High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin Omp32

Journal of Biological Chemistry

Volumn 281, Issue 11, 2006, Pages 7413-7420

  Zachariae, Ulrich ^a   Klühspies, Thomas ^a   De, Sharmila ^a,b   Engelhardt, Harald ^a   Zeth, Kornelius ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^b Physics Department   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CELL MEMBRANES; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; NEGATIVE IONS; OPTICAL RESOLVING POWER; PHYSIOLOGY; PROTEINS; SUBSTRATES;

DYNAMICS SIMULATION; PHYSIOLOGICAL ADAPTATION; SUBSTRATE BINDING; THREONINES;

CRYSTAL STRUCTURE;

ARGININE; CARBOXYLIC ACID; MALIC ACID; MEMBRANE PROTEIN; MONOMER; PORIN; THREONINE; ANION; BACTERIAL PROTEIN; ION; ION CHANNEL; LIGAND; LIPID; MALIC ACID DERIVATIVE; OMP32 PROTEIN, BACTERIA; OUTER MEMBRANE PROTEIN; VOLTAGE DEPENDENT ANION CHANNEL;

ARTICLE; BINDING SITE; CELL MEMBRANE CONDUCTANCE; CLUSTER ANALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; DELFTIA ACIDOVORANS; ELECTRICITY; ENZYME SUBSTRATE COMPLEX; IMMOBILIZATION; ION CURRENT; LIPID MEMBRANE; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN MOTIF; CELL MEMBRANE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DOSE RESPONSE; ELECTRON; ELECTROPHYSIOLOGY; ENZYME SPECIFICITY; ESCHERICHIA COLI; HYDROGEN BOND; METABOLISM; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TRANSPORT; TEMPERATURE; TIME; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS); DELFTIA ACIDOVORANS;

ANIONS; BACTERIAL OUTER MEMBRANE PROTEINS; BACTERIAL PROTEINS; BINDING SITES; CELL MEMBRANE; CRYSTALLOGRAPHY, X-RAY; DELFTIA ACIDOVORANS; DOSE-RESPONSE RELATIONSHIP, DRUG; ELECTRONS; ELECTROPHYSIOLOGY; ESCHERICHIA COLI; HYDROGEN BONDING; ION CHANNELS; IONS; LIGANDS; LIPIDS; MALATES; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PORINS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN TRANSPORT; SUBSTRATE SPECIFICITY; TEMPERATURE; TIME FACTORS; VOLTAGE-DEPENDENT ANION CHANNELS;

EID: 33646354636     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M510939200     Document Type: Article

References (53)

1. Nikaido, H. (2003) Microbiol. Mol. Biol. Rev. 67, 593-656
2. Koebnik, R., Locher, K. P., and van Gelder, P. (2000) Mol. Microbiol. 37, 239-253
3. Schulz, G. E. (2003) Adv. Protein Chem. 63, 47-70
4. Schirmer, T. (1998) J. Struct. Biol. 121, 101-109
5. Schirmer, T., Keller, T. A., Wang, Y. F., and Rosenbusch, J. P. (1995) Science 267, 512-514
6. Forst, D., Welte, W., Wacker, T., and Diederichs, K. (1998) Nat. Struct. Biol. 5, 37-46
7. Weiss, M. S., Abele, U., Weckesser, J., Welte, W., Schlitz, E., and Schulz, G. E. (1991) Science 254, 1627-1630
8. Cowan, S. W., Schirmer, T., Rummel, G., Steiert, M., Ghosh, R., Pauptit, R. A., Jansonius, J. N., and Rosenbusch, J. P. (1992) Nature 358, 727-733
9. Kreusch, A., and Schulz, G. E. (1994) J. Mol. Biol. 243, 891-905
10. Hirsch, A., Breed, J., Saxena, K., Richter, O. M., Ludwig, B., Diederichs, K., and Welte, W. (1997) FEBS Lett. 404, 208-210
11. Dutzler, R., Rummel, G., Alberti, S., Hernandez-Alles, S., Phale, P., Rosenbusch, J., Benedi, V., and Schirmer, T. (1999) Structure Fold. Des. 7, 425-434
12. Engelhardt, H., Gerbl-Rieger, S., Krezmar, D., Schneider-Voss, S., Engel, A., and Baumeister, W. (1990) J. Struct. Biol. 105, 92-102
13. Baldermann, C., Lupas, A., Lubieniecki, J., and Engelhardt H. (1998) J. Bacteriol. 180, 3741-3749
14. Horowitz, H., Gilroy, Sh., Feinstein, S., and Gilardi, G. (1990) J. Clin. Microbiol. 28, 143-145
15. Willems, A., de Vos, P., and de Ley, J. (1992) in The Prokaryotes Vol. III (Balows, A., Trüper, H. G., Dworkin, M., Harder, W., and Schleifer, K. H., eds), pp. 2583-2590, Springer-Verlag, New York
16. Gödde, C., Liebergesell, M., and Steinbüchel, A. (1999) FEMS Microbiol. Lett. 173, 365-372
17. Ye, J., and van den Berg, B. (2004) EMBO J. 23, 3187-3195
18. van den Berg, B., Black, P. N., Clemons, W. M., Jr., and Rapoport, T. A. (2004) Science 304, 1506-1509
19. Berezkhovskii, A. M., and Bezrukov, S. M. (2005) Biophys. J. 88, 17-19
20. Dutzler, R., Schirmer, T., Karplus, M., and Fischer, S. (2002) Structure (Camb.) 10, 1273-1284
21. Robertson, K. M., and Tieleman, D. P. (2002) FEBS Lett. 528, 53-57
22. Nestorovich, E. M., Danelon, C., Winterhalter, M., and Bezrukov, S. M. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 9789-9794
23. Ceccarelli, M., Danelon, C., Laio, A., and Parrinello, M. (2004) Biophys. J. 87, 58-64
24. Mathes, A., and Engelhardt, H. (1998) Biophys. J. 75, 1255-1262
25. Zeth, K., Diederichs, K., Welte, W., and Engelhardt, H. (2000) Structure Fold. Des. 8, 981-992
26. Zachariae, U., Helms, V., and Engelhardt, H. (2003) Biophys. J. 85, 954-962
27. Suenaga, A., Komeiji, Y., Uebayasi, M., Meguro, T., Saito, M., and Yamato, I. (1998) Biosci. Rep. 18, 39-48
28. Danelon, C., Suenaga, A., Winterhalter, M., and Yamato, I. (2003) Biophys. Chem. 104, 591-603
29. Kabsch, W. (1988) J. Appl. Cryst. 21, 67-71
30. Vagin, A., and Teplyakov, A. (2000) Acta Crystallogr. Sect. D 56, 1622-1624
31. Collaborative Computational Project, No. 4 (1994) Acta Crystallogr. Sect. D 50, 760-763
32. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Acta Crystallogr. Sect. A 47, 110-119
33. Morris, R. J., Perrakis, A., and Lamzin, V. S. (2003) Methods Enzymol. 374, 229-244
34. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Cryst. 26, 283-291
35. Matthews, B. W. (1968) J. Mol. Biol. 33, 491-497
36. Woolf, T. B., and Roux, B. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 11631-11635
37. Woolf, T. B., and Roux, B. (1996) Proteins 24, 92-114
38. Im, W., and Roux, B. (2002) J. Mol. Biol. 319, 1177-1197
39. Im, W., and Roux, B. (2002) J. Mol. Biol. 322, 851-869
40. Jorgensen, W. L., Chandrasekhar, J., Madura, J., Impey, R., and Klein, M. (1983) J. Chem. Phys. 79, 926-935
41. Brooks, B., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S., and Karplus, M. (1983) J. Comput. Chem. 4, 187-217
42. MacKerell, A. D., Bashford, D., Bellot, M., Dunbrack, R. L., Evanseck, J. D., Field., M. J., Fischer, S., Gao, J., Guo, H., Ha, S., McCarthy, D. J., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiórkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) J. Phys. Chem. B 102, 3586-3616
43. Ryckaert, J., Ciccotti, G., and Berendsen, H. (1977) J. Comput. Chem. 23, 327-341
44. Essmann, U., Perera, L., Berkowitz, M., Darden, T., Lee, H., and Pedersen, L. (1995) J. Chem. Phys. 103, 8577-8593
45. Grizot, S., and Buchanan, S. K. (2004) Mol. Microbiol. 51, 1027-1037
46. Prinz, T., and Tommassen, J. (2000) FEMS Microbiol. Lett. 183, 49-53
47. Meyer, J. E. W., Hofnung, M., and Schulz, G. E. (1997) J. Mol. Biol. 266, 761-775
48. Zachariae, U., Koumanov, A., Engelhardt, H., and Karshikoff, A. (2002) Protein Sci. 11, 1309-1319
49. Domene, C., Bond, P. J., and Sansom, M.S. P. (2003) Adv. Prot. Chem. 66, 159-193
50. Kosztin, I., and Schulten, K. (2004) Phys. Rev. Lett. 93, 238102
51. Winterhalter, M. (1999) Colloids Surf. 149, 547-551
52. Jordy, M., Andersen, C., Schülein, K., Ferenci, T., and Benz, R. (1996) J. Mol. Biol. 259, 666-678
53. Buchanan, S. K., Smith, B. S., Venkatramani, L., Xia, D., Esser, L., Palnitkar, M., Chakraborty, R., van der Helm, D., and Deisenhofer, J. (1999) Nat. Struct. Biol. 6, 56-63