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The search for a new model structure of β-Factor XIIa

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Abstract

We present the search for a new model of β-factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modellers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and β-factor XIIa, in particular.

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References

  1. Furie, B.and Furie, B.C., Cell, 53 (1988) 505.

    Google Scholar 

  2. Broze, G.J., Jr., Annu. Rev. Med., 46 (1995) 103.

    Google Scholar 

  3. Revak, S.D., Cochrane, C.G., Johnson, A.R. and Hugli, T.E., J. Clin. Invest., 54 (1974) 619.

    Google Scholar 

  4. Fujikawa, K. and Davie, E.W., Methods Enzymol., 80 (1981) 198.

    Google Scholar 

  5. McMullen, B.A. and Fujikawa, K., J. Biol. Chem., 260 (1985) 5328.

    Google Scholar 

  6. Fujikawa, K. and McMullen, B.A., J. Biol. Chem., 258 (1983) 10924.

    Google Scholar 

  7. Cool, D.E. and MacGillivray, R.T.A., J. Biol. Chem., 262 (1987) 13662.

    Google Scholar 

  8. Cool, D.E., G.V. Louie, C.-J.S., Zoller, M.J., Brayer, G.D. and MacGillivray, R.T.A., J. Biol. Chem., 260 (1985) 13 666.

    Google Scholar 

  9. Ramos, M.J., J. Mol. Graphics, 9 (1991) 91.

    Google Scholar 

  10. Mosimann, S., Meleshko, R. and James, M.N.G., Proteins: Structure, Function Genetics, 23 (1995) 301.

    Google Scholar 

  11. OWL: Bleasby, A.J. and Wootton, J.C., Prot. Engng, 3 (1990) 153.

    Google Scholar 

  12. Akrigg, D., Bleasby, A.J., Dix, N.I.M., Findlay, J.B.C., North, A.C.T., Parry-Smith, D.J., Wootton, J.C., Blundell, T.L., Gardner, S.P., Hayes, F., Islam, S., Sternberg, M.J.E., Thornton, J.M., Tickle, I.J. and Murray-Rust, P., Nature, 335 (1988) 745.

    Google Scholar 

  13. BLAST: Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J., J. Mol. Biol., 215 (1990) 403.

    Google Scholar 

  14. CLUSTAL W: Thompson, J.D., Higgins, D.G. and Gibson, T.J., Nucleic Acids Res., 22 (1994) 4673.

    Google Scholar 

  15. PROCHECK v.2.1.4.: Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M., J. Appl. Cryst., 26 (1993) 283.

    Google Scholar 

  16. PREDICTPROTEIN: Rost, B., Meth. Enzym., 266 (1996) 525.

    Google Scholar 

  17. SWISS-MODEL (Automated Protein Modelling Server) Pro-Mod: Peitsch, M.C., Biotechnology, 13 (1995) 658; Biochem. Soc. Trans., 24 (1996) 274.

    Google Scholar 

  18. CHARMm (release version c23f3), Molecular Simulations Incorporated.

  19. SWISS-PROT: Appel, R.D., Bairoch, A. and Hochstrasser, D.F., Trends Biochem. Sci., 19 (1994) 258.

    Google Scholar 

  20. AMBER (version 4.1);Weiner, S.J. and Kollman, P.A., J. Am. Chem. Soc., 106 (1984) 765.

    Google Scholar 

  21. Pearson, W.R. and Lipman, D.J., Proc. Natl. Acad. Sci. USA, 85 (1988) 2444.

    Google Scholar 

  22. Biosym Technologies, 9685 Scranton Road, San Diego, CA (92121-4778).

  23. Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F. and Weng, J., Protein Data Bank in Crystallographic Databases-Information Content, Software Systems, Scientific Applications, eds. F.H.Allen, G.Bergerhoff, R.Sievess, Data Commission of the International Union of Crystallography, Bonn/Cambridge/Chester, (1987) 107-132.

  24. Protein Data Bank, Release # 75 (1996) Brookhaven National Laboratory, Upton, NY.

  25. Lamba, D., Bauer, M., Huber, R., Fischer, S., Rudolph, R., Kohnert, U. and Bode, W., J. Mol. Biol., 258 (1996) 117.

    Google Scholar 

  26. QUANTA (version 4.0), 1994, Molecular Simulations Inc., 16 New England Executive Park, Burlington MA.

  27. Sreenivasan, U. and Axelsen, P.H., Biochemistry, 31 (1992) 12 785.

    Google Scholar 

  28. Brown, D., Minoux, H. and Maigret, B., Comp. Phys. Commun., 103 (1997) 170.

    Google Scholar 

  29. Hartley, B.S. and Kauffman, D.L., Biochem. J., 101 (1966) 229.

    Google Scholar 

  30. Ford, R.P., Esnouf, M.P., Burgess, A.I. and Sarphie, A.F., J. Immunoassay, 17 (1996) 119.

    Google Scholar 

  31. Henriques, E.F., Ramos, M.J. and Reynolds, C.A., J. Comput. Aided Mol. Des., 11 (1997) 547.

    Google Scholar 

  32. Ramakrishnan, C. and Ramachandran, G.N., Biophys., 5 (1965) 909.

    Google Scholar 

  33. Rodriguez, R. and Vriend, G., website article at http:// swift.embl-heidelberg.de/future/ articles/ text/ gambling.html (1998).

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Authors and Affiliations

  1. CEQUP/Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007, Porto, Portugal

    Elsa S. Henriques, André Melo, José A.N.F. Gomes & Maria João Ramos

  2. Centro de Ciencias Exatas, Departamento de Fisica, Universidade Federal do Espirito Santo, Av. Fernando Ferrari s/n, Goiabeiras, Vitoria, ES 29060-900, Brazil

    Welly B. Floriano

  3. Laboratoire de Chimie Theorique UMR CNRS 7565, Université de Nancy I, Domaine Scientifique Victor Grignard, B.P. 239, 54506, Vandoeuvre les Nancy Cedex, France

    Nathalie Reuter & Bernard Maigret

  4. LMOPS, Bât. IUT, Université de Savoie, Campus Scientifique, Savoie Technolac, 73376, Le Bourget du Lac, France

    David Brown

  5. Instituto de Quimica, Departamento de Fisico-Quimica, Cidade Universitaria, CT Bloco A sala 412, Rio de Janeiro RJ, 21949-900, Brazil

    Marco A.C. Nascimento

Authors
  1. Elsa S. Henriques
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  2. Welly B. Floriano
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  3. Nathalie Reuter
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  4. André Melo
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  5. David Brown
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  6. José A.N.F. Gomes
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  7. Bernard Maigret
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  8. Marco A.C. Nascimento
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  9. Maria João Ramos
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Henriques, E.S., Floriano, W.B., Reuter, N. et al. The search for a new model structure of β-Factor XIIa. J Comput Aided Mol Des 15, 309–322 (2001). https://doi.org/10.1023/A:1011128521816

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