Dynamic structure of subtilisin-eglin c complex studied by normal mode analysis

Proteins: Structure, Function and Genetics

Volumn 32, Issue 3, 1998, Pages 324-333

  Ishida, Hisashi ^a   Jochi, Yasumasa ^a   Kidera, Akinori ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Binding free energy; Dynamics of a complex; Internal and external motions; Normal mode analysis of a complex; Subtilisin eglin c complex

Indexed keywords

SUBTILISIN;

ARTICLE; CALCULATION; ENTROPY; ENZYME INHIBITION; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE;

MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SERPINS; SUBTILISINS;

EID: 0032529585     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980815)32:3<324::AID-PROT8>3.0.CO;2-H     Document Type: Article

References (33)

1. Gilson, M.K., Given, J.A., Bush, B.L., McCammon, J.A. The statistical-thermodynamic basis for computation of binding affinities: A critical review. Biophys. J. 72:1047-1069, 1997.
2. Janin, J. Elusive affinities. Proteins 21:30-39, 1995.
3. Lengauer, T., Rarey, M. Computational methods for biomolecular docking. Curr. Opin. Struct. Biol. 6:402-406, 1996.
4. Steinberg, I.Z., Scheraga, H.A. Entropy changes accompanying association reactions of proteins. J. Biol. Chem. 238:172-181, 1963.
5. Page, M.I., Jencks, W.P. Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. Proc. Natl. Acad. Sci. USA 68:1678-1683, 1971.
6. Murphy, K.P., Xie, D., Thompson, K.S., Amzel, L.M., Freire, E. Entropy in biological binding processes: Estimation of translational entropy loss. Proteins 18:63-67, 1994.
7. Bode, W., Papamokos, E., Musil, D. The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, subtilisin structure and interface geometry. Eur. J. Biochem. 166:673-692, 1987.
8. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B. et al. The Protein Data Bank: A computer based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
9. Hiromi, K., Akasaka, K., Mitsui, Y., Tonomura, B., Murao, S. "Protein Protease Inhibitor - The Case of Streptomyces Subtilisin Inhibitor (SSI)." New York: Elsevier, 1985.
10. Ascenzi, P., Amiconi, G., Menegatti, E., Guarneri, M., Bolognesi, M., Schnebli, H.P. Binding of the recombinant proteinase inhibitor eglin c from leech Hirudo medicinalis to human leukocyte elastase, bovine alpha-chymotrypsin and subtilisin Carlsberg: Thermodynamic study. J. Enzym. Inhib. 2:167-172, 1988
11. Makhatadze, G.I., Privalov, P.L. Energetics of protein structure. Adv. Protein Chem. 47:307-425, 1995.
12. Tidor, B., Karplus, M. The contribution of vibrational entropy to molecular association. The dimerization of insulin. J. Mol. Biol. 238:405-414, 1994.
13. Brady, G.P., Sharp, K.A. Energetics of cyclic dipeptide crystal packing and solvation. Biophys. J. 72:913-927, 1997.
14. Duan, Y., Wilkosz, P., Rosenberg, J.M. Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases. J. Mol. Biol. 264:546-555, 1996.
15. Jackson, R.M., Sternberg, M.J.E. A continuum model for protein-protein interactions: Application to the docking problem. J. Mol. Biol. 250:258-275, 1995.
16. Novotny, J., Bruccoleri, R.E., Davis, M., Sharp K.A. Empirical free enrgy calculations: Ablind test and further improvements to the method. J. Mol. Biol. 268:401-411, 1997.
17. Nishikawa, T., Go, N. Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property. Proteins 2:308-329, 1987.
18. Brooks, B., Karplus, M. Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. USA 82:4995-4999, 1985.
19. Seno, Y., Go, N. Deoxymyoglobin studied by the conformational normal mode analysis. I. Dynamics of globin and the heme-globin interaction. J. Mol. Biol. 216:95-109, 1990.
20. Eckart, C. Some studies concerning rotating axes and polyatomic molecules. Phys. Rev. 47:552-558, 1935.
21. Braun, W., Yoshioki, S., Go, N. Formulation of static and dynamic conformational energy analysis of biopolymer systems consisting of two or more molecules. J. Phys. Soc. Jpn. 53:3269-3275, 1984.
22. Higo, J., Seno, Y., Go, N. Formulation of static and dynamic conformational energy analysis of biopolymer systems consisting of two or more molecules - Avoiding a singularity in the previous method. J. Phys. Soc. Jpn. 54:4053-4058, 1985.
23. Wako, H., Endo, S., Nagayama, K., Go, N. FEDER/2: Program for static and dynamic conformational energy analysis of macro-molecules in dihedral angle space. Comput. Phys. Commun. 91:233-251, 1995.
24. Momany, F.A., McGuire, R.F., Burgess, A.W., Scheraga, H.A. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for naturally occurring amino acids. J. Phys. Chem. 79:2361-2381, 1975.
25. Némethy, G., Pottle, M.S., Scheraga, H.A. Energy parameters in polypeptides. 9. Updating geometric parameters, nonbonded interactions, and hydrogen bond interactions for naturally occurring amino acids. J. Phys. Chem. 87: 1883-1887, 1983.
26. Noguti, T., Go, N. Amethod of rapid calculation of a second derivative matrix of conformational energy for large molecules. J. Phys. Soc. Jpn. 52:3685-3690, 1983.
27. Abe, H., Braun, W., Noguti, T., Go, N. Rapid calculation of first and second derivatives of conformational energy with respect to dihedral angles for proteins. General recurrent equations. Comput. Chem. 8:239-247, 1984.
28. Wako, H., Go, N. Algorithm for rapid calculation of hessian of conformational energy function of proteins by supercomputer. J. Comput. Chem. 8:625-635, 1987.
29. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950, 1991.
30. Dauter, Z., Betzel, Ch., Genov, N., Pipon, N., Wilson, K.S. Complex between the subtilisin from a mesophilic bacterium and the leech inhibitor eglin-c. Acta Crystallogr. B47:707-730, 1991.
31. McQuarrie, D.A. "Statistical Mechanics." New York: Harper-Collins, 1976.
32. Kidera, A., Go, N. Normal mode refinement: Crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data. J. Mol. Biol. 225:457-475, 1992.
33. Kidera, A., Go, N. Normal mode refinement: Crystallographic refinement of protein dynamic structure. II. Application to human lysozyme. J. Mol. Biol. 225:477-486, 1992.