Computational study of IAG-nucleoside hydrolase: Determination of the preferred ground state conformation and the role of active site residues

Biochemistry

Volumn 44, Issue 21, 2005, Pages 7805-7817

  Mazumder Shivakumar, Devleena ^a,b   Bruice, Thomas C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOBASE; NUCLEOSIDE HYDROLASE; SOLVENT ACCESSIBLE SURFACE AREA (SASA); WATER SOLVENTS;

BOUNDARY CONDITIONS; CATALYSIS; COMPUTATIONAL METHODS; COMPUTER SIMULATION; CONFORMATIONS; HYDROGEN BONDS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; SOLVENTS; SUBSTRATES; X RAY CRYSTALLOGRAPHY;

ENZYMES;

ADENOSINE; ASPARTIC ACID; GUANOSINE; HYDROGEN; INOSINE DERIVATIVE; NUCLEIC ACID BASE; NUCLEOSIDASE; PROTEIN IAG NH; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; ELECTRICITY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ASSAY; ENZYME CONFORMATION; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; POISSON DISTRIBUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTON TRANSPORT; STOCHASTIC MODEL; X RAY CRYSTALLOGRAPHY;

ADENOSINE; ANIMALS; ASPARTIC ACID; BINDING SITES; CALCIUM; CATIONS, DIVALENT; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; GUANOSINE; INOSINE; MODELS, MOLECULAR; N-GLYCOSYL HYDROLASES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTONS; RIBOSE; SUBSTRATE SPECIFICITY; THERMODYNAMICS; TRYPANOSOMA VIVAX;

SASA;

EID: 19644382751     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi047394h     Document Type: Article

References (37)

1. Hammond, D. J., and Gutteridge, W. E. (1984) Purine and pyrimidine metabolism in the Trypanosomatidae, Mol. Biochem. Parasitol. 13, 243-261.
2. Berens, R. L., Krug, E. D., and Marr, J. J. (1995) Purine and Pyrimidine Metabolism, Academic Press, London, U.K.
3. Parkin, D. W., Horenstein, B. A., Abdulah, D. R., Estupinan, B., and Schramm, V. L. (1991) Nucleoside hydrolase from Crithidia fasciculata, Metabolic role, purification, specificity, and kinetic mechanism, J. Biol. Chem. 266, 20658-20665.
4. Parkin, D. W. (1996) Purine-specific nucleoside N-ribohydrolase from Trypanosoma brucei brucei. Purification, specificity, and kinetic mechanism, J. Biol. Chem. 271, 21713-21719.
5. Versees, W., Decanniere, K., Pelle, R., Depoorter, J., Brosens, E., Parkin, D. W., and Steyaert, J. (2001) Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax, J. Mol. Biol. 307, 1363-1379.
6. Estupinan, B., and Schramm, V. L. (1994) Guanosine-inosine-preferring nucleoside N-glycohydrolase from Crithidia fasciculata, J. Biol. Chem. 269, 23068-23073.
7. Horenstein, B. A., Parkin, D. W., Estupinan, B., and Schramm, V. L. (1991) Transition-state analysis of nucleoside hydrolase from Crithidia fasciculata, Biochemistry 30, 10788-10795.
8. Schramm, V. L. (2003) Enzymatic transition state poise and transition state analogues, Acc. Chem. Res. 36, 588-596.
9. Gopaul, D. N., Meyer, S. L., Degano, M., Sacchettini, J. C., and Schramm, V. L. (1996) Inosine-uridine nucleoside hydrolase from Crithidia fasciculata. Genetic characterization, crystallization, and identification of histidine 241 as a catalytic site residue. Biochemistry 35, 5963-5970.
10. Mazumder, D., and Bruice, T. C. (2002) Exploring nucleoside hydrolase catalysis in silico: molecular dynamics study of enzymebound substrate and transition state, J Am. Chem. Soc. 124, 14591-14600.
11. Mazumder, D., Kahn, K., and Bruice, T. C. (2002) Computer simulations of trypanosomal nucleoside hydrolase: determination of the protonation state of the bound transition-state analogue, J. Am. Chem. Soc. 124, 8825-8833.
12. Mazzella, L. J., Parkin, D. W., Tyler, P. C., Furneaux, R. H., and Schramm, V. L. (1996) Mechanistic diagnoses of N-ribohydrolases and purine nucleoside phosphorylase, J. Am. Chem. Soc. 118, 2111-2112.
13. Versees, W., Decanniere, K., Van Holsbeke, E., Devroede, N., and Steyaert, J. (2002) Enzyme-substrate interactions in the purine-specific nucleoside hydrolase from Trypanosoma vivax, J. Biol. Chem. 277, 15938-15946.
14. Vandemeulebroucke, A., Versees, W., De Vos, S., Van Holsbeke, E., and Steyaert, J. (2003) Pre-steady-state analysis of the nucleoside hydrolase of Trypanosoma vivax. Evidence for half-of-the-sites reactivity and rate-limiting product release, Biochemistry 42, 12902-12908.
15. Versees, W., Loverix, S., Vandemeulebroucke, A., Geerlings, P., and Steyaert, J. (2004) Leaving group activation by aromatic stacking: an alternative to general acid catalysis, J. Mol. Biol. 338, 1-6.
16. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) CHARMM: a program for macromolecular energy, minimization and dynamics calculations, J. Comput. Chem. 4, 187-217.
17. Brunger, A. T., and Karplus, M. (1988) Polar hydrogen positions in proteins: empirical energy placement and neutron-diffraction comparison, Proteins 4, 148-156.
18. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Zakrzewski, V. G., Montgomery, J. A., Jr., Stratmann, R. E., Burant, J. C., Dapprich, S., Millam, J. M., Daniels, A. D., Kudin, K. N., Strain, M. C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G. A., Ayala, P. Y., Cui, Q., Morokuma, K., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Cioslowski, J., Ortiz, J. V., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Gonzalez, C., Challacombe, M., Gill, P. M. W., Johnson, B. G., Chen, W., Wong, M. W., Andres, J. L., Head-Gordon, M., Replogle, E. S., Pople, J. A. (1998) Gaussian 98, Gaussian, Inc., Pittsburgh, PA.
19. SYBYL. 7.0, Tripos Inc., St. Louis, Missouri, 63144.
20. Brooks, C. L., III, Karplus, M. (1989) Solvent effects on protein motion and protein effects on solvent motion, J. Mol. Biol. 208, 159-181.
21. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of N-alkanes, J. Comput. Phys. 23, 327-341.
22. Nina, M., and Roux, B. (1997) Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations, J. Phys. Chem. B101, 5239-5248.
23. Banavali, N. K., and Roux, B. (2002) Atomic radii for continuum electrostatics calculations on nucleic acids, J. Phys. Chem. B106, 11026-11035.
24. Hubbard, S. J., and Thornton, J. M. (1993), NACCESS: computer program, Department of Biochemistry and Molecular Biology, University College London, U.K.
25. Lee, B., and Richards, F. M. (1971) The interpretation of protein structures: estimation of static accessibility, J. Mol. Biol. 55, 379-380.
26. Wessel, P., and Smith, W. H. F. (1998) New, improved version of the generic mapping tools released, EOS Trans. AGU 79, 579-580.
27. Laaksonen, L. (1992) A graphics program for the analysis and display of molecular dynamics trajectories, J. Mol. Graph. 10, 33-34.
28. Bergman, D. L., Laaksonen, L., and Laaksonen, A. (1997) Visualization of solvation structures in liquid mixtures, J. Mol. Graphics Modell. 15, 301-306.
29. Tirion, M. M. (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis, Phys. Rev. Lett. 77, 1905-1908.
30. Tama, F., and Sanejouand, Y. H. (2001) Conformational change of proteins arising from normal mode calculations, Protein Eng. 14, 1-6.
31. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD - visual molecular dynamics, J. Mol. Graphics 14, 33-38.
32. Saenger, W. (1984) in Principles of Nucleic Acid Structure, pp 51-78, Springer-Verlag, New York.
33. 3H]thymidine kinetic isotope effect in human thymidine phosphorylase, J. Am. Chem. Soc. 126, 6882-6883.
34. Roday, S., Amukele, T., Evans, G. B., Tyler, P. C., Furneaux, R. H., and Schramm, V. L. (2004) Inhibition of ricin A-chain with pyrrolidine mimics of the oxacarbenium ion transition state, Biochemistry 43, 4923-4933.
35. a′ of participating groups in enzymic reactions, J. Am. Chem. Soc. 81, 4552-4556.
36. 5-steroid isomerase, Biochemistry 37, 10499-10506.
37. Andersen, J. F., Sanders, D. A. R., Gasdaska, J. R., Weichsel, A., Powis, G., and Montfort, W. R. (1997) Human thioredoxin homodimers: regulation by pH, role of aspartate 60, and crystal structure of the aspartate 60 → asparagine mutant, Biochemistry 35, 13979-13988.