Modeling the structure of pyrococcus furiosus rubredoxin by homology to other X-ray structures (original) (raw)

Abstract

The three-dimensional structure of rubredoxin from the hyperthermophilic archaebacterium, Pyrococcus furiosus, has been modeled from the X-ray crystal structures of three homologous proteins from Clostridiumpusteuriunum, Desulfovibrio gigas, and Desulfovibrio vulgaris. All three homology models are similar. When comparing the positions of all heavy atoms and essential hydrogen atoms to the recently solved crystal structure (Day, M.W., et al., 1992, Protein Sci. I, 1494-1507) of the same protein, the homology models differ from the X-ray structure by 2.09 A root mean square (RMS). The X-ray and the zinc-substituted NMR structures (Blake, P.R., et al., 1992b, Protein Sci. I, 1508-1521) show a similar level of difference (2.05 A RMS). On average, the homology models are closer to the X-ray structure than to the NMR structures (2.09 vs. 2.42 A RMS).

Loading...

Loading Preview

Sorry, preview is currently unavailable. You can download the paper by clicking the button above.

References (42)

  1. Abola, E.E., Bernstein, F.C.. Bryant, S.H., Koetzle, T.F., & Weng, J. (1987). Protein Data Bank. In Crystallographic Databases-fnfor- mation Content, Software Systems, Scientific Applications (Allen, F.H., Bergerhoff, G., & Sievers, R., Eds.), pp. 107-132. Commis- sion of the International Union of Crystallography, BonnICam- bridge/Chester.
  2. Adams, M.W.W. &Kelly, R.M., Eds. (1992). Biocatalysisat Extreme Temperatures: Enzyme Systems Near and Above 100 "C. American Chemical Society, Washington, D.C.
  3. Adman, E.T., Sieker, L.C., & Jensen, L.H. $1991). Structure of rub- redoxin from Desulfovibrio vulgaris at 1.5 A resolution. J. Mol. Biol. 217, 337-352.
  4. Bernstein, F.C.. Koet.de, T.F., Williams, G.J.B., Meyer, E.F., Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977). The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
  5. Blake, P.R., Day, M.W., Hsu, B.T., Joshua-Tor, L., Park, J.-B., Zhou, Z.H., Hare, D.R., Adams, M.W. W., Rees, D.C., & Summers, M.F. (1992a). Comparison of the X-ray structure of native rubredoxin from Pyrococcusfuriosus with the NMR structure of the zinc-sub- stituted protein. Protein Sci. I , 1522-1525.
  6. Blake, P.R., Park, J.-B., Bryant, EO., Shigetoshi, A., Magnuson, J.K., Eculston, E., Howard, J.B., Summers, M.F., & Adams, M.W.W. (1991). Determinants of protein hyperthermostability: 1. Purifica- tion, amino acid sequence and secondary structure by NMR of the rubredoxin from the hyperthermophilic archaebacterium, Pyrococ- cus furiosus. Biochemistry 30, 10885-10895.
  7. Blake, P.R., Park, J.-B., Zhou, Z.H., Hare, D.R., Adams, M.W.W., & Summers, M.F. (1992b). Solution-state structure by NMR of zinc- substituted rubredoxin from the marine hyperthermophilic archae- bacterium Pyrococcus furiosus. Protein Sci. I , 1508-1521.
  8. Bradley, E.A., Stewart, D.E., Adams, M.W.W., & Wampler, J.E.
  9. Investigations of the thermostability of rubredoxin models using molecular dynamics simulations. Protein Sci. 2, 650-665.
  10. Bull, H.B. & Breese, K. (1973). Thermal stability of proteins. Arch. Bio- chem. Biophys. 158, 681-686.
  11. Chandrasekhar, I., Clore, G.M., Szabo, A., Gronenborn, A.M., & Brooks, B.R. (1992). A 500 ps molecular dynamics simulation study of interleukin-lb in water, correlation with nuclear magnetic reso- nance spectroscopy and crystallography. J. Mol. Biol. 226,239-250.
  12. Clore, G . M . , Wingfield, P.T., & Gronenborn, A.M. (1991). High- resolution three-dimensional structure of interleukin 10 in solution by three-and four-dimensional nuclear magnetic resonance spectros- copy. Biochemistry 30, 2315-2323.
  13. Costantino, H.R., Brown, S.H., & Kelly, R.M. (1990). Purification and characterization of an a-glucosidase from a hyperthermophilic archaebacterium Pyrococcus furiosus exhibits a temperature opti- mum of 105 to 115°C. J. Bucteriol. 172, 3654-3660.
  14. Dauter, Z., Sieker, L.C., &Wilson, K.S. (199?). Refinement of rub- redoxin from Desulfovibrio vulgaris at 1 .O A with and without re- straints. Acta Crystallogr. B48, 42-59.
  15. Day, M.W., Hsu, B.T., Joshua-Tor, L., Park, J.-B., Zhou, Z.H., Ad- ams, M.W.W., & Rees, D.C. (1992). X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus. Protein Sci. 1 , 1494-1507.
  16. Finzel, B.C., Clancy, L.L., Holland, D.R., Muchmore, S.W., Waten- paugh, K.D., & Einspahr, H.M. (1989). Crystal structure of recom- binant human interleukin-lo at 2.OA resolution. J. Mol. Biol. 209, Frey, M., Sieker, L., Payan, F., Haser, R., Bruschi, M., Pepe, G., & LeGall, J. (1987). Rubredoxin from Desulfovibrio gigas. A molec- ular model of the oxidized form at 1.4 angstroms resolution. J. Mol.
  17. Fontana, A. (1991). How nature engineers protein (therm0)stability. In Life Under Extreme Conditions (di Prisco, G., Ed.), pp. 89-1 13. Springer-Verlag, Berlin.
  18. Hall, D. & Pavitt, N. (1984). An appraisal of molecular force fields for the representation of polypeptides. J. Comp. Chem. 5 , 441-450.
  19. Lim, W.K.L., Brouillete, C., & Hardman, J.K. (1992). Thermal stabil- ities of mutant Escherichia coli tryptophan synthase a subunits. Arch. Biochem. Biophys. 292, 34-41.
  20. Lovenberg, W. & Sobel, B.E. (1965). Rubredoxin: A new electron trans- fer protein from Clostridiumpasteurianum. Proc. Natl. Acad. Sci.
  21. Merz, K.M., Murcko, M.A., &Kollman, P.A. (1991). Inhibitionofcar- 179-791. Bid. 197, 525-541. USA 54, 193-199.
  22. bonic anhydrase. J. Am. Chem. SOC. 113, 4484-4490.
  23. Papavassiliou, P. & Hatchikian, E.C. (1985). Isolation and character- ization of a rubredoxin and a two (4Fe-4s) ferredoxin from Ther- rnodesulfobacterium commune. Biochim. Biophys. Acta 810, 1-1 I .
  24. Priestle, J.P., Schar, H.-P., & Grutter,M.G. (1989). Crystallographic refinement of interleukin-I 6 at 2.0 A resolution. Proc. Natl. Acad. Sci. USA 86, 9667-9671.
  25. Schwartz, R.M. & Dayhoff, M.O. (1978). Matrices for detecting distant relationships. In Atlas of Protein Sequence and Structure Supple- ment 3 (Dayhoff, M.O., Ed.), pp. 353-358. National Biomedical Research Foundation, Washington, D.C.
  26. Singh, U.C., Wiener, P.K., Caldwell, J.W., & Kollman, P.A. (1986). AMBER (USCF), Version 3.0. Department of Pharmaceutical Chemistry, University of California, California.
  27. Stellwagen, E. & Wilgus, H. (1978). Relationship of protein thermosta- bility to accessible surface area. Nature 275, 342-343.
  28. Stenkamp, R.E., Sieker, L.C., & Jensen, L.H. (1990). The structure 0 : rubredoxin from Desulfovibrio desulfuricans strain 27774 at 1.5 A resolution. Proteins Struct. Funct. Genet. 8 , 352-364.
  29. Stewart, D.E. (1989). The structure, interactions, and dynamics of elec- tron transport proteins from Desulfovibrio: A molecular modeling and computational study. Ph.D. Dissertation, University of Geor- gia, Athens, Georgia.
  30. Stewart, D.E. & Wampler, J.E. (1991). Molecular dynamics simulations of the cytochrome c3-rubredoxin complex from Desulfovibrio vul- garis. Proteins Struct. Funct. Genet. 11, 142-152.
  31. Stewart, D.E., Weiner, P.K., & Wampler, J.E. (1987). Prediction of the structure of proteins using related structures, energy minimization and computer graphics. J. Mol. Graph. 5 , 137-144.
  32. Veerapandian, B., Gilliland, G.L., Raag, R., Svensson, A.L., Masui, Y., Hirai, Y., & Poulos, T.L. (1991). Functional implications of in- terleukin-10 based on the three-dimensional structure. Proteins Struct. Funct. Genet. 12, 10-23.
  33. Wampler, J.E. (1991). Specos SA: A computer program for managing, graphing and manipulating laboratory data. Anal. Instrum. 19, 203-230.
  34. Wampler, J.E., Bradley, E.A., Adams, M.W.W., & Stewart, D.E. (1992). Computational approaches to modeling and analyzing ther- mostability in proteins. In Biocatalysis at Extreme Temperatures: Enzyme Systems Near and Above 100 "C (Adams, M.W.W. & Kelly, R.M., Eds.), pp. 153-173. American Chemical Society, Washing- ton, D.C.
  35. Wampler, J.E., Stewart, D.E.. & Gallion, S.L. (1990). Molecular dy- namics simulations of proteins and protein-protein complexes. In Computer Simulation Studies in Condensed Matter Physics I1 (Lan- dau, D.P., Mon, K.K.,&Schiittler, H.-B., Eds.), pp. 68-84. Springer- Verlag, New York.
  36. Watenpaugh, K.D., Sieker, L.C., & Jensen, L.H. (1979). The structure of rubredoxin at 1.2 A resolution. J. Mol. Biol. 131, 509-522.
  37. Watenpaugh, K.D., Sieker, L.C., & Jensen,.L.H. (1980). Crystallo- Mol. Biol. 138, 615-633. graphic refinement of rubredoxin at 1.2 Angstroms resolution. J.
  38. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G . , Profeta, S., & Weiner, P. (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 165-784.
  39. Whitlow, M. &Teeter, M.M. (1986). An empirical examination of po- tential energy minimization using the well-determined structure of the protein crambin. J. Am. Chem. Soc. 108, 7163-7172.
  40. Zuber, H. (1978). Comparative studies of thermophilic and mesophilic enzymes: Objectives, problems, results. In Biochemistry of Ther- mophily (Friedman, S.M., Ed.), pp. 267-285. Academic Press, New York.
  41. Zulli, F., Schneiter, R., Urfer, R., & Zuber, H . (1991). Engineering ther- mostability and activity of lactate dehydrogenases from bacilli. Biol. Chem. Hoppe-Seyler 372, 363-372.
  42. Zwickl, P., Fabry, S., Bogedain, C., Haas, A., & Hensel, R. (1990). Glyceraldehyde-3-phosphate dehydrogenase from the hyperthermo- philic archaebacterium Pyrococcus woesei: Characterization of the enzyme, cloning and sequencing of the gene, and expression in Esch- erichia coli. J. Bacteriol. 172, 4329-4338.