suppl:970-972.
10. Goulding CW, Perry LJ: Protein production in Escherichia coli for structural studies by X-ray crystallography. J Struct Biol 2003, 142:133-143.
11. Mammalian Gene Collection [http://mgc.nci.nih.gov/]
12. ATCC [http://www.atcc.org/]
13. Loll PJ: Membrane protein structural biology: the high throughput challenge. J Struct Biol 2003, 142:144-153.
14. Expert Protein Analysis System ExPASy Molecular Biology Server [http://www.expasy.ch/]
15. Miroux B, Walker JE: Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels. J Mol Biol 1996, 260:289-298.
16. Sui H, Han B-G, Lee JK, Walian P, Jap BK: Structural basis of water-specific transport through the AQP1 water channel. Nature 2001, 414:872-878.
17. Jermutus L, Ryabova LA, Pluckthun A: Recent advances in producing and selecting functional proteins by using cell-free translation. Curr Opin Biotechnol 1998, 9:534-548.
18. Kigawa T, Yabuki T, Yoshida Y, Tsutsui M, Ito Y, Shibata T, Yokoyama S: Cell-free production and stable-isotope labeling of milligram quantities of proteins. FEBS Lett 1999, 442:15-19.
19. Sawasaki T, Ogasawara T, Morishita R, Endo Y: A cell-free protein synthesis system for high-throughput proteomics. Proc Natl Acad Sci USA 2002, 99:14652-14657.
20. Rapid Translation System [http://www.roche-applied-science.com/sis/proteinexpression/]
21. Anatrace [http://www.anatrace.com/]
22. Montelione GT, Zheng D, Huang YJ, Gunsalus KC, Szyperski T: Protein NMR spectroscopy in structural genomics. Nat Struct Biol 2000, 7 Suppl:982-985.
23. Ferre-D'Amare AR, Burley SK: Dynamic light scattering in evaluating crystallizability of macromolecules. Methods Enzymol 1997, 276:157-166.
24. Hendrickson WA, Horton JR, LeMaster DM: Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J 1990, 9:1665-1672.
25. Pebay-Peyroula E, Rummel G, Rosenbusch JP, Landau EM: X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science 1997, 277:1676-1681.
26. Ostermeier C, Michel H: Crystallization of membrane proteins. Curr Opin Struct Biol 1997, 7:697-701.
27. Deisenhofer J, Epp O, Miki K, Huber R, Michel H: Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3 Å resolution. Nature 1985, 318:618-624.
28. Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen B, Link TA, Ramaswamy S, Jap BK: Complete structure of the 11-subunit bovine mitochondrial cytochrome bcl complex. Science 1998, 281:64-71.
29. Carter CW Jr, Carter CW: Protein crystallization using incomplete factorial experiments. J Biol Chem 1979, 254:12219-12223.
30. Cudney R, Patel S, Weisgraber K, Newhouse Y, McPherson A: Screening and optimization strategies for macromolecular crystal growth. Acta Crystallogr D 1994, 50:414-423.
31. Jancarik J, Kim S-H: Sparse matrix sampling: a screening method for crystallization of proteins. J Appl Crystallogr 1991, 24:409-411.
32. Hampton Research [http://www.hamptonresearch.com/]
33. Hui R, Edwards A: High-throughput protein crystallization. J Struct Biol 2003, 142:154-161.
34. Stevens RC: High throughput protein crystallization. Curr Opin Struct Biol 2000, 10:558-563.
35. van der Woerd M, Ferree D, Pusey M: The promise of macromolecular crystallization in microfluidic chips. J Struct Biol 2003, 142:180-187.
36. Hansen CL, Skordalakes E, Berger JM, Quake SR: A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion. Proc Natl Acad Sci USA 2002, 99:16531-16536.
37. Fluidigm [http://www.fluidigm.com/]
38. Landau EM, Rosenbusch JP: Lipidic cubic phases: a novel concept for the crystallization of membrane proteins. Proc Natl Acad Sci USA 1996, 93:14532-14535.
39. Faham S, Bowie JU: Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure. J Mol Biol 2002, 316:1-6.
40. 2H-labeled proteins. J Am Chem Soc 1998, 120:4825-4831.
41. Tycko R, Blanco FJ, Ishii Y: Alignment of biopolymers in strained gels: a new way to create detectable dipole-dipole couplings in high-resolution biomolecular NMR. J Am Chem Soc 2000, 122:9340-9341.
42. Melesh MF, Opella SJ: Dipolar waves as NMR maps of helices in proteins. J Magn Reson 2003, 163:288-299.
43. Marassi FM, Opella SJ: Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints. Protein Sci 2003, 12:403-411.
44. Oxenoid K, Sonnichsen FD, Sanders CR: Topology and secondary structure of the N-terminal domain of diacylglycerol kinase. Biochemistry 2002, 41:12876-12882.
45. Fu R, Cross TA: Solid-state nuclear magnetic resonance investigation of protein and polypeptide structure. Annu Rev Biophys Biomol Struct 1999, 28:235-268.
46. Marassi F, Opella SJ: A solid-state NMR index of helical membrane protein structure and topology. J Magn Reson 2000, 144:150-155.
47. Wang J, Denny J, Tian C, Kim S, Mo Y, Kovacs F, Song Z, Nishimura K, Gan Z, Fu R, et al.: Imaging membrane protein helical wheels. J Magn Reson 2000, 144:162-167.
48. Grigorieff N, Ceska TA, Downing KH, Baldwin JM, Henderson R: Electron-crystallographic refinement of the structure of bacteriorhodopsin. J Mol Biol 1996, 259:393-421.
49. Kimura Y, Vassylyev DG, Miyazawa A, Kidera A, Matsushima M, Mitsuoka K, Murata K, Hirai T, Fujiyoshi Y: Surface of bacteriorhodopsin revealed by high-resolution electron crystallography. Nature 1997, 389:206-211.
50. Jap BK, Walian PJ: Crystallization of proteins: two-dimensional. In Nature Encyclopedia of Life Sciences London: Nature Publishing Group, April 2001. (doi:10.1038/npg.els.0003041)
51. Locher KP, Lee AT, Rees DC: The E. coli BtuCD structure: a framework for ARC transporter architecture and mechanism. Science 2002, 296:1091-1098.
52. Ferguson AD, Chakraborty R, Smith BS, Esser L, van der Helm D, Deisenhofer J: Structural basis of gating by the outer membrane transporter FecA. Science 2002, 295:1715-1719.
53. Kraulis PJ: MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991, 24:946-950.
54. Merritt EA, Bacon DJ: Raster3D: photorealistic molecular graphics. Methods Enzymol 1997, 277:505-524.