Exploring the conformational space of cyclic peptides by a stochastic search method

Journal of Molecular Graphics and Modelling

Volumn 22, Issue 5, 2004, Pages 319-333

  Rayan, Anwar ^a   Senderowitz, Hanoch ^b   Goldblum, Amiram ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b Peptor Ltd   (Israel)

Author keywords

Complex combinatorial; Conformations; Cyclic peptides; Ensembles; Flexibility; Multidimensional space; Stochastic search algorithm; Structure prediction

Indexed keywords

CONFORMATIONS; CRYSTAL STRUCTURE; MOLECULAR STRUCTURE; PROTEINS; RANDOM PROCESSES;

CYCLIC PEPTIDES; RING CLOSURE;

POLYPEPTIDES;

AMINO ACID; CYCLOPEPTIDE;

ALGORITHM; CONFERENCE PAPER; CONFORMATION; DATA BASE; EXTRACTION; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; RING CLOSING METATHESIS; STOCHASTIC MODEL;

ALGORITHMS; DATA INTERPRETATION, STATISTICAL; PEPTIDES, CYCLIC; PROTEIN CONFORMATION; STOCHASTIC PROCESSES;

EID: 1942455320     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2003.12.012     Document Type: Conference Paper

References (70)

1. Cuniasse P., Raynal I., Yiotakis A., Dive V. Accounting for conformational variability in NMR structure of cyclopeptides: ensemble averaging of interproton distance and coupling constant restraints. J. Am. Chem. Soc. 119:1997;5239-5248.
2. Li H., Sampson N. Structural analysis of fertilin beta cyclic peptide mimics that are ligands for alpha(6)beta(1) integrin. J. Pept. Res. 59:2002;45-54.
3. Groth M., Malicka J., Rodziewicz-Motowidlo S., Czaplewski C., Klaudel L., Wiczk W., Liwo A. Determination of conformational equilibrium of peptides in solution by NMR spectroscopy and theoretical conformational analysis: application to the calibration of mean-field solvation models. Biopolymers. 60:2001;79-95.
4. Matter H., 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. 117:1995;3347-3359.
5. Malicka J., Groth M., Czaplewski C., Wiczk W., Liwo A. Conformational studies of cyclic enkephalin analogues with L- or D-proline in position 3. Biopolymers. 63:2002;217-231.
6. Unger R., Moult J. Finding the lowest free energy conformation of a protein is an NP-hard problem: proof and implications. Bull. Math Biol. 55:1993;1183-1198.
7. MacKerell A.D., Bashford D., Bellott M., Dunbrack R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Reiher W.E., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Yin D., Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:1998;3586-3616.
8. Zhang W.J., Nikiforovich G.V., Perodin J., Richard D.E., Escher E., Marshall G.R. Novel cyclic analogs of angiotensin II with cyclization between positions 5 and 7: conformational and biological implications. J. Med. Chem. 39:1996;2738-2744.
9. Sefler A.M., Lauri G., Barlett P.A. A convenient method for determining cyclic peptide conformation from 1D H-1-NMR information. Int. J. Pept. Protein Res. 48:1996;129-138.
10. de Bakker P.I.W., DePristo M.A., Burke D.F., Blundell T.L. Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized born solvation model. Proteins. 51:2003;21-40.
11. Gohlke H., Klebe G. Statistical potentials and scoring functions applied to protein-ligand binding. Curr. Opin. Struct. Biol. 11:2001;231-235.
12. Gan H.H., Tropsha A., Schlick T. Lattice protein folding with two- and four-body statistical potentials. Proteins. 43:2001;161-174.
13. Guarnieri F., Weinstein H. Conformational memories and the exploration of biologically relevant peptide conformations: an illustration for the gonadotropin-releasing hormone. J. Am. Chem. Soc. 118:1996;5580-5589.
14. Guarnieri F., Wilson S.R. Conformational memories and a simulated annealing program that learns - application to Ltb(4). J. Comput. Chem. 16:1995;648-653.
15. Hassan S.A., Guarnieri F., Mehler E.L. A new approach for folding peptides: conformational memories with a new implicit solvent model. Biophys. J. 78:2000;1978. (Pos Part 2).
16. Kolossvary I., Guida W.C. Low mode search. An efficient, automated computational method for conformational analysis: application to cyclic and acyclic alkanes and cyclic peptides. J. Am. Chem. Soc. 118:1996;5011-5019.
17. Senderowitz H., Guarnieri F., Still W.C. A smart Monte Carlo technique for free-energy simulations of multiconformational molecules, Direct calculations of the conformational populations of organic-molecules. J. Am. Chem. Soc. 117:1995;8211-8219.
18. Senderowitz H., Still W.C. MC(JBW): simple but smart Monte Carlo algorithm for free energy simulations of multiconformational molecules. J. Comput. Chem. 19:1998;1736-1745.
19. Lee J., Scheraga H.A., Rackovsky S. New optimization method for conformational energy calculations on polypeptides: conformational space annealing. J. Comput. Chem. 18:1997;1222-1232.
20. Goodman J.M., Still W.C. An unbounded systematic search of conformational space. J. Comput. Chem. 12:1991;1110-1117.
21. Glick M., Rayan A., Goldblum A. A stochastic algorithm for global optimization and for best populations: a test case of side chains in proteins. Proc. Natl. Acad. Sci. USA. 99:2002;703-708.
22. Behrens S., Matha B., Bitan G., Gilon C., Kessler H. Structure-activity relationship of the ring portion in backbone-cyclic C-terminal hexapeptide analogs of substance P. Int. J. Pept. Protein Res. 48:1996;569-579.
23. Boer J., Gottschling D., Schuster A., Semmrich M., Holzmann B., Kessler H. Design and synthesis of potent and selective alpha(4)beta(7) integrin antagonists. J. Med. Chem. 44:2001;2586-2592.
24. Bradley E.K., Ng S.C., Simon R.J., Spellmeyer D.C. Synthesis, molecular modelling, and NMR structure determination of four cyclic peptide antagonists of endothelin. Bioorg. Med. Chem. 2:1994;279-296.
25. Breton C., Chellil H., Kabbaj-Benmansour M., Carnazzi E., Seyer R., Phalipou S., Morin D., Durroux T., Zingg H., Barberis C., Mouillac B. Direct identification of human oxytocin receptor-binding domains using a photoactivatable cyclic peptide antagonist - comparison with the human V-1a vasopressin receptor. J. Biol. Chem. 276:2001;26931-26941.
26. Burgess K., Lim D., Mousa S.A. Synthesis and solution conformation of cyclo RGDRGD: a cyclic peptide with selectivity for the alpha V beta 3 receptor. J. Med. Chem. 39:1996;4520-4526.
27. Cucchi P., Meini S., Quartara L., Giolitti A., Zappitelli S., Rotondaro L., Maggi C.A. Interaction of linear and cyclic peptide antagonists at the human B-2 kinin receptor. Peptides. 23:2002;1457-1463.
28. Goldberg J. Cyclic peptide antibiotics self-assembly required. Trends Biotechnol. 19:2001;379-379.
29. Kasher R., Oren D.A., Barda Y., Gilon C. Miniaturized proteins: the backbone cyclic proteinomimetic approach. J. Mol. Biol. 292:1999;421-429.
30. Karle I.L. Aspects of peptide folding and aggregation. Acc. Chem. Res. 32:1999;693-701.
31. Schmiedeberg N., Schmitt M., Rolz C., Truffault V., Sukopp M., Burgle M., Wilhelm O.G., Schmalix W., Magdolen V., Kessler H. Synthesis, solution structure, and biological evaluation of urokinase type plasminogen activator (uPA)-derived receptor binding domain mimetics. J. Med. Chem. 45:2002;4984-4994.
32. Williams E., Williams G., Gour B.J., Blaschuk O.W., Doherty P. A novel family of cyclic peptide antagonists suggests that N-cadherin specificity is determined by amino acids that flank the HAV motif. J. Biol. Chem. 275:2000;4007-4012.
33. Zanotti G., Saviano M., Saviano G., Tancredi T., Rossi F., Pedone C., Benedetti E. Structure of cyclic peptides: the crystal and solution conformation of cyclo(Phe-Phe-Aib-Leu-Pro). J. Pept. Res. 51:1998;460-466.
34. Stavrakoudis A., Makropoulou S., Tsikaris V., Sakarellos-Daitsiotis M., Sakarellos C., Demetropoulos I.N. Computational screening of branched cyclic peptide motifs as potential enzyme mimetics. J. Pept. Sci. 9:2003;145-155.
35. Lucke A.J., Tyndall J.D.A., Singh Y., Fairlie D.P. Designing supramolecular structures from models of cyclic peptide scaffolds with heterocyclic constraints. J. Mol. Graph. 21:2003;341-355.
36. Valero M.L., Camarero J.A., Haack T., Mateu M.G., Domingo E., Giralt E., Andreu D. Native-like cyclic peptide models of a viral antigenic site: finding a balance between rigidity and flexibility. J. Mol. Recognit. 13:2000;5-13.
37. Kohli R.M., Walsh C.T., Burkart M.D. Biomimetic synthesis and optimization of cyclic peptide antibiotics. Nature. 418:2002;658-661.
38. Kinsella T.M., Ohashi C.T., Harder A.G., Yam G.C., Li W.Q., Peelle B., Pali E.S., Bennett M.K., Molineaux S.M., Anderson D.A., Masuda E.S., Payan D.G. Retrovirally delivered random cyclic peptide libraries yield inhibitors of interleukin-4 signaling in human B cells. J. Biol. Chem. 277:2002;37512-37518.
39. Hahn M., Winkler D., Welfle K., Misselwitz R., Welfle H., Wessner H., Zahn G., Scholz C., Seifert M., Harkins R., Schneider-Mergener J., Hohne W.G. Cross-reactive binding of cyclic peptides to an anti-TGF alpha antibody fab fragment: an X-ray structural and thermodynamic analysis. J. Mol. Biol. 314:2001;293-309.
40. Horton D.A., Bourne G.T., Smythe M.L. Exploring privileged structures: the combinatorial synthesis of cyclic peptides. J. Comput. Aided Mol. Des. 16:2002;415-430.
41. Fairlie D.P., Abbenante G., March D.R. Macrocyclic peptidomimetics - forcing peptides into bioactive conformations. Curr. Med. Chem. 2:1995;654-686.
42. MacDonald M., Aube J. Approaches to cyclic peptide beta-turn mimics. Curr. Org. Chem. 5:2001;417-438.
43. Kessler H., Gratias R., Hessler G., Gurrath M., Muller G. Conformation of cyclic peptides. Principle concepts and the design of selectivity and superactivity in bioactive sequences by 'spatial screening'. Pure Appl. Chem. 68:1996;1201-1205.
44. Sukopp M., Marinelli L., Heller M., Brandl T., Goodman S.L., Hoffman R.W., Kessler H. Designed beta-turn mimic based on the allylic-strain concept: evaluation of structural and biological features by incorporation into a cyclic RGD peptide (cyclo(-L-arginylglcyl-L-alpha-aspartyl-)). Helv. Chim. Acta. 85:2002;4442-4452.
45. Desai P., Prachand M., Coutinho E., Saran A., Bodi J., Suli-Vargha H. Activity and conformation of a cyclic heptapeptide possessing the message sequence His-Phe-Arg-Trp of alpha-melanotropin. Int. J. Biol. Macromol. 30:2002;187-195.
46. Descours A., Moehle K., Renard A., Robinson J.A. A new family of beta-hairpin mimetics based on a trypsin inhibitor from sunflower seeds. Chem. Biochem. 3:2002;318-323.
47. Keasar C., Rosenfeld R. Empirical modifications to the AMBER/OPLS potential for predicting the solution conformations of cyclic peptides by vacuum calculations. Fold. Des. 3:1998;379-388.
48. Nikiforovich G.V., Kover K.E., Zhang W.J., Marshall G.R. Cyclopentapeptides as flexible conformational templates. J. Am. Chem. Soc. 122:2000;3262-3273.
49. Loiseau N., Gomis J.M., Santolini J., Delaforge M., Andre F. Predicting the conformational states of cyclic tetrapeptides. Biopolymers. 69:2003;363-385.
50. Grover A.A., Kishore R. Characterization of a novel type VII beta-turn conformation for a bio-active tetrapeptide rigin - a synergy between theoretical and experimental results. Eur. J. Biochem. 267:2000;1455-1463.
51. Krause K., Pineda L.F., Peteranderl R., Reissmann S. Conformational properties of a cyclic peptide bradykinin B-2 receptor antagonist using experimental and theoretical methods. J. Pept. Res. 55:2000;63-71.
52. Baysal C., Meirovitch H. Efficiency of simulated annealing for peptides with increasing geometrical restrictions. J. Comput. Chem. 20:1999;1659-1670.
53. Morita H., Kayashita T., Takeya K., Itokawa H., Shiro M. Conformation of cyclic heptapeptides: solid and solution state conformation of yunnanin A. Tetrahedron. 53:1997;1607-1616.
54. Baysal C., Meirovitch H. Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR data. Biopolymers. 50:1999;329-344.
55. A. Rayan, E. Noy, D. Chema, A. Levitzki, A. Goldblum, Stochastic algorithm for kinase homology model construction, Curr. Med. Chem. 11 (2004) 675-692.
56. Glick M., Goldblum A. A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays. Proteins. 38:2000;273-287.
57. Oliva B., Bates P.A., Querol E., Aviles F.X., Sternberg M.J.E. An automated classification of the structure of protein loops. J. Mol. Biol. 266:1997;814-830.
58. D.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross, T.E.I. Cheatham, D.M. Ferguson, G.L. Seibel, U.C. Singh, P.K. Weiner, P.A. Kollman, AMBER, University of California, San Francisco, Version 4.1, 1995.
59. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Res. 28:2000;235-242.
60. Viles J.H., Mitchell J.B.O., Gough S.L., Doyle P.M., Harris C.J., Sadler P.J., Thornton J.M. Multiple solution conformations of the integrin-binding cyclic pentapeptide cyclo(-Ser-D-Leu-Asp-Val-Pro-) Analysis of the (phi, psi) space available to cyclic pentapeptides. Eur. J. Biochem. 242:1996;352-362.
61. Clark M., Cramer R.D., Vanopdenbosch N. Validation of the general-purpose tripos 5.2 force-field. J. Comput. Chem. 10:1989;982-1012.
62. Allen F.H., Bellard S., Brice M.D., Cartwright B.A., Doubleday A., Higgs H., Hummelink T., Hummelinkpeters B.G., Kennard O., Motherwell W.D.S., Rodgers J.R., Watson D.G. Cambridge crystallographic data center - computer-based search, retrieval, analysis and display of information. Acta Crystallogr. Sect. B - Struct. Commun. 35:1979;2331-2339.
63. Moriarty D.F., Colon W. Peptide fragments from the DNA binding protein Fis: influence of proline on secondary structure. Biochemistry. 41:2002;159.
64. Brachais L., Duclohier H., Mayer C., Davoust D. Influence of proline-14 substitution on the secondary structure in a synthetic analog of alamethicin. Biopolymers. 36:1995;547-558.
65. Kricheldorf H.R., Haupt E.T.K., Muller D. Secondary structure of peptides. Part 17. Cis-trans isomerism of solid proline-containing oligopeptides as revealed by C-13 Nmr Cp/Mas spectroscopy. Magn. Reson. Chem. 24:1986;41-52.
66. Amodeo P., Saviano G., Borin G., Calderan A., Ruzza P., Tancredi T. Solution conformational analysis of sodium complexed [Gly6]- and [Gly9]-antamanide analogs. J. Pept. Res. 51:1998;180-187.
67. Karle I.L. Flexibility in peptide molecules and restraints imposed by hydrogen bonds, the AiB residue, and core inserts. Biopolymers. 40:1996;157-180.
68. Diblasio B., Lombardi A., Yang X., Pedone C., Pavone V. Beta-Alanyl-Beta-Alanine in cyclic beta-turned peptides. Biopolymers. 31:1991;1181-1188.
69. Karle I.L. Folding, aggregation and molecular recognition in peptides. Acta Crystallogr. Sect. B - Struct. Commun. 48:1992;341-356.
70. Fiser A., Do R.K.G., Sali A. Modeling of loops in protein structures. Protein Sci. 9:2000;1753-1773.