Structural genomics of membrane proteins

Protein Data Bank[http://www.rcsb.org/pdb]

Membrane Proteins of Known 3D Structure[http://blanco.biomol.uci.edu/MembraneProteins_xtal.html]

Wallin E, von Heijne G: Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms.Protein Sci 1998, 7:1029–1038.

Russell RB, Eggleston DS: New roles for structure in biology and drug discovery.Nat Struct Biol 2000, 7 Suppl:928–930.

Heinemann U: Structural genomics in Europe: slow start, strong finish?Nat Struct Biol 2000, 7 Suppl:940–942.

Terwilliger T: Structural genomics in North America.Nat Struct Biol 2000, 7 Suppl:935–939.

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.

Mycobacterium tuberculosisMembrane Protein Collaboratory[http://magnet.fsu.edu/~rhudy/grant/tb-start.html]

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.

Goulding CW, Perry LJ: Protein production inEscherichia colifor structural studies by X-ray crystallography.J Struct Biol 2003, 142:133–143.

Mammalian Gene Collection[http://mgc.nci.nih.gov/]

ATCC[http://www.atcc.org/]

Loll PJ: Membrane protein structural biology: the high throughput challenge.J Struct Biol 2003, 142:144–153.

Expert Protein Analysis System ExPASy Molecular Biology Server[http://www.expasy.ch/]

Miroux B, Walker JE: Over-production of proteins inEscherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels.J Mol Biol 1996, 260:289–298.

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.

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.

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.

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.

Rapid Translation System[http://www.roche-applied-science.com/sis/proteinexpression/]

Anatrace[http://www.anatrace.com/]

Montelione GT, Zheng D, Huang YJ, Gunsalus KC, Szyperski T: Protein NMR spectroscopy in structural genomics.Nat Struct Biol 2000, 7 Suppl:982–985.

Ferre-D'Amare AR, Burley SK: Dynamic light scattering in evaluating crystallizability of macromolecules.Methods Enzymol 1997, 276:157–166.

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.

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.

Ostermeier C, Michel H: Crystallization of membrane proteins.Curr Opin Struct Biol 1997, 7:697–701.

Deisenhofer J, Epp O, Miki K, Huber R, Michel H: Structure of the protein subunits in the photosynthetic reaction centre ofRhodopseudomonas viridisat 3 Å resolution.Nature 1985, 318:618–624.

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 bc1 complex.Science 1998, 281:64–71.

Carter CW Jr, Carter CW: Protein crystallization using incomplete factorial experiments.J Biol Chem 1979, 254:12219–12223.

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.

Jancarik J, Kim S-H: Sparse matrix sampling: a screening method for crystallization of proteins.J Appl Crystallogr 1991, 24:409–411.

Hampton Research[http://www.hamptonresearch.com/]

Hui R, Edwards A: High-throughput protein crystallization.J Struct Biol 2003, 142:154–161.

Stevens RC: High throughput protein crystallization.Curr Opin Struct Biol 2000, 10:558–563.

van der Woerd M, Ferree D, Pusey M: The promise of macromolecular crystallization in microfluidic chips.J Struct Biol 2003, 142:180–187.

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.

Fluidigm[http://www.fluidigm.com/]

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.

Faham S F, Bowie JU: Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure.J Mol Biol 2002, 316:1–6.

Zwahlen C, Vincent SJF, Gardner KH, Kay LE: Significantly improved resolution for NOE correlations from valine and isoleucine (Cγ2) ethyl groups in15N,13C- and15N,13C,2H-labeled proteins.J Am Chem Soc 1998, 120:4825–4831.

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.

Melesh MF, Opella SJ: Dipolar waves as NMR maps of helices in proteins.J Magn Reson 2003, 163:288–299.

Marassi FM, Opella SJ: Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints.Protein Sci 2003, 12:403–411.

Oxenoid K, Sonnichsen FD, Sanders CR: Topology and secondary structure of the N-terminal domain of diacylglycerol kinase.Biochemistry 2002, 41:12876–12882.

Fu R, Cross TA: Solid-state nuclear magnetic resonance investigation of protein and polypeptide structure.Annu Rev Biophys Biomol Struct 1999, 28:235–268.

Marassi F, Opella SJ: A solid-state NMR index of helical membrane protein structure and topology.J Magn Reson 2000, 144:150–155.

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.

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.

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.

Jap BK, Walian PJ: Crystallization of proteins: two-dimensional.In Nature Encyclopedia of Life Sciences London: Nature Publishing Group 2001. (doi:10.1038/npg.els.0003041)

Locher KP, Lee AT, Rees DC: TheE. coliBtuCD structure: a framework for ABC transporter architecture and mechanism.Science 2002, 296:1091–1098.

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.

Kraulis PJ: MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures.J Appl Crystallogr 1991, 24:946–950.

Merritt EA, Bacon DJ: Raster3D: photorealistic molecular graphics.Methods Enzymol 1997, 277:505–524.