Conformational investigation of α,β-dehydropeptides. XVI. β-turn tendency in Ac-Pro-ΔXaa-NHMe: Crystallographic and theoretical studies

Journal of Peptide Science

Volumn 12, Issue 8, 2006, Pages 538-549

  Broda, Malgorzata A ^a   Ciszak, Ewa M ^b   Koziol, Anna E ^c   Pietrzynski, Grzegorz ^d   Rzeszotarska, Barbara ^a  

^a UNIVERSITY OF OPOLE   (Poland)

^b UNIVERSITY OF ALABAMA IN HUNTSVILLE   (United States)

^c MARIA CURIE SK ODOWSKA UNIVERSITY   (Poland)

^d Supratek Pharma Inc   (Canada)

Author keywords

, dehydropeptides; turn; DFT calculation; Extended form; Hydrogen bonds; Peptide conformation; Solute solvent interaction; X ray crystallography

Indexed keywords

ALPHA,BETA DEHYDROBUTYRINE PEPTIDE; PEPTIDE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CORRELATION FUNCTION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DIASTEREOISOMER; HYDROGEN BOND; MOLECULAR STABILITY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; THEORETICAL STUDY;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; PEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SOLVENTS;

EID: 33747221168     PISSN: 10752617     EISSN: 10991387     Source Type: Journal    
DOI: 10.1002/psc.763     Document Type: Article

References (58)

1. Broda MA, Siodlak D, Rzeszotarska B. Conformational investigation of α,β-dehydropeptides. XV. N-Acetyl-α,β-dehydroamino acid N′ N′-dimethylamides: conformational properties from infrared and theoretical studies. J. Pept. Sci. 2005; 11: 546-555.
2. Joshi RM, Chauhan VS. Synthesis of peptides based on α,β-didehydro-α-amino acids. In Methods of Organic Chemistry (Houben-Weyl). Synthesis of Peptides and Peptidomimetics. Vol. E22c, Goodman M, Felix A, Moroder L, Toniolo C (eds). Thieme: Stuttgart, New York, 2003; 636-662. references cited therein.
3. Pietrzynski G, Rzeszotarska B. α,β-Dehydroamino acids as peptide modifiers: conformational aspects. Pol. J. Chem. 1995; 69: 1595-1614, references cited therein.
4. Jain R, Chauhan VS. Conformational characteristics of peptides containing α,β-dehydroamino acid residues. Biopolymers (Peptide Sci.) 1996; 40: 105-119, references cited therein.
5. Singh TP, Kaur P. Conformation and design of peptides with α,β-dehydro-amino acid residues. Prog. Biophys. Mol. Biol. 1997; 66: 141-165, references cited therein.
6. Mathur P, Ramakumar S, Chauhan VS. Peptide design using α,β-dehydro amino acids: from β-turns to helical hairpins. Biopolymers (Peptide Sci.) 2004; 76: 150-161. references therein.
7. Vijayaraghavan R, Makker J, Kumar P, Dey S, Singh TP. Design of peptides with α,β-dehydro-residue: syntheses, crystal structures and molecular conformations of two ΔPhe-Trp containing peptides. J. Mol. Struct. 2003; 654: 103-110.
8. 3. J. Mol. Struct. 2003; 658: 135-141.
9. Ciszak E, Pietrzynski G, Rzeszotarska B. Conformational investigation of α,β-dehydropeptides. III. Molecular and crystal structure of acetyl-L-prolyl-α,β-dehydrovaline methylamide. Int. J. Pept. Protein Res. 1992; 39: 218-222.
10. Thormann M, Hofmann H-J. Conformational properties of peptides containing dehydro amino acids. J. Mol. Struct (Theochem) 1998; 431: 79-96.
11. Vijayaraghavan R, Kumar P, Dey S, Singh TP. Design of peptides with α,β-dehydro residues: a peptide with a branched β-carbon dehydro residue at (i + 1) position, methyl N-(benzyloxycarbonyl)-α,β-didehydrovalyl-L-tryptophanate. Acta Crystallogr. 2001; C57: 1220-1221.
12. Makker J, Dey S, Mukherjee R, Vijayaraghavan R, Kumar P, Singh TP. Design of peptides with α,β-dehydro-residues: synthesis, crystal structure and molecular conformation of a tetrapeptide Z-ΔVal-Val-ΔPhe-Ile-Ome. J. Mol. Struct. 2003; 654: 119-124.
13. 3: comparison with (Z) substituted α,β-dehydro-peptides. Int. J. Pept. Protein Res. 1996; 48: 347-356.
14. Crisma M, Formaggio F, Toniolo C, Yoshikawa T, Wakamiya T. Flat peptides. J. Am. Chem. Soc. 1999; 121: 3272-3278.
15. Pietrzynski G, Rzeszotarska B, Ciszak E, Lisowski M. Turn tendency of model α,β-dehydropeptides. Pol. J. Chem. 1994; 68: 1015-1021.
16. 3: NMR and IR studies. Int. J. Pept. Protein Res. 1992; 40: 524-531.
17. 3 in crystals. Int. J. Pept. Protein Res. 1993; 41: 394-398.
18. Gupta A, Chauhan VS. Conformation of dehydropeptides. Synthesis and solution structure of model peptides containing (E) and (Z) dehydroaminobutyric acid residues. Int. J. Pept. Protein Res. 1993; 41: 421-426.
19. 3: CD studies in various solvents. Int. J. Pept. Protein Res. 1993; 42: 466-474.
20. Jack RW, Bierbaum G, Sahl H-G. Lantibiotics and Related Peptides. Springer-Verlag: Berlin, 1998.
21. Jack RW, Jung G. Lantibiotics and microcins: polypeptides with unusual chemical diversity. Curr. Opin. Chem. Biol. 2000; 4: 310-317.
22. Guder A, Wiedemann I, Sahl H-G. Posttranslationally modified bacteriocins-the lantibiotics. Biopolymers (Peptide Sci.) 2000; 55: 62-73.
23. McAuliffe O, Ross PR, Hill C. Lantibiotics: structure, biosynthesis and mode of action. FEMS Microbiol Rev. 2001; 25: 285-308.
24. Bower CK, Bothwell MK, McGuire J. Lantibiotics as surface active agents for biomedical applications. Colloids Surf., B: Biointerfaces 2001; 22: 259-265.
25. Hoffmann A, Pag U, Wiedemann I, Sahl H-G. Combination of antibiotic mechanisms in lantibiotics. Farmaco 2001; 57: 685-691.
26. Wiedemann I, Breukink E, van Kraaij C, Kuipers OP, Bierbaum G, de Kruijff B, Sahl H-G. Specific binding of nisin to the peptidoglycan precursor lipid II combines pore formation and inhibition of cell wall biosynthesis for potent antibiotic activity. J. Biol. Chem. 2001; 276: 1772-1779.
27. Noda K, Shimohigashi Y, Izumiya N. α,β-Dehydroamino acids and peptides. In The Peptides. Analysis, Synthesis, Biology, Vol. 5, Gross E, Meienhofer J (eds). Academic Press: New York-London, 1983; 285-339.
28. Li KW, Wu J, Xing W, Simon JA. Total synthesis of the antitumor depsipeptide FR-901.228. J. Am. Chem. Soc. 1996; 116: 7237-7238.
29. Santamaría A, Cabezas N, Avendaño C. Synthesis of tryptophan-dehydrobutyrine diketopiperazines and analogues. Tetrahedron 1999; 55: 1173-1186.
30. Pedras MSC, Taylor JT, Nakashima TT. A novel chemical signal from "blackleg" fungus: beyond phytotoxins and phytoalexins. J. Org. Chem. 1993; 58: 4778-4780.
31. Ward DE, Vazquez A, Pedras MSC. Understanding host-selective phytotoxicity: synthesis and biological discrimination of phomalide and its (Z)-isomer. J. Org. Chem. 1996; 61: 8008-8009.
32. Lukomska J, Kasprzykowski F, Lankiewicz L, Grzonka Z. Peptide toxins of cyanobacteria. Wiad. Chem. 2002; 56: 57-82; CA 2002; 137: 104 855.
33. Sano T, Kaya K. Two new 2-(E)-amino-2-butenoic acid (Dhb)-containing microcystins from Oscillatoria agardhii. Tetrahedron 1998; 54: 463-470.
34. Sano T, Beattie KA, Codd GA, Kaya K. Two (Z)-dehydrobutyrine containing microcystins from hepatotoxic bloom of Oscillatoria agardhii from Soulseat Loch, Scotland. J. Nat. Prod. 1998; 61: 851-853.
35. Beattie KA, Raya K, Sano T, Codd GA. Three dehydrobutyrine-containing microcystins Nostoc. Phytochemistry 1998; 47: 1289-1292.
36. Brittain S, Mohamed ZA, Wang J, Lehmann VKB, Carmichael WW, Rinehart K. Isolation and characterization of microcystins from a river Nile strain of Oscillatoria tenuis Agardh ex Gomont. Toxicon 2000; 38: 1759-1771.
37. 7]microcystin-RR of Planktothrix rubescens as compared to different microcystins. Toxicon 2001; 39: 1923-1932.
38. Gupta A, Chauhan VS. Synthetic and conformational studies on dehydroalanine containing model peptides. Biopolymers 1990; 30: 395-403.
39. Pietrzynski G, Rzeszotarska B. Conformational investigation of α,β-dehydropeptides. II. Synthesis of model dipeptides. Bull. Pol. Acad. Sci. Chem. 1991; 39: 1-6.
40. Lehmann MS, Larsen KL. A method for location of the peaks in step-scan measured Bragg reflexions. Acta Crystallogr. 1974; A30: 580-584.
41. Jaskólski M. Ph Dissertation. Rentgenograficzne badania struktury krysztalow dwupiperydyloetanu. A. Mickiewicz University, Poznan: Poland, 1979.
42. Sheldrick GM. SHELXLS93. Program for Crystal Structure Solution. University of Göttingen: Germany, 1993.
43. Sheldrick GM. SHELXL97. Program for Crystal Structure Refinement. University of Göttingen: Germany. 1997.
44. Venkatachalam CM. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 1968; 6: 1425-1436.
45. Hutchinson EG, Thornton JM. A revised set potentials for β-turn formation in proteins. Protein Sci. 1994; 3: 2207-2216.
46. Hudáky I, Baldoni HA, Perczel A. Peptide models XXXVIII. Proline conformers from X-ray ciystallographic database and from ab initio computations. J. Mol. Struct. (Theochem) 2002; 582: 233-249.
47. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T Jr, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian 03, Revision B.04 Gaussian: Pittsburgh, PA, 2003.
48. Cossi M, Barone V, Cammi R, Tomasi J. Ab initio study of solvated molecules: A new implementation of the polarizable continuum model. Chem. Phys. Lett. 1996; 255: 327-335.
49. Perczel A, McAllister MA, Császár P, Csizmadia IG. Peptide models 6. New β-turn conformations from ab initlo calculations confirmed by X-ray data of proteins. J. Am. Chem. Soc. 1993; 115: 4849-4858.
50. Lewitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 1976; 104: 59-107.
51. Broda MA, Rzeszotarska B, Smelka L, Rospenk M. Conformational investigation of α,β-dehydropeptides. VIII. N-Acetyl-α,β-dehydroamino acid N′ methylamides: conformation and electron density perturbation from infrared and theoretical studies. J. Pept. Res. 1997; 50: 342-351.
52. Broda MA, Rzeszotarska B, Smelka L, Pietrzynski G. Conformational investigation of α,β-dehydropeptides. IX. N-Acetyl-(E)-α,β-dehydrobutyrine N′ methylamide: stereoelectronic properties from infrared and theoretical studies. J. Pept. Res. 1998; 52: 72-79.
53. Möhler K, Gussmann M, Hofmann H-J. Structural and energetic relations between β-turns. J. Comput. Chem. 1997; 18: 1415-1430.
54. Görbitz CH, Etter MC. Hydrogen bond connectivity pattern and hydrophobic interactions in crystal structures of small acyclic peptides. Int. J. Pept. Proteín Res. 1992; 39: 93-110.
55. Steiner T. The hydrogen bond in the solid state. Angew. Chem., Int. Ed. Engl. 2002; 41: 48-76.
56. Aubry A, Protas J, Boussard G, Marraud M. Conformations moleculaires à l'etat solide des deux diastéréoisoméres de la N-isobutyrylprolylalanine-isopropylamide. Comparaison avec les conformations adoptées en solution. Acta Crystallogr. 1977; B33: 2399-2406.
57. Aubry A, Cung MT, Marraud M. βI and βII-turn conformations in model dipeptides with the Pro-Xaa sequences. J. Am. Chem. Soc. 1985; 107: 7640-7647.
58. Boussard G, Marraud M, Aubry A. Experimental investigation on the backbone folding of proline-containing model tripeptides. Biopolymers 1979; 18: 1297-1331.