Dynamics of fusarium solani cutinase investigated through structural comparison among different crystal forms of its variants

Proteins: Structure, Function and Genetics

Volumn 26, Issue 4, 1996, Pages 442-458

  Longhi, Sonia ^a   Nicolas, Anne ^a   Creveld, Lucia ^b   Egmond, Maarten ^b   Verrips, C Theo ^b   De Vlieg, Jakob ^b   Martinez, Chrislaine ^a   Cambillau, Christian ^a  

^a Centre National de la Recherche Scientifique   (France)

^b UNILEVER RESEARCH VLAARDINGEN   (Netherlands)

Author keywords

comparative structural analysis; cutinase; molecular dynamics simulation; mutant structures; X ray crystallography

Indexed keywords

ARTICLE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; FUSARIUM SOLANI; GENETIC POLYMORPHISM; LIPOLYSIS; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

CARBOXYLIC ESTER HYDROLASES; CRYSTALLOGRAPHY, X-RAY; FUSARIUM; MUTAGENESIS; PROTEIN CONFORMATION;

EID: 0030470263     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199612)26:4<442::AID-PROT5>3.0.CO;2-D     Document Type: Article

References (62)

1. Smith, J.L., Hendrickson, W.A., Honzatko, R.B., Sheriff, S. Structural heterogeneity in protein crystals. Biochemistry 25:5018-5027, 1986.
2. Clore, G.M., Gronenborn, A.M., Kjaer, M., Poulsen, F.M. The determination of the three-dimensional structure of barley serine proteinase inhibitor 2 by nuclear magnetic resonance, distance geometry and restrained molecular dynamics. Protein Eng. 1:305-311, 1987.
3. Housset, D., Kim, K., Fuchs, J., Woodward, C., Wlodawer, A. Crystal structure of a Y35G mutant of bovine pancreatic trypsin inhibitor. J. Mol. Biol. 220:757-770, 1991.
4. Hua, Q., Weiss, M.A. Toward the solution structure of human insulin: Sequential 2D 1H NMR assignment of a despentapeptide analogue and comparison with crystal structure. Biochemistry 29:10545-10555, 1990.
5. Kline, A.D., Braun, W., Wuthrich, K. Determination of the complete three-dimensional structure of the α-amylase inhibitor tendamistat in acqueous solution by nuclear magnetic resonance and distance geometry. J. Mol. Biol. 204: 675-685, 1988.
6. Pflugrath, J.W., Wiegand, G., Huber, R., Vertesy, L. Crystal structure determination, refinement and the molecular model of the α-amylase inhibitor Hoe-467A. J. Mol. Biol. 189:383-386, 1986.
7. Urbanova, M., Dukor, R.K., Pancoska, P., Gupta, V.P., Keiderling, T.A. Comparison of α-lactalbumin and lysozyme using vibrational circular dichroism: Evidence for a difference in crystal and solution structures. Biochemistry 30:10479-10485, 1991.
8. Weiss, M.A., Nguyen, D.T., Khait, I., Inouye, K., Frank, B.H., Beckage, M., O'Shea, E., Shoelson, S.E., Karplus, M., Neuringer, L.J. Two-dimensional NMR and photo-CIDNP studied of the insulin monomer: Assignment of aromatic resonances with application to protein folding, structure and dynamics. Biochemistry 28:9855-9873, 1989.
9. Wittekind, M., Rajagopal, P., Branchini, B.R., Reizer, J., Saier, M.H.Jr., Klevit, R.E. Solution structure of the phosphocarrier protein HPr from Bacillus subtilis by two-dimensional NMR spectroscopy. Protein Sci. 1:1363-1376, 1992.
10. Artymiuk, P.J., Blake, C.C.F., Grace, D.E.P., Oatley, S.J., Phillips, D.C., Sternberg, M.J.E. Crystallographic studies of the dynamic properties of lysozyme. Nature 280:563-568, 1979.
11. Phillips, G.N. Jr. Comparison of the dynamics of myoglobin in different crystal forms. Biophys. J. 57:381-383, 1990.
12. Taubes, G. X-ray movies start to capture enzyme molecules in action. Science 266:364-365, 1994.
13. Vonrhein, C., Schlauderer, G.J., Schulz, G.E. Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure 3:483-490, 1995.
14. Bennett, W.S.Jr., Steitz, T.A. Structure of a complex between yeast hexokinase A and glucose: Detailed comparisons of conformation and active site conformation with the native hexokinase B monomer and dimer. J. Mol. Biol. 140:211-230, 1980.
15. Dixon, M.M., Nicholson, H., Shewchuk, L., Baase, W.A., Matthews, B.W. Structure of a hinge-bending bacteriophage T4 lysozyme mutant, Ile -> Pro. J. Mol. Biol. 227: 917-933, 1992.
16. Zhang, X., Wozniak, J.A., Matthews, B.W. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J. Mol. Biol. 250:527-552, 1995.
17. Anderson, B.F., Baker, H.M., Norris, G.E., Rumball, S.V., Baker, E.N. Apolactoferrin structure demonstrates ligandinduced conformational change in transferring. Nature 344:784-787, 1990.
18. Brzozowski, A.M., Derewenda, U., Derewenda, Z.S., Dodson, G., Lawson, D., Turkenburg, J.P. A model for interfacial activation in lipases from the structure of a fungal lipase-inhibitor complex. Nature 351:491-494, 1991.
19. Derewenda, U., Brzozowski, A.M., Lawson, D., Derewenda, Z.S. Catalysis at the interface: The anatomy of a conformational change in a triglyceride lipase. Biochemistry 31:1532-1541, 1992.
20. van Tilbeurg, H., Egloff, M.P., Martinez, C., Rugani, N., Verger, R., Cambillau, C. Interfacial activation of the lipase-procolipase complex by mixed micelles revealed by x-ray crystallography. Nature 362:814-820, 1993.
21. Egloff, M.P., Marguet, F., Buono, G., Verger, R., Cambillau, C., van Tilbeurg, H. The 2.46 Å resolution structure of the pancreatic lipase-procolipase complex inhibited by a C11 alkyl phosphonate. Biochemistry 34:2751-2762, 1995.
22. Grochulski, P., Bouthillier, F., Kazlauskas, R.J., Serreqi, A.N., Schrag, J.D., Ziomek, E., Cygler, M. Analogs of reaction intermediates identify a unique substrate binding site in Candida rugosa lipase. Biochemistry 33:3494-3500, 1994.
23. Karplus, M., Petsko, G.A. Molecular dynamics simulation in biology. Nature 347:631-639, 1990.
24. Braatz, J.A., Paulsen, M.D., Ornstein, R.L. 3 nsec molecular dynamics simulation of the protein ubiquitin and comparison with x-ray crystal and solution NMR structures. J. Biomol. Struct. Dyn. 9:935-949, 1992.
25. Chandrasekhar, I., Clore, J.M., Szabo, A., Gronenborn, A.M., Brooks, B.R. A 500 ps molecular dynamics simulation study of interleukin-1b in water. J. Mol. Biol. 226: 239-250, 1992.
26. Brunne, R.M., Liepinsh, E., Otting, G., Wuthrich, K., van Gunsteren, W.F. Hydratation of proteins: A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J. Mol. Biol. 231:1040-1048, 1993.
27. Storch, E.M., Daggett, V. Molecular dynamics simulation of cytochrome β5: Implications for protein-protein recognition. Biochemistry 34:9682-9693, 1995.
28. Kolattukudy, P.E. (1984) Cutinase from fungi and pollen. In "Lipases". Borgstrom, B., Brockman, H. (eds.). Elsevier, Amsterdam, The Netherlands. 1984:471-504.
29. Lauwreys, M., De Geus, P., De Meuter, J., Stanssens, P., Matthyssens, G. Cloning, expression and characterization of cutinase, a fungal lipolytic enzyme. Lipases Struct. Mech. Genet. Eng. 16:243-251, 1991.
30. Martinez, C., De Geus, P., Lauwereys, M., Matthyssens, G., Cambillau, C. Fusarium solani cutinase is a lipolytic enzyme with a catalytic serine accessible to the solvent. Nature 356:615-618, 1992.
31. Martinez, C., De Geus, P., Stanssens, P., Lauwereys, M., Cambillau, C. Engineering cysteine mutants to obtain crystallographic phases with a cutinase from Fusarium solani pisi. Protein Eng. 6:157-165, 1993.
32. Ollis, D.L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S.M., Harel, M., Remington, S.J., Silman., I., Shrag, J., Sussman, J.L., Verschueren, K.H.G., Goldman. A. The α/β hydrolase fold. Protein Eng. 5:197-211, 1992.
33. Martinez, C., Nicolas, A., van Tilbeurgh, H., Egloff, M.P., Cudrey, C., Verger, R., Cambillau, C. Cutinase, a lipolytic enzyme with a preformed oxyanion hole. Biochemistry 33: 83-89, 1994.
34. Nicolas, A., Egmond, M., Verrips, C.T., de Vlieg, J., Longhi, S., Cambillau, C., Martinez, C. Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state. Biochemistry 35:398-410, 1996.
35. van Gemeren, I.A., Musters, W., van den Hondel, C.A., Verrips, C.T. Construction and heterologous expression of a synthetic copy of the cutinase cDNA from Fusarium solani pisi. J. Biotechnol. 40:155-162, 1995.
36. Dulau, L., Cheyrou, A., Aigle, M. Direct mutagenesis using PCR. Nucl. Acid Res. 17:2873, 1989.
37. Ho, S.N., Hunt, H.D., Horton, R.M., Pullen, J.K., Pease, L.R. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51-59, 1989.
38. Kadowaki, H., Kadowaki, T, Wondisford, F.E., Taylor, S.I. Use of polymerase chain reaction catalyzed by Taq DNA polymerase for site-specific mutagenesis. Gene 76:161-166, 1989.
39. Sambrook, J., Fritsch, E.F., Maniatis, T. (eds.). "Molecular Cloning: A Laboratory Manual." Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1989.
40. Smith, L.M., Fung, S., Hunkapiller, M.W., Hunkapiller, T.J., Hood, L.E. The synthesis of oligonucleotides containing an aliphatic amino group at the 5′ terminus: Synthesis of fluorescent DNA primers for use in DNA sequence analysis. Nucleic Acid Res. 13:2399-2412, 1985.
41. Smith, L.M., Sanders, J.Z., Kaiser, R.J., Hughes, P., Dodd, C., Connell, C.R., Heiner, C., Kent, S.B., Hood, L.E. Fluorescence detection in automated DNA sequence analysis. Nature 321:674-679, 1986.
42. Sanger, F., Nicklen, S., Coulson, A.R. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. 74:5463-5467, 1977.
43. Orr-Weaver, T.L., Szostak, J.M. Multiple, tandem plasmid integration in Saccharomyces cerevisiae. Mol. Cell Biol. 3:747-749, 1983.
44. Lopes, T.S., Klootwijk, J., Veenstra, A.E., van der Aar, P.C., van Heerikhuizen, H., Raue, H.A., Planta, R.J. Highcopy-number integration into the ribosomal DNA of Saccharomyces cerevisiae: A new vector for high-level expression. Gene 79:199-206, 1989.
45. Manivasakam, P., Schiestl, R.H. High efficiency transformation of Saccharomyces cerevisiae by electroporation. Nucleic Acid Res. 21:4414-4415, 1993.
46. Abergel, C., Martinez, C., Fontecilla-Camps, J., Cambillau, C., De Geus, P., Lauwereys, M. Crystallization and preliminary x-ray study of a recombinant cutinase from Fusarium solani pisi. J. Mol. Biol. 215:215-216, 1990.
47. Kabsch, W. Automatic indexing of rotation diffraction patterns. J. Appl. Crystallogr. 21:67-71, 1988.
48. Kabsch, W. Evaluation of single crystal x-ray diffraction from a position-sensitive detector. J. Appl. Crystallogr. 21: 916-924, 1988.
49. Leslie, A.G.W. In "Joint CCP4 and ESF-EACMB Newsletter on Protein Crystallography". No. 26. Warrington, UK: Daresbury Laboratory, 1992.
50. Howard, A.J. , Gilliland, G.L., Finzel, B.C., Poulos, T.L., Olhendorf, D.H., Salemme, F.R. The use of an imaging proportional counter in macromolecular crystallography. J. Appl. Crystallogr. 20:383-387, 1987.
51. Navaza, J. AMoRe: An automated package for molecular replacement. Acta Crystallogr. A 50:157-163, 1994.
52. Brünger, A.T. X-PLOR version 3.1 Manual. New Haven, CT: Yale University, 1993.
53. Roussel, A., Cambillau, C. In: "Silicon Graphics Geometry Partners Directory". Mountain View, CA: Silicon Graphics, 1991:86.
54. van Gunsteren, W.F., Berendsen, H.J.C. Groningen Molecular Simulation (GROMOS) Library Manual, Biomos, Groningen, The Netherlands, 1987
55. van Buuren, A.R., Marrink, S.J., Berendsen, H.J.C. A molecular dynamics study of the decane/water interface. J. Phys. Chem. 97:9206-9212, 1993.
56. Mark, A.E., van Helden, S.P., Smith, P.E., Janssen, L.H.M., van Gunsteren, W.F. Convergence properties of free energy calculations: α-Cyclodextrin complexes as a case study. J. Am. Chem. Soc. 116:6293-6302, 1994.
57. Smith, L.J., Mark, A.E., Dobson, C.M., van Gunsteren, W.F. Comparison of MD simulations and NMR experiments for hen lysozyme: Analysis of local fluctuations, cooperative motions and global changes. Biochemistry 34: 10918-10931, 1995.
58. Berendsen, H.J.C., Grigera, J.R., Straatsma, T.P. The missing term in effective pair potentials. J. Phys. Chem. 91:6269-6271, 1987.
59. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A., Haak, J.R. Molecular dynamics with coupling to an external bath. J. Phys. Chem. 81:3684-3690, 1984.
60. van Gunsteren, W.F., Berendsen, H.J.C. Computer simulation of molecular dynamics: Methodology, applications and perspectives. Angew. Chem. Int. Ed. Engl. 29:992-1023, 1990.
61. Hüenenberger, P.H., Mark. A.E., van Gunsteren, W.F. Fluctuation and cross-correlation analysis of protein motions observed in nanoseconds molecular simulations. J. Mol. Biol. 252:492-503, 1995.
62. Uppenberg, J., Hansen, M.T., Patkar, S., Jones, T.A. The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica. Structure 2:293-308, 1994.