Quantification of the Influence of Single-Point Mutations on Haloalkane Dehalogenase Activity: A Molecular Quantum Similarity Study

Journal of Chemical Information and Computer Sciences

Volumn 40, Issue 3, 2000, Pages 839-846

  Robert, David ^a   Gironés, Xavier ^a   Carbó Dorca, Ramon ^a  

^a UNIVERSITY OF GIRONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

HALOALKANE DEHALOGENASE; HYDROLASE;

ARTICLE; CHEMISTRY; GENETICS; METABOLISM; POINT MUTATION; QUANTUM THEORY; STRUCTURE ACTIVITY RELATION;

HYDROLASES; POINT MUTATION; QUANTUM THEORY; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0034181927     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci9903408     Document Type: Article

References (65)

1. Oxender, D. L.; Fox, C. F., Eds. Protein Engineering., Alan R. Liss: New York, 1987; pp 221-224.
2. Leatherbarrow, R. J.; Fersht, A. J. Protein Engineering. Protein Eng. 1986, 1, 7-16.
3. Hellberg, S.; Sjostrom, M.; Skagerberg, B.; Wold, S. Peptide quantitative structure-activity relationships, a multivariate approach. J. Med. Chem. 1987, 30, 1126-1135.
4. Kato, A.; Yutani, K. Correlation of surface properties with conformational stabilities of wild-type and six mutant tryptophan synthase alpha-subunits substituted at the same position. Protein Eng. 1988, 2, 153-156.
5. Lee, C.; Levitt, M. Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core. Nature 1991, 352, 448-451.
6. Collantes, E. R.; Dunn, W. J., III. Amino acid side-chain descriptors for quantitative structure-activity relationship studies of peptide analogues. J. Med. Chem. 1995, 38, 2705-2713.
7. Zbilut, J. P.; Giuliani, A.; Webber, C. L., Jr.; Colosimo, A. Recurrence quantification analysis in structure-function relationships of proteins: An overview of a general methodology applied to the case of TEM-1 beta-lactamase. Protein Eng. 1998, 11, 87-93.
8. Rozeboom, H. J.; Kingma, J.; Janssen, D. B.; Dijkstra, B. W. Crystallisation of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. J. Mol. Biol. 1988, 200, 611-612.
9. Franken, S. M.; Rozeboom, H. J., Kalk, K. H.; Dijkstra, B. W. Crystal structure of haloalkane dehalogenase: An enzyme to detoxify halogenated alkanes. EMBO J. 1991, 10, 1297-1302.
10. Verschueren, K. H. G.; Franken, S. M.; Rozeboom, H. J.; Kalk, K. H.; Dijkstra, B. W. Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction mechanism. J. Mol Biol. 1993, 232, 856-872.
11. Verschueren, K. H. G.; Seljee, F.; Rozeboom, H. J.; Kalk, K. H.; Dijkstra, B. W. Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase. Nature 1993, 363, 693-698.
12. Ridder, I. S.; Rozeboom, H. J.; Dijkstra, B. W. Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15A. Acta Crystallogr. 1999, D55, 1273-1290.
13. Hutchison, C. A., III; Phillips, S.; Edgell, M. H.; Gillam, S.; Jahnke, P.; Smith, M. Mutagenesis at a specific position in a DNA sequence. J. Biol. Chem. 1978, 253, 6551-6560.
14. Pries, F.; Kingma, J.; Pentega, M.; Van Pouderoyen, G.; Jeronimus-Stratingh, C. M.; Bruins, A. P.; Janssen, D. B. Site-directed mutagenesis and oxygen isotope incorporation studies of the nucleophilic aspartate of haloalkane dehalogenase. Biochemistry 1994, 33, 1242-1247.
15. Pries, F., Kingma, J.; Janssen, D. B. Activation of an Asp-124-Asn mutant of haloalkane dehalogenase by hydrolytic deamidation of asparagine. FEBS Lett. 1995, 358, 171-174.
16. Pries, F.; Kingma, J.; Krooshof, G. H.; Jeronimus-Stratingh, C. M.; Bruins, A. P.; Janssen. D. B. Histidine 289 is essential for hydrolysis of the alkyl-enzyme intermediate of haloalkane dehalogenase. J. Biol. Chem. 1995, 270, 10405-10411.
17. Schanstra, J. P.; Janssen, D. B. Kinetics of halide release of haloalkane dehalogenase: Evidence for a slow conformational change. Biochemistry 1996, 35, 5624-5632.
18. Schanstra, J. P.; Ridder, I. S.; Heimericks, G. J.; Rink, R.; Poelarends, G. J.; Kalk, K. H.; Dijkstra, B. W.; Janssen, D. B. Kinetic characterization and X-ray structure of a mutant of haloalkane dehalogenase with higher catalytic activity and modified substrate range. Biochemistry 1996, 35, 13186-13195.
19. Schanstra, J. P.; Ridder, A.; Kingma, J.; Janssen, D. B. Influence of mutation of Val226 on the catalytic rate of haloalkane dehalogenase. Protein Eng. 1997, 10, 53-61.
20. Carhó, R.; Arnau, J.; Leyda, L. How similar is a molecule to another? An electron density measure of similarity between two molecular structures. Int. J. Quantum Chem. 1985, 17, 1185-1189.
21. Carbó-Dorca, R.; Besalú, E. A general survey of molecular quantum similarity. THEOCHEM 1998, 451, 11-23.
22. Carbó-Dorca, R.; Amat, L.; Besalti, E.; Lobato, M. Quantum Similarity. In Advances in Molecular Similarity, Carbô-Dorca, R.; Mezey, P. G., Eds.; JAI Press: Greenwich, CT, 1998; Vol. 2, pp 1-42.
23. Carbó-Dorca, R. Fuzzy sets and boolean tagged sets; vector semispaces and convex sets; quantum similarity measures and ASA density functions; diagonal vector spaces and quantum chemistry. In Advances in Molecular Similarity, Carbó-Dorca, R., Mezey, P. G., Eds.; JAI Press: Greenwich, CT, 1998: Vol. 2, pp 43-72.
24. Besalú, E.; Carbó, R.; Mestres, J.; Solà, M. Foundations and Recent Developments on Molecular Quantum Similarity. Top. Curr. Chem. 1995, 173, 31-62.
25. Carbó, R.; Besalú, E. Theoretical Foundations of Quantum Molecular Similarity. In Molecular Similarity and Reactivity: From Quantum Chemical to Phenomenological Approaches; Carbó, R., Ed.; Kluwer Amsterdam, 1995: pp 3-30.
26. Carbó-Dorca, R.; Besalú, E.; Amat, L.; Fradera, X. Quantum Molecular Similarity Measures: Concepts, Definitions, and Applications to Quantitative Structure - Property Relationships. In Advances in Molecular Similarity, Carbó-Dorca, R., Mezey, P. G., Eds.; JAI Press: Greenwich, CT, 1996; Vol. 1, pp 1-42.
27. Carbó, R.; Besalú, E.; Amat. L.; Fradera, X. Quantum molecular similarity measures (QMSM) as a natural way leading towards a theoretical foundation of quantitative structure-properties relationships. J. Math. Chem. 1995, 18, 237-246.
28. Fradera, X.; Amat, L.; Besalú, E.; Carbó-Dorca, R. Application of Molecular Quantum Similarity to QSAR. Quant. Struct.-Act. Relat. 1997, 16, 25-32.
29. Lobato, M.; Amat, L.; Carbó-Dorca, R. Structure-Activity Relationships of a Steroid Family using Quantum Similarity Measures and Topolocical Quantum Similarity Indices. Quant. Struct.-Act. Relat. 1997. 16, 465-472.
30. Amat, L.; Robert, D.; Besalú, E.; Carbó-Dorca, R. Molecular Quantum Similarity Measures Tuned 3D QSAR: An Antitumoral Family Validation Study. J. Chem. Inf. Comput. Sci. 1998, 38, 624-631.
31. Robert, D.; Amat, L.; Carbó-Dorca, R. Three-Dimensional Quantitative Structure-Activity Relationships from Tuned Molecular Quantum Similarity Measures. Prediction of the Corticosteroid-Binding Globulin Binding Affinity for a Steroid Family. J. Chem. Inf. Comput. Sci. 1999, 39, 333-344.
32. Robert, D.; Gironés, X.; Carbó-Dorca, R. Facet Diagrams for Quantum Similarity Data. J. Comput.-Aided Mol. Des. 1999, 13, 597-610.
33. Robert, D.; Carbó-Dorca, R. Aromatic Compounds Aquatic Toxicity QSAR using Quantum Similarity Measures. SAR QSAR Environ. Res. 1999, 10, 401-422.
34. Gironés, X.; Amat, L.; Carbó-Dorca, R. Molecular Quantum Similarity Measures Used to Characterize Molecular Toxicology. Institute of Computational Chemistry, Technical Report IT-IQC-98-29. Also: SAR QSAR Environ. Res., in press.
35. Gironés, X.; Amat, L.; Carbó-Dorca, R. Molecular Quantum Similarity Measures Used to Characterize Molecular Toxicology. Institute of Computational Chemistry, Technical Report IT-IQC-98-29. Also: SAR QSAR Environ. Res., in press.
36. Constans, P.; Carbó, R. Atomic Shell Approximation: Electron Density Fitting Algorithm Restricting Coefficients to Positive Values. J. Chem. Inf. Comput. Sci. 1995, 35, 1046-1053.
37. Amat, L.; Carbó-Dorca, R. Quantum Similarity Measures under Atomic Shell Approximation: First-Order Density Fitting using Elementary Jacobi Rotations. J. Comput. Chem. 1997, 18, 2023-2039.
38. Amat, L.; Carbó-Dorca, R. Fitted Electronic Density Functions from H to Rn for Use in Quantum Similarity Measures: cis-Diammine- Dichloroplatinum (II) Complex as an Application Example. J. Comput. Chem. 1999, 20, 911-920.
39. Cox, T. F.; Cox, M. A. A. Multidimensional Scaling; Chapman & Hall: London, 1994.
40. Cuadras, C. M.; Arenas, C. A distance based regression model for prediction with mixed data. Commun. Stat. Theor. Method. 1990, 19, 2261-2279.
41. Allen, D. M. The relationship between variable selection and data augmentation and a method for prediction. Technometrics 1974, 16, 125-127.
42. Wold, S.; Eriksson, L. Statistical validation of QSAR results. In Chemometric Methods in Molecular Design; Van der Waterbeemd, H., Ed.; VCH: New York. 1995; pp 309-318.
43. Kunkel, T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 488-492.
44. Keuning, S.; Janssen, D. B.; Witholt, B. Purification and characterization of hydrolytic haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. J. Bacteriol. 1985, 163, 635-639.
45. Allen, F. H.; Bellard, S.; Brice, M. D.; Cartwright, B. A.; Doubleday: A.; Higgs, H.; Hummelink, T.; Hummelink-Peters, B. G.; Kennard, O.; Motherwell, W. D. S.; Rodgers, J. R.; Watson, D. G. The Cambridge Crystal Data Centre: Computer-Based Search, Retrieval, Analysis and Display of Information. Acta Crystallogr. 1979, B35, 2331-2339.
46. Allinger, N. L. Conformational Analysis 130. MM2. A Hydrocarbon Force Field Utilizing V1 and V2 Torsional Terms. J. Am. Chem. Soc. 1977, 99, 8127-8134.
47. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta S., Jr.; Weiner, P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 1984, 106, 765-784.
48. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 1986, 7, 230-252.
49. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. AMI: A New General Purpose Quantum Chemical Molecular Model. J. Am. Chem. Soc. 1985, 107, 3902-3909.
50. Stewart, J. J. P. Optimization of parameters for semiempirical methods. I. Method. J. Comput. Chem. 1989, 10, 209-220.
51. Stewart, J. J. P. Optimization of parameters for semiempirical methods. II. Applications. J. Comput. Chem. 1989, 10, 221-264.
52. Hyperchem, Release 3 for Windows. Molecular Modeling System; Hypercube, Inc. and Autodesk, Inc: Sausalito, CA, 1993.
53. AMPAC 6.01, Semichem: Shawnee, KS, 1994.
54. Coitiño, E. L.; Irving, K.; Rama, J.; Ventura, O. N. Theoretical Studies of Hydrogen-Bonded Complexes Using Semiempirical Methods. J. Mol. Struct. (THEOCHEM) 1990, 69, 405.
55. Lii, J.-H.; Gallion, S.; Bender, C.; Wikström, H.; Allinger, N. L.; Flurchick, K. M.; Teeter, M. M. Molecular Mechanics (MM2) Calculations on Peptides and on the Protein Crambin Using the Cyber 205. J. Comput. Chem. 1989, 10, 503-513.
56. Damborský, J.; Boháć, M.; Prokop, M.; Kutý, M.; Koča, J. Computational site-directed mutagenesis of haloalkane dehalogenase in position 172. Protein Eng. 1998, 11, 901-907.
57. Damborský, J. Quantitative structure-function and structure-stability relationships of purposely modified proteins. Protein Eng. 1998, 11, 21-30.
58. Hansch, C.; Leo, A.; Hoekman, D. Exploring QSAR: Hydrophobic, Electronic, and Steric Constants; American Chemical Society: Washington, D.C., 1995.
59. Damborský, J. Quantitative structure-function relationships of the single-point mutants of haloalkane dehalogenase: A multivariate approach. Quant. Struct.-Act. Relat. 1997, 16, 126-135.
60. Nakai, K.; Kidera A.; Kanehisa, M. Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 1988, 2, 93-100.
61. Tomii, K.; Kanehisa, M. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 1996, 9, 27-36.
62. Kawashima, S.; Ogata, H.; Kanehisa, M. AAindex: Amino acid index database. Nucleic Acids Res. 1999, 27, 368-369.
63. Jones, D. D. Amino acid properties and side-chain orientation in proteins: A cross correlation approach. J. Theor. Biol. 1975, 50, 167-183.
64. Weber, A. L.; Lacey, J. C. Genetic code correlations: Amino acids and their anticodon nucleotides. J. Mol. Evol. 1978, 11, 199-210.
65. Zimmerman, J. M.; Eliezer, N.; Simha, R. The characterization of amino acid sequences in proteins by statistical methods. J. Theor. Biol. 1968, 21, 170-201.