Molecular Dynamics as a pattern recognition tool: An automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Site

Biophysical Chemistry

Volumn 133, Issue 1-3, 2008, Pages 36-44

  Tatsis, Vasileios A ^a   Stavrakoudis, Athanassios ^a   Demetropoulos, Ioannis N ^b  

^a UNIVERSITY OF IOANNINA   (Greece)

^b UNIVERSITY OF WESTERN MACEDONIA   (Greece)

Author keywords

Computer aided molecular design; Cyclic branched peptides; Implicit solvation molecular dynamics; Pattern recognition; QSAR; Serine proteases

Indexed keywords

AMINO ACID; TRYPSIN;

ARTICLE; AUTOMATION; BINDING AFFINITY; CHIRALITY; COMPUTER AIDED DESIGN; ENZYME ACTIVE SITE; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; THREE DIMENSIONAL IMAGING;

AUTOMATION; BINDING SITES; PEPTIDES; STEREOISOMERISM; TRYPSIN;

EID: 38749138838     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2007.11.008     Document Type: Article

References (63)

1. Pauling L., Corey R.B., and Branson H.R. The structure of proteins: two hydrogen bonded helical conformations of the polypeptide chain. Proc. Natl. Acad. Sci. U. S. A. 37 (1951) 205-211
2. Eisenberg D. The discovery of the-helix and-sheet, the principal structural features of proteins. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 11207-11210
3. Quemeneur E., Moutiez M., Charbonnier J.B., and Menez A. Engineering cyclophilin into a proline-specific endopeptidase. Nature 391 (1998) 301-304
4. Iengar P., and Ramakrishnan C. Knowledge-based modeling of the serine protease triad into non-protease. Protein Eng. 8 (1999) 649-655
5. Imperiali B., and Ottesen J.J. Uniquely folded mini-protein motifs. J. Pept. Res. 54 (1999) 177-184
6. Drakopoulou E., Zinn-Justin S., Guenneugues M., Gilquin B., Menez A., and Vita C. Changing the structural content of a functional β-hairpin. J. Mol. Biol 271 (1996) 11979-11987
7. Zinn-Justin S., Guenneugues M., Drakopoulou E., Gilquin B., Vita C., and Menez A. Transfer of a beta-hairpin from the functional site of snake curaremimetic toxins to the alpha/beta scaffold of scorpion toxins: three-dimensional solution structure of the chimeric protein. Biochemistry 35 (1996) 8535-8543
8. Vita C., Vizzanova J., Drakopoulou E., Zinn-Austin S., Gilquin B., and Menez A. Novel miniproteins engineered by the transfer of active sites to small natural scaffolds. Biopolymers (Pept. Sci.) 47 (1998) 93-100
9. Martin L., Barthe P., Combes O., Roumestand C., and Vita C. Engineering novel bioactive mini-proteins on natural scaffolds. Tetrahedron 56 (2000) 9451-9460
10. Cruishshank P., and Sheehan J.C. Synthetic peptide models of enzyme active sites. II. L-Threonyl-L-alanyl-L-seryl-Lhistidyl-L-aspartic, acid an active esterase model. J. Am. Chem. Soc. 86 (1963) 2070-2071
11. Sheehan J.C., Bennett G.B., and Schneider J.A. Synthetic peptide models of enzyme active sites. III. Stereoselective esterase models. J. Am. Chem. Soc. 88 (1966) 3455-3456
12. Vandersteen A.M., and Janda K.D. A Re-examination of two linear pentapeptides claimed to be serine protease mimics. J. Am. Chem. Soc. 118 (1996) 8787-8790
13. Photaki L., and Sakarellou-Daitsiotou M. Synthesis and catalytic properties of peptides containing amino acids involved in the active centres of hydrolytic enzymes. J. Chem. Soc. Perkin Trans. I (1976) 589-591
14. Vorherr T., Altmann K.-H., and Mutter M. Single-center model for the active site of alpha-chymotrypsin. Helv. Chim. Acta 69 (1986) 410-414
15. Clough J.M., Jones R.V.H., McCann H., Moriss D.J., and Martin W. Synthesis and hydrolysis studies of a peptide containing the reactive triad of serine proteases with an associated linker to a dye on a solid phase support. Org. Biomol. Chem. 1 (2003) 1486-1497
16. Fitzsimons M.P., and Barton J.K. Design of a Synthetic Nuclease: DNA Hydrolysis by a Zinc-Binding Peptide Tethered to a Rhodium Intercalator. J. Am. Chem. Soc. 119 (1997) 3379-3380
17. Hahn K.W., Klis W.A., and Stewart J.M. Design and synthesis of a peptide having chymotrypsin-like esterase activity. Science 248 (1990) 1544-1547
18. Chao T.M., Perez J.J., and Loew G.H. Characterization of the bioactive form of linear peptide antagonists at the δ-opioid receptor. Biopolymers 38 (1996) 759-768
19. Attassi M.Z., and Manshouri T. Design of peptide enzymes (pepzymes): surface-simulation synthetic peptides that mimic the chymotrypsin and trypsin active sites exhibit the activity and specificity of the respective enzyme. Proc. Natl. Acad. Sci. U. S. A. 90 (1993) 8282-8286
20. Marrone T.J., and McCammon J.A. Pepzyme dynamics and conformation: A Molecular Dynamics Study in Water. J. Am. Chem. Soc. 116 (1994) 6987-6988
21. Corey D.R., and Phillips M.A. Cyclic peptides as proteases: a reevaluation. Proc. Natl. Acad. Sci. U. S. A. 91 (1994) 4106-4109
22. Walse B., Ullner M., Lindbladh C., Bulow L., Drakenberg T., and Taleman O. Structure of a cyclic peptide with a catalytic triad, determined by computer simulation and NMR spectroscopy. J. Comput.-Aided Mol. Des. 10 (1996) 11-22
23. 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly]. J. Comput.-Aided Mol. Des. 10 (1996) 213-232
24. Gea A., Farcy N., Rosel N.R., Martins J.C., Clercq P.J., and Madder A. Solid-Supported Synthesis of Highly Functionalized Tripodal Peptides with Flexible but Preorganized Geometry: towards Potential Serine Protease Mimics. Eur. J. Org. Chem. 18 (2006) 4135-4146
25. Mutter M., and Vuillemier S. A chemical approach to protein design: template-assisted synthetic proteins (TASP). Angew. Chem. 28 (1989) 535-676
26. Tuchschererer G., and Mutter M. Protein design as a challenge for peptide chemists. J. Pept. Sci. 1 (1995) 3-10
27. Bloomberg G.B., Askin D., Gargaro A.R., and Tanner M.J.A. Synthesis of a branched cyclic peptide using a strategy employing Fmoc chemistry and two additional orthogonal protecting groups. Tetrahedron Lett. 34 (1993) 4709-4712
28. Satow Y., Cohen G.H., Padlan E.A., and Davies D.R. Phosphocholine binding immunoglobulin Fab McPC603: an X-ray diffraction study at 2.7 Å. J. Mol. Biol. 190 (1986) 593-604
29. Jones R.C.F., Tankard M., and Higton A.M. Studies towards a hydrophobic serine protease model. Bioorganic Med. Chem. Letters 1 (1991) 353-356
30. Catry M.A., and Madder A. Synthesis of functionalised nucleosides for incorporation into nucleic acid-based serine protease mimics. Molecules 12 (2007) 114-129
31. Stavrakoudis A., Demetropoulos I.N., Sakarellos C., Sakarellos-Daitsiotis M., and Tsikaris V. Design, synthesis and catalytic activity of a serine protease synthetic model. Lett. Pept. Sci. 4 (1997) 481-487
32. Stavrakoudis A., Makropoulou S., Tsikaris V., Sakarellos Daiotsiotis M., Sakarellos C., and Demetropoulos I.N. Computational screening of branched cyclic peptide motifs as potential enzyme mimetics. J. Pept. Sci. 9 (2003) 145-155
33. Tatsis V.A., Stavrakoudis A., and Demetropoulos I.N. LysinebasedTrypsinActSite(LysTAS): a configurational tool of the TINKER software to evaluate Lysine based branched cyclic peptides as potential chymotrypsin-mimetics. Mol. Simul. 32 (2006) 643-644
34. J.W. Ponder, TINKER Software Tool, Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, http://dasher.wustl.edu/tinker/.
35. Demetropoulos I.N., and Gresh N. A supermolecular study of the effect of hydration on the conformational behaviour of leucine-enkephalin. J. Comput.-Aided Mol. Des. 5 (1991) 81-94
36. Collet O., Premilat S., Maigret B., and Scheraga H.A. Comparison of explicit and implicit treatments of solvation: application to angiotensin II. Biopolymers 42 (1997) 363-371
37. Roux B., and Simonson T. Implicit solvent models. Biophys. Chemist. 78 (1999) 1-20
38. Ooi T., Oobatake M., Nemethy G., and Scheraga H.A. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc. Natl. Acad. Sci. U.S.A 84 (1987) 3086-3090
39. Lee B., and Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55 (1971) 379-380
40. Tunon I., Silla E., and Pascual-Ahuir J.L. Molecular surface area and hydrophobic effect. Protein Eng. 5 (1992) 715-716
41. Fraternalli F., and van Gunsternen W.F. An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution. J. Mol. Biol. 256 (1996) 939-948
42. Lazaridis T., and Karplus M. "New View" of protein folding reconciled with the old through multiple unfolding simulations. Science 278 (1997) 1928-1931
43. Cummings M.D., Hart N.T., and Read R.J. Atomic solvation parameters in the analysis of protein-protein docking results. Protein Sci. 4 (1995) 2087-2089
44. Eisenberg D., and McLachlan A.D. Solvation energy in protein folding and binding. Nature 319 (1986) 199-203
45. Wesson L., and Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1 (1992) 227-235
46. Still W.C., Tempczyk A., Hawley R.C., and Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112 (1990) 6127-6129
47. Constanciel R., and Contreras R. Self consistent field theory of solvent effects representation by continuum models: introduction of desolvation contribution. Theo Chim. Acta 65 (1984) 1-11
48. Born M. Volume and hydration heat of ions. Z. Phys. 1 (1920) 45-48
49. Hawkins G.D., Cramer C.J., and Truhlar D.G. Pairwise descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 246 (1995) 122-129
50. Hawkins G.D., Cramer C.J., and Truhlar D.G. Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J. Phys. Chem. 100 (1996) 19824-19839
51. Kraut J. How do enzymes work?. Science 242 (1988) 533-540
52. Beeman D. Some multistep methods for use in molecular dynamics calculations. J. Comp. Phys. 20 (1976) 130-139
53. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., DiNola A., and Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
54. Wang J., Cieplak P., and Kollman P.A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?. J. Comput. Chem. 21 (2000) 1049-1074
55. Foloppe N., and Jr MacKerell A.D. All-atom empirical force field for nucleic acids: 1) parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21 (2000) 86-104
56. Wallace A.C., Laskowski R.A., and Thornton J.M. Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci. 5 (1996) 1001-1013
57. McDonald I.K., and Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238 (1994) 777-793
58. Hutchinson E.G., and Thornton J.M. PROMOTIF-a program to identify and analyze structural motifs in proteins. Protein Sci. 5 (1996) 212-220
59. Jaramillo A., and Wodak S.J. Computational protein design is a challenge for implicit solvation models. Biophys. J. 88 (2005) 156-171
60. Matter H., and Kessler H. Structures, dynamics, and biological activities of 15 cyclic hexapeptide analogs of the alpha-amylase inhibitor tendamistat (HOE 467) in solution. J. Am. Chem. Soc. 117 (1994) 3347-3359
61. Hammes-Schiffer S., and Benkovic S.J. Relating protein motion to catalysis. Ann. Rev. Biochem. 75 (2006) 519-541
62. Benkovic S.J., and Hammes-Schiffer S. A perspective on enzyme catalysis. Science 301 (2003) 1196-1202
63. Colvin M.E., Cramer C.J., Dykstra C.E., Jensen J.H., Krimm S., Rivail J.-L., Thakkar A.J., and Yanez M. Molecular quantum mechanics to biodynamics: essential connections. J. Mol. Struct., Theochem 764 (2006) 1-8