Understanding the binding of procyanidins to pancreatic elastase by experimental and computational methods

Biochemistry

Volumn 49, Issue 25, 2010, Pages 5097-5108

  Brás, Natércia F ^a   Gonçalves, Rui ^a   Fernandes, Pedro A ^a   Mateus, Nuno ^a   Ramos, Maria João ^a   De Freitas, Victor ^a  

^a UNIVERSITY OF PORTO   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

AGGREGATE FORMATION; BIMOLECULAR QUENCHING CONSTANT; BINDING ABILITIES; BINDING MODES; BLUE SHIFT; CIRCULAR DICHROISM; CRUCIAL FUNCTIONS; DYNAMICS SIMULATION; ELASTASE; EMISSION WAVELENGTH; FLUORESCENCE INTENSITIES; FLUORESCENCE QUENCHING; FOOD INDUSTRIES; GRAPE SEEDS; HELIX CONTENT; HUMAN DIET; HYDROPHOBIC CHARACTER; MOLECULAR DOCKING; MOLECULAR DYNAMICS SIMULATIONS; NEPHELOMETRY; POLYPHENOLIC COMPOUND; POLYPHENOLS; PROCYANIDINS; SECONDARY METABOLITES; SECONDARY STRUCTURES; SHEET COMPONENTS; SOLVENT-ACCESSIBLE SURFACE AREA; TETRAMERS; TRYPTOPHAN RESIDUES; WATER MOLECULE;

AMINO ACIDS; BINDING ENERGY; COMPUTATIONAL METHODS; DOCKING; DYNAMIC LIGHT SCATTERING; ENZYMES; FLUORESCENCE; METABOLITES; MOLECULAR DYNAMICS; MOLECULAR MODELING; MOLECULES; NEPHELOMETERS; PHENOLS; QUENCHING;

DICHROISM;

GRAPE SEED EXTRACT; PANCREATIC ELASTASE; POLYPHENOL; PROCYANIDIN DERIVATIVE; TRYPTOPHAN;

ALPHA HELIX; ARTICLE; CIRCULAR DICHROISM; ENZYME BINDING; FLUORESCENCE; HYDROPHOBICITY; LIGHT SCATTERING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NEPHELOMETRY; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; SIMULATION;

CIRCULAR DICHROISM; PANCREATIC ELASTASE; PROANTHOCYANIDINS; PROTEIN BINDING; SPECTROMETRY, FLUORESCENCE;

SUS; VITACEAE;

EID: 77953906402     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi100410q     Document Type: Article

References (44)

1. Daniel, K. G., Landis-Piwowar, K. R., Chen, D., Wan, S. B., Chan, T. H., and Dou, Q. P. (2006) Methylation of green tea polyphenols affects their binding to and inhibitory poses of the proteasome beta 5 subunit Int. J. Mol. Med. 18 (4) 625-632
2. Pezzato, E., Sartor, L., Dell Aica, I., Dittadi, R., Gion, M., Belluco, C., Lise, M., and Garbisa, S. (2004) Prostate carcinoma and green tea: PSA-triggered basement membrane degradation and MMP-2 activation are inhibited by (-)epigallocatechin-3-gallate Int. J. Cancer 112 (5) 787-792
3. Xue, Z. P., Feng, W. H., Cao, J. K., Cao, D. D., and Jiang, W. B. (2009) Antioxidant activity and total phenolic contents in peel and pulp of Chinese jujube (Ziziphus jujuba Mill) fruits J. Food Biochem. 33 (5) 613-629
4. Goncalves, R., Soares, S., Mateus, N., and De Freitas, V. (2007) Inhibition of trypsin by condensed tannins and wine J. Agric. Food Chem. 55 (18) 7596-7601
5. Soares, S., Mateus, N., and De Freitas, V. (2007) Interaction of different polyphenols with bovine serum albumin (BSA) and human salivary alpha-amylase (HSA) by fluorescence quenching J. Agric. Food Chem. 55 (16) 6726-6735
6. Mateus, N., Silva, A. M. S., Santos-Buelga, C., Rivas-Gonzalo, J. C., and de Freitas, V. (2002) Identification of anthocyanin-flavanol pigments in red wines by NMR and mass spectrometry J. Agric. Food Chem. 50 (7) 2110-2116
7. McDougall, G. J. and Stewart, D. (2005) The inhibitory effects of berry polyphenols on digestive enzymes Biofactors 23 (4) 189-195
8. de Freitas, V., Carvalho, E., and Mateus, N. (2003) Study of carbohydrate influence on protein-tannin aggregation by nephelometry Food Chem. 81 (4) 503-509
9. DellAica, I., Niero, R., Piazza, F., Cabrelle, A., Sartor, L., Colalto, C., Brunetta, E., Lorusso, G., Benelli, R., Albini, A., Calabrese, F., Agostini, C., and Garbisa, S. (2007) Hyperforin blocks neutrophil activation of matrix metalloproteinase-9, motility and recruitment, and restrains inflammation-triggered angiogenesis and lung fibrosis J. Pharmacol. Exp. Ther. 321 (2) 492-500
10. Baxter, N. J., Lilley, T. H., Haslam, E., and Williamson, M. P. (1997) Multiple interactions between polyphenols and a salivary proline-rich protein repeat result in complexation and precipitation Biochemistry 36 (18) 5566-5577
11. Frazier, R. A., Papadopoulou, A., Mueller-Harvey, I., Kissoon, D., and Green, R. J. (2003) Probing protein-tannin interactions by isothermal titration microcalorimetry J. Agric. Food Chem. 51 (18) 5189-5195
12. Horne, J., Hayes, J., and Lawless, H. T. (2002) Turbidity as a measure of salivary protein reactions with astringent substances Chem. Senses 27 (7) 653-659
13. Jobstl, E., OConnell, J., Fairclough, J. P. A., and Williamson, M. P. (2004) Molecular model for astringency produced by polyphenol/protein interactions Biomacromolecules 5 (3) 942-949
14. Maiti, T. K., Ghosh, K. S., and Dasgupta, S. (2006) Interaction of (-)-epigallocatechin-3-gallate with human serum albumin: Fluorescence, Fourier transform infrared, circular dichroism, and docking studies Proteins: Struct., Funct., Bioinf. 64 (2) 355-362
15. Pascal, C., Pate, F., Cheynier, V., and Delsuc, M. A. (2009) Study of the interactions between a proline-rich protein and a flavan-3-ol by NMR: residual structures in the natively unfolded protein provides anchorage points for the ligands Biopolymers 91 (9) 745-756
16. Pascal, C., Poncet-Legrand, C., Imberty, A., Gautier, C., Sarni-Manchado, P., Cheynier, V., and Vernhet, A. (2007) Interactions between a nonglycosylated human proline-rich protein and flavan-3-ols are affected by protein concentration and polyphenol/protein ratio J. Agric. Food Chem. 55 (12) 4895-4901
17. Rawel, H. A., Meidtner, K., and Kroll, J. (2005) Binding of selected phenolic compounds to proteins J. Agric. Food Chem. 53 (10) 4228-4235
18. Simon, C., Barathieu, K., Laguerre, M., Schmitter, J. M., Fouquet, E., Pianet, I., and Dufourc, E. J. (2003) Three-dimensional structure and dynamics of wine tannin-saliva protein complexes. A multitechnique approach Biochemistry 42 (35) 10385-10395
19. Nadarajah, D., Atkinson, M. A. L., Huebner, P., and Starcher, B. (2008) Enzyme kinetics and characterization of mouse pancreatic elastase Connect. Tissue Res. 49 (6) 409-415
20. Wurtele, M., Hahn, M., Hilpert, K., and Hohne, W. (2000) Atomic resolution structure of native porcine pancreatic elastase at 1.1 angstrom Acta Crystallogr., Sect. D: Biol. Crystallogr. 56, 520-523
21. DellAica, I., Caniato, R., Biggin, S., and Garbisa, S. (2005) Matrix proteases, green tea, and St. Johns wort: biomedical research catches up with folk medicine, in International Conference on Enzymes - Old Molecules with New Clinical Applications, Padova, Italy.
22. Sartor, L., Pezzato, E., DellAica, I., Caniato, R., Biggin, S., and Garbisa, S. (2002) Inhibition of matrix-proteases by polyphenols: chemical insights for anti-inflammatory and anti-invasion drug design Biochem. Pharmacol. 64 (2) 229-237
23. Teichmann, J., Lange, U., Hardt, P., Schnell-Kretschmer, H., Stracke, H., Bretzel, R. G., and Klor, H. U. (2001) Decreased pancreatic elastase I stool content: an independent risk factor of the osteoporosis in elderly women Bone 28 (5) S194-S194
24. Rathmann, W., Haastert, B., Icks, A., Giani, G., Hennings, S., Mitchell, J., Curran, S., and Wareham, N. J. (2001) Low faecal elastase 1 concentrations in type 2 diabetes mellitus Scand. J. Gastroenterol. 36 (10) 1056-1061
25. Geissman, T. A. and Yoshimura, N. N. (1966) Synthetic proanthocyanidin Tetrahedron Lett. 7 (24) 2669-2673
26. Delcour, J. A., Ferreira, D., and Roux, D. G. (1983) Synthesis of condensed tannins. Part 9. The condensation sequence of leucocyanidin with (+)-catechin and with the resultant procyanidins J. Chem. Soc., Perkin Trans. 1, 1711-1717
27. de Freitas, V., Glories, Y., Bourgeois, G., and Vitry, C. (1998) Characterisation of oligomeric and polymeric procyanidins from grape seeds by liquid secondary ion mass spectrometry Phytochemistry 49 (5) 1435-1441
28. González-Manzano, S., Mateus, N., de Freitas, V., and Santos-Buelga, C. (2008) Influence of the degree of polymerisation in the ability of catechins to act as anthocyanin copigments Eur. Food Res. Technol. 227 (1) 83-92
29. Gonçalves, R., Soares, S., Mateus, N., and de Freitas, V. (2007) Inhibition of trypsin by condensed tannins and wine J. Agric. Food Chem. 55 (18) 7596-7601
30. Whitmore, L. and Wallace, B. A. (2004) DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data Nucleic Acids Res. 32, W668-W673
31. Geller, M., Swanson, S. M., and Meyer, E. F. (1990) Dynamic properties of the 1st steps of the enzymatic reaction of porcine pancreatic elastase (PPE). 2. Molecular-dynamics simulation of a Michaelis complex - PPE and the hexapeptide Thr-Pro-Nval-Leu-Tyr-Thr J. Am. Chem. Soc. 112 (24) 8925-8931
32. Sreenivasan, U. and Axelsen, P. H. (1992) Buried water in homologous serine proteases Biochemistry 31 (51) 12785-12791
33. Wilmouth, R. C., Edman, K., Neutze, R., Wright, P. A., Clifton, I. J., Schneider, T. R., Schofield, C. J., and Hajdu, J. (2001) X-ray snapshots of serine protease catalysis reveal a tetrahedral intermediate Nat. Struct. Biol. 8 (8) 689-694
34. Jones, G., Willett, P., Glen, R. C., Leach, A. R., and Taylor, R. (1997) Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 267 (3) 727-748
35. Verdonk, M. L., Cole, J. C., Hartshorn, M. J., Murray, C. W., and Taylor, R. D. (2003) Improved protein-ligand docking using GOLD Proteins: Struct., Funct., Genet. 52 (4) 609-623
36. 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, D. A., Raghavachari, K., Foresman, J. B., Cioslowski, J., Ortiz, J. V., Baboul, A. G., 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., Chen, W., Wong, M. W., Andres, J. L., Gonzalez, C., Head-Gordon, M., Replogle, E. S., and Pople, J. A. (2003) Gaussian 03, Gaussian, Inc., Pittsburgh, PA.
37. Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - the Resp model J. Phys. Chem. 97 (40) 10269-10280
38. Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., L o, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., and Woods, R. J. (2005) The Amber biomolecular simulation programs J. Comput. Chem. 26 (16) 1668-1688
39. Izaguirre, J. A., Catarello, D. P., Wozniak, J. M., and Skeel, R. D. (2001) Langevin stabilization of molecular dynamics J. Chem. Phys. 114 (5) 2090-2098
40. Case, D. A., Darden, T. A., Cheatham, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Merz, H. M., Wang, B., Pearlman, D. A., Crowley, M., Brozell, S., Tsui, V., Gohlke, H., Mongan, J., Hornak, V., Cui, G., Beroza, P., Schafmeister, C., Caldwell, J. W., Ross, W. S., and Kollman, P. A. (2004) AMBER 8, University of California, San Francisco.
41. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A 2nd generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 117 (19) 5179-5197
42. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of Cartesian equations of motion of a system with constraints - molecular dynamics of N-alkanes J. Comput. Phys. 23 (3) 327-341
43. Prendergast, F. G., Lu, J., and Callahan, P. J. (1983) Oxygen quenching of sensitized terbium luminescence in complexes of terbium with small organic-ligands and proteins J. Biol. Chem. 258 (7) 4075-4078
44. Simon, L. M., Kotorman, M., Garab, G., and Laczko, I. (2001) Structure and activity of alpha-chymotrypsin and trypsin in aqueous organic media Biochem. Biophys. Res. Commun. 280 (5) 1367-1371