Structural Biology of Membrane Proteins Program Reannounced

Release Date:
10/21/1998
Contact:
Dr. Peter C. Preusch, NIGMS
301-594-5938
preuschp@nigms.nih.gov

NIGMS announces its continued interest in supporting research on membrane protein structures at atomic resolution. Recent spectacular successes in solving the structures of membrane proteins ( Table 1) suggest that the study of membrane proteins by X-ray crystallography, electron microscopy, and NMR is indeed feasible. However, the comprehensive list of known membrane protein structures listed in Table 1 is dwarfed by the thousands of soluble protein structures that are known and reported in the Protein Data Bank.

The National Advisory General Medical Sciences Council has endorsed a special effort in this area at several of its open meetings, most recently in May, 1998. A new program announcement, PA-99​-004, was issued on October 16, 1998, to replace our earlier announcement in this subject area [PA-95-035].In the new announcement, NIGMS and NIDDK have been joined by NIAMS, NIEHS, NINDS, and NIMH in urging researchers to address this area of science.

The announcement has no closing date and proposals in this area will continue to be of interest for the indefinite future. Applications will be accepted on the usual NIH receipt dates.

In addition to regular research grant (R01), program project (P01), and SBIR/STTR grants, which are mentioned in PA-99-004, applicants may also wish to consider applying for support using the R21 grant mechanism under the NIGMS program of Exploratory Studies for High Risk/High Impact Research [PA-97-049].

Several additional items have been published relating to NIGMS interest in this subject area and to address the "no crystal, no grant" issue regarding the review of crystallographic proposals. See: FAS​EB Journal 10, 529, March, 1996 ; Nature Structural Biology 5, 11-14, January, 1998; Proteins: Structure, Function, and Genetics 26(1), i-ii, September, 1996 (155K PDF file).

NIGMS has developed a set of Criteria for the Evaluation of Structure Determination Proposals. These are non-binding suggestions that were distributed to relevant study sections by the Center for Scientific Review and also appeared in the Nature Structural Biology article mentioned above. They represent suggested guidelines for discussion and do not in any way replace or alter the official NIH review criteria as published in the NIH Guide, June 27, 1997.

For more information about NIGMS support for the structural biology of membrane proteins, contact:

Dr. Peter C. Preusch
Program Director
Division of Pharmacology, Physiology, and Biological Chemistry
National Institute of General Medical Sciences
45 Center Drive, MSC 6200
Bethesda, MD 20892-6200
Phone: 301-594-5938
FAX: 301-480-2802
preuschp@nigms.nih.gov

or contact:

Dr. John C. Norvell
Program Director
Division of Cell Biology and Biophysics
National Institute of General Medical Sciences
45 Center Drive, MSC 6200
Bethesda, MD 20892-6200
Phone: 301-594-0533
FAX: 301-480-2004
norvellj@nigms.nih.gov


Table 1. Structures Including Membrane-Embedded Domains Solved at High Resolution

Protein(s) First Solved Number of Models Highest Resolution References
Bacteriorhodopsin 1990 9 2.3 A [1-9]





Bacterial Photoreaction Centers 1984 13 2.2 A [7-21]





Light Harvesting Complexes 1994 2 2.4 A [22-24]





Photosystem I 1996 1 4.0 A [25]





Porins 1990 27 1.8 A [26-41]





Ferric Enterobactin Receptor 1998 1 IP* [42-43]





Alpha-Hemolysin 1996 1 1.9 A [44]





Potassium Channel KcsA 1998 1 3.2 A [45]





Mechanosensitive Channel MSCL 1998 1 IP* [46]





Prostaglandin Synthase-I 1993 5 3.4 A [47-49]





Prostaglandin Synthase-II 1996 7 3.0 A [50-51]





Squalene-hopene cyclase 1997 1 2.8 A [52]





Cytochrome Oxidase 1995 7 2.7 A [53-57]





Cytochrome bc1 Complex 1996 6 2.9 A [58-61]





This list includes structures solved for substantially intact proteins that include a membrane-embedded domain. The list does not include structures solved for extramembrane domains of membrane proteins, membrane-embedded fragments, small peptides, or peripheral membrane proteins not tightly associated with the lipid core. Several entries represent families of proteins that include functionally and structurally distinct members (e.g., porins). A more detailed table is available on request.

The list is based on structures reported in the literature or in the Protein Data Bank (including items submitted, but not yet released) as of 12/22/98. Brackets in the reference list give PDB entry numbers. IP indicates "In progress; published resolution of refined model not yet available." NIGMS is interested in tracking progress in this area. If you note omissions to this list, please contact preuschp@nigms.nih.gov.

References Cited:

1. Model for the structure of bacteriorhodopsin based on high resolution electron cryo-microscopy. Henderson, R., Baldwin, J.M., Ceska, T.A., Zemlin, F., Beckmann, E., & Downing, K.H., J. Mol. Biol. 213, 899-929 (1990). [1BRD]

2. Electron-crystallographic refinement of the structure of bacteriorhodopsin. Grigorieff, N., Ceska, T.A., Downing, K.H., Baldwin, J.M., & Henderson, R., J. Mol. Biol. 259, 393-421 (1996). [2BRD]

3. Surface of bacteriorhodopsin revealed by high-resolution electron crystallography. Kimura, Y., Vassylyev, D.G., Miyazawa, A., Kidera, A., Matsushima, M., Mitsuoka, K., Murata, K., Hirai, T., & Fujiyoshi, Y., Nature 389, 206-211 (1997). [1AT9]

4. X-ray structure of bacteriorhodopsin at 2.5 Angstroms from microcrystals grown in lipidic cubic phases. Pebay-Peyroula, E., Rummel, G., Rosenbusch, J.P., & Landau, E.M., Science 277, 1676-1681 (1997). [1AP9]

5. Proton transfer pathways in bacteriorhodopsin at 2.3 Angstrom resolution. Luecke, H., Richter, H.-T., & Lanyi, J.K., Science 280, 1934-1937 (1998). [1BRX]

6. Structure of the bacteriorhodopsin-lipid complex from heterogeneously nucleated 3-D crystals. Essen, L.-O., Siegert, R., Lehmann, W.D., & Oesterhelt (in prep.) [1BRR]

7. X-ray structure analysis of a membrane protein complex. Electron density map of 3 Angstrom resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis. Deisenhofer, J., Epp, O., Miki, K., Huber, R., & Michel, H., J. Mol. Biol. 180, 385-98 (1984). [1PRC]

8. Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3 Angstroms resolution. Deisenhofer, J., Epp, O., Miki, K., Huber, R., & Michel, H., Nature 318, 618-24 (1985). [1PRC]

9. Crystallographic refinement at 2.3 Angstrom and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis. Deisenhofer, J., Epp, O., Sinning, I., & Michel, H., J. Mol. Biol. 246, 429-457 (1995). [1PRC]

10. The coupling of light-induced electron transfer: proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, Qb. Lancaster, C.R.D., & Michel, H., Structure 5, 1339-1359 (1997). [2PRC, 3PRC, 4PRC]

11. Ubiquinone reduction and protonation in the reaction centre of Rhodopseudomonas viridis: structures and their functional implications. Lancaster, C.R.D., Biochim. Biophys. Acta 1365, 143 (1998). [2PRC, 3PRC, 4PRC]

12. Structure of Rhodopseudomonas sphaeroides R-26 reaction center. Chang, C.-H., Tiede, D.M., Tang, J., Smith, U., Norris, J.R., & Schiffer, M., FEBS Lett. 205, 82-86 (1986). [2RCR]

13. Structure of the membrane-bound protein photosynthetic reaction center from Rhodobacter sphaeroides. Chang, C.-H., El-Kabbani, O., Tide, D., Norris, J., & Schiffer, M., Biochemistry 30, 5352-5360 (1991). [2RCR]

14. Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction. Allen, J.P., Feher, G., Yeates, T.O., Rees, D.C., Deisenhofer, J., & Michel, H., Proc. Nat. Acad. Sci., U.S.A. 83, 8589-8593 (1986). [4RCR]

15. Structure and Function of Bacterial Photosynthetic Reaction Centers. Feher, G., Allen, J.P., Okamura, M.Y., & Rees, D.C., Nature 339, 111-116 (1989). [4RCR]

16. New crystal form of the photosynthetic reaction centre from Rhodobacter sphaeroides of improved diffraction quality. Buchanan, S.K., Fritzsch, G., Ermler, U., & Michel, H., J. Mol. Biol. 230, 1311-1314 (1993). [1PCR]

17. Structure of the photosynthetic reaction center from Rhodobacter sphaeroides at 2.65 Angstroms resolution: cofactors and protein-cofactor interactions. Ermler, U., Fritzsch, G., Buchanan, S.K., & Michel, H., Structure 2, 925-936 (1994) [1PCR]

18. Structure of the photochemical reaction center of a spheroidene containing purple bacterium, Rhodobacter sphaeroides Y, at 3 Angstroms. Arnoux, B., Gaucher, J.F., Ducruix, A., Reiss-Husson, F. [submitted to PDB 12/94, not published]. [1YST]

19. Crystallographic analyses of site-directed mutants of the photosynthetic reaction center from Rhodobacter sphaeroides. Charino, A.J., Lous, E.J., Huber, M., Allen, J.P., Schenck, C.C., Paddock, M.L., Feher, G., & Rees, D.C., Biochemistry 33, 4584-4593 (1994). [1PSS, 1PST]

20. Light-induced structural changes in photosynthetic reaction center: implications for mechanism of electron-proton transfer. Stowell, M.H.B., McPhillips, T.M., Rees, D.C., Soltis, S.M., Abresch, E., & Feher, G., Science 276, 812-816 (1997). [1AIG, 1AIJ]

21. Structural studies of wild-type and mutant reaction centers from an antenna-deficient strain of Rhodobacter sphaeroides: monitoring the optical properties of the complex from bacterial cell to crystal. McCauley-Hecht, K.E., Fyfe, P.K., Ridge, J.P., Prince, S., Hunter, C.N., Isaacs, N.W., Cogdell, R.J., & Jones, M.R., Biochemistry 37, 4740-4750 (1998). [1MPS]

22. Atomic model of plant light-harvesting complex by electron crystallography. Kuhlbrandt, W., Wang, D.N., & Fujiyoshi, Y., Nature 367, 614-621 (1994). [Not submitted to PDB]

23. Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria. McDermott, G., Prince, S.M., Freer, A.A., Hawthornthwaite-Lawless, A.M., Papiz, M.Z., Cogdell, R.J., & Isaacs, N.W., Nature 374, 517-521 (1995). [1KZU]

24. The crystal structure of the light-harvesting complex II (B800-850 from Rhodospirillum molischianum. Koepke, J., Hu, X., Muenke, C., Schulten, K., & Michel, H., Structure 15, 581-597 (1996). [1LGH]

25. Photosystem I at 4 A resolution represents the first structural model of a joint photosynthetic reaction centre and core antenna system. Krauss, N., Schubert, W.D., Klukas, O., Fromme, P., Witt, H.T., & Saenger, W., Nat. Struct. Biol. 3, 965-973 (1996). [2PPS]

26. The structure of porin from Rhodobacter capsulatus at 3 Angstroms resolution. Weiss, M.S., Wacker, T., Weckesser, J., Welte, W., & Schulz, G.E., FEBS Lett 267, 268-272 (1990) [3POR]

27. The structure of porin from Rhodobacter capsulatus at 1.8 A resolution. Weiss, M.S., Kreusch, A., Schiltz, E., Nestel, U., Welte, W., Weckesser, J., Schulz, G.E., FEBS Lett 280, 379-382 (1991). [2POR]

28. Molecular architecture and electrostatic properties of a bacterial porin. Weiss, M.S., Abele, U., Weckesser, J., Welte, W. Schiltz, E., & Schulz, G.E., Science 254, 1627-1630 (1991). [2POR]

29. Structure of porin refined at 1.8 A resolution. Weiss, M.S. & Schulz, G.E., J. Mol. Biol. 227, 493-509 (1992). [2POR]

30. Structure of the membrane channel porin from Rhodopseudomonas blastica at 2.0 A resolution. Kreusch, A., Neubuser, A., Schiltz, E., Weckesser, J., & Schulz, G.E., Protein Sci. 3, 58-63 (1994). [1PRN]

31. Refined structure of the porin from Rhodopseudomonas blastica. Comparison with the porin from Rhodobacter capsulatus. Kreusch, A. & Schulz, G.E., J. Mol. Biol. 243, 891-905 (1994). [2POR, 1PRN]

32. Porin mutants with new channel properties. Schmidt, B., Maveyraud, L., Kromer, M., & Schulz, G.E., Protein Sci. 7, 1603-1611 (1998). [1BH3, 3PRN-8PRN].

33. Crystal structures explain functional properties of two E. coli porins. Cowan, S.W., Schirmer, T., Rummel, G., Steiert, M., Ghosh, R., Pauptit, R.A., Jansonius, J.N., & Rosenbusch, J.P., Nature 358, 727-733 (1992). [1OPF, 1PHO]

34. The structure of OmpF porin in a tetragonal crystal form. Cowan, S.W., Garavito, R.M., Jansonius, J.N., Jenkins, J.A., Karlsson, R., Konig, N., Pai, E.F., Pauptit, R.A., Rizkallah, P.J., Rosenbusch, J.P., Rummel, G., & Schirmer, T., Structure 3, 1041-1050 (1995). [2OMF]

35. Structural and functional alterations of a colicin resistant mutant of OmpF-porin from Escherichia coli. Jeanteur, D., Schirmer, T., Fourel, D., Simonet, V., Rummel, G., Widmer, C., Rosenbusch, J.P., Pattus, F., & Pages, J.M., Proc. Nat. Acad. Sci., U.S.A. 91, 10675-10679 (1994). [1MPF]

36. Structural and functional characterization of porin mutants selected for larger pore size. I. crystallographic analysis. Lou, K.-L., Saint, N., Prilipov, A., Rummel, G., Benson, S.A., Rosenbusch, J.P., & Schirmer, T., J. Biol. Chem. 271, 20669-20675 (1996). [1GFM, N, O, P, Q]

37. Structural basis for sugar translocation through maltoporin channels of 3.1 A resolution. Schirmer, T., Keller, T.A., Wang, Y.F., & Rosenbusch, J.P., Science 267, 512-514 (1995). [1MPM, 1MPN, 1MPN, 1MPQ]

38. Crystal structures of various maltooligosaccharides bound to maltoporin reveal a specific sugar translocation pathway. Dutzler, R., Wang, Y.F., Rizkallah, P., Rosenbusch, J.P., & Schirmer, T., Structure 4, 127-134 (1996). [1MPM, 1MPN, 1MPO]

39. Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin. Wang, Y.F., Dutzler, R., Rizkallah, P.J., Rosenbusch, J.P., & Schirmer, T., J. Mol. Biol. 272, 56-63 (1997). [1AF6, 1MPQ].

40. Structure of maltoporin from Salmonella typhimurium ligated with a nitrophenylmaltotrioside. Meyer, J.E., Hofnung, M., & Schulz, G.E., J. Mol. Biol. 266, 761-775 (1997). [1MPR]

41. Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose. Forst, D., Welte, W., Wacker, T., & Diederichs, K., Nature Structural Biology 5, 37-46, 1998. [1A0S, 1A0T]

42. Crystallization and preliminary X-ray analysis of ferric enterobactin receptor FepA, an integral membrane protein from Eschericia coli. Smith, B.S., Kobe, B., Kurumbail, R., Buchanan, S.K., Venkatramani, L., van der Helm, D., & Deisenhofer, J., Acta Crystallogr D Biol Crystallogr 54, 697-699 (1998). [1FEP]

43. Crystal structure of the ferric enterobactin receptor from E. coli. Buchanan, S., Smith, B., Venkatramani, L., Xia, D., Palnitkar, M., Chakraborty, R., van der Helm, D., & Deisenhofer, J., presented at American Crystallographic Association meeting, July, 1998, abstr. #E0031. [1FEP]

44. Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Song, L., Hobaugh, M.R., Shustak, C., Cheley, S., Bayley, H., & Gouaux, J.E., Science 274, 1859-1866 (1996). [7AHL]

45. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Doyle, D.A., Cabral, J.M., Pfuetzner, R.A., Kuo, A., Gulbis, J.M., Cohen, S.L., Chait, B.T., & MacKinnon, R., Science 280, 69-77 (1998). [1BL8]

46. Structure of the MSCL homologue from Mycobacterium tuberculosis: a gated mechanosensitive channel. Chang, G., Spencer, R.H., Lee, A.T., Barclay, M.T., & Rees, D.C., in press. [1MSL]

47. The x-ray crystal structure of the membrane protein prostaglandin H2 synthase-1. Picot, D., Loll. P.J., & Garavito, R.M., Nature 367, 243-249 (1994). [1PHR]

48. The structural basis of aspirin activity from the crystal structure of inactivated prostaglandin H2 synthase. Loll, P.J., Picot, D., & Garavito, R.M., Nature Structural Biology 2, 637-643 (1995). [1PTH]

49. Synthesis and use of iodinated non-steroidal antiinflammatory drug analogs as crystallographic probes of the prostaglandin H2 synthase cyclooxygenase site. Loll, P.J., Picot, D., Ekabo, O., & Garavito, R.M., Biochemistry 35, 7330 (1996). [1PGE, 1PGF, 1PGG]

50. Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents. Kurumbail, R.G., Stevens, A.M., Gierse, J.K., McDonald, J.J., Stegeman, R.A., Pak, J.Y., Gildehause, D., Miyashiro, J.M., Penning, T.D., Seibert, K., Isakson, P.C., & Stallings, W.C., Nature 384, 644-648 (1996). [1CX2, 3PGH, 4COX, 5COX, 6COX]

51. Flexibility of the NSAID binding site in the structure of human cyclooxygenase-2. Luong, C., Miller, A., Barnett, J., Chow, J., Ramesha, C., & Browner, M.F., Nature Structural Biology 3, 927-33 (1996). [Not submitted to PDB]

52. Structure and Function of a Squalene Cyclase Wendt, K.U., Poralla, K., & Schulz, G.E., Science 277, 1811-15 (1997). [1SQC]

53. Structure at 2.8 A resolution of cytochrome C oxidase from Paracoccus denitrificans. Iwata, S., Ostermeier, C., Ludwig, B., Michel, H., Nature 376, 660-669 (1995). [Not submitted to PDB].

54. Structure at 2.7 Angstrom resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody Fv fragment. Ostermeier, C., Harrenga, A., Ermler, U., & Michel, H., Proc. Nat. Acad. Sci., U.S.A. 94, 10547, (1997). [1AR1]

55. Structures of metal sites of oxidized bovine heart cytochrome C oxidase at 2.8 A. Tsukihara, T., Aoyama, H., Yamashita, E., Tomizaki, T., Yamaguchi, H., Shinzawa--Itoh, K., Nakashima, R., Yaono, R., & Yoshikawa, S., Science 269, 1069-1074 (1995). [1OCC]

56. The whole structure of the 13 -- submit oxidized cytochrome C oxidase at 2.8 A. Tsukihara, T., Aoyama, H., Yamashita, E., Tomizaki, T., Yamaguchi, H., Shinzawa-Itoh, K., Nakashima, R., Yaono, R., & Yoshikawa, S., Science 272, 1136-1144 (1996). [1OCC]

57. Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase. Yoshikawa, S., Shinzawa-Itoh, K., Nakashima, R., Yaono, R., Yamashita, E., Inoue, N., Yao, M., Fei, M.J., Libeu, C.P., Mizushima, T., Yamaguchi, H., Tomizaki, T., & Tsukihara, T., Science 280, 1723-1729 (1998). [1OCO, 1OCR, 1OCZ, 2OCC]

58. Crystal structure of the cytochrome bcl complex from bovine heart mitochondria. Xia, D., Yu, C.A., Kim, H., Xia, J.Z., Kachurin, A.M., Zhang, L., Yu, L., & Deisenhofer, J., Science 277, 60-66 (1997). [1QCR]

59. X-ray structural studies of the mitochondrial complex III dimer from different vertebrate sources. Berry, E.A., Zhang, Z., Huang, L.-S., & Kim, S.-H., Biophys. J. 72, 2:A137 (abstract) (1997). Crystal structure of chicken mitochondrial bc1 complex. Zhang, Z.L., Berry, E.A., Huang, L.S., Chi, Y.-I., Kim, K.-K., Hung, L.W., & Kim, S.-H., American Crystallographic Association Annual Meeting, July 19-25, p. 86 (1997). [1BCC-3BCC]

60. Electron transfer by domain movement in cytochrome bc1. Zhang, Z., Huang, L.S., Shulmeister, V.M., Chi, V.M., Kim, K.-K., Hung, L.-W., Crofts, A.R., Berry, E.A., & Kim, S.-H., Nature 392, 677-684 (1998). [1BCC, 3BCC]

61. Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex. Iwata, S., Lee, J.W., Okada, K., Lee, J.K., Iwata, M., Rasmussen, B., Link, T.A., Ramaswamy, S., & Jap, B.K., Science 281, 64-71 (1998). [1BE3, 1BGY]