Preferred conformation of peptides rich in Ac8c, a medium-ring alicyclic Cα,α-disubstituted glycine

Journal of Peptide Science

Volumn 2, Issue 1, 1996, Pages 14-27

  Moretto, Vittorio ^a   Formaggio, Fernando ^a   Crisma, Marco ^a   Bonora, Gian Maria ^a   Toniolo, Claudio ^a   Benedetti, Ettore ^b   Santini, Antonello ^b   Saviano, Michele ^b   Di Blasio, Benedetto ^b   Pedone, Carlo ^b  

^a UNIVERSITY OF PADOVA   (Italy)

^b UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

310 helix; Cyclic amino acid; Peptide conformation; X ray diffraction; bend

Indexed keywords

1 AMINOCYCLOOCTANECARBOXYLIC ACID; 1-AMINOCYCLOOCTANECARBOXYLIC ACID; 4 AMINOBUTYRIC ACID; AMINO ACID; DRUG DERIVATIVE; GLYCINE; PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; INFRARED SPECTROSCOPY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION; X RAY DIFFRACTION;

AMINO ACIDS; AMINO ACIDS, CYCLIC; GAMMA-AMINOBUTYRIC ACID; GLYCINE; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; X-RAY DIFFRACTION;

EID: 0029677673     PISSN: 10752617     EISSN: None     Source Type: Journal    
DOI: 10.1002/psc.43     Document Type: Article

References (61)

1. G. R. Marshall in: Intra-Science Chemistry Report, N. Kharasch (Ed.), p. 305-316, Gordon and Breach, New York 1971.
2. I. L. Karle and P. Balaram (1990). Structural characteristics of α-helical peptide molecules containing Aib residues. Biochemistry 29, 6747-6756.
3. P. Balaram (1992). Non-standard amino acids in peptide design and protein engineering. Curr. Opin. Struct Biol. 2, 845-851.
4. C. Toniolo and E. Benedetti (1991). Structures of polypeptides from α-amino acids disubstituted at the α-carbon. Macromolecules 24, 4004-4009.
5. α,α-Symmetrically disubstituted glycines: useful building blocks in the design of conformationally restricted peptides. Janssen Chim. Acta 11, 10-16.
6. S. S. Zimmerman, M. S. Pottle, G. Némethy and H. A. Scheraga (1977). Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP. Macromolecules 10, 1-9.
7. C. M. Venkatachalam (1968). Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three-linked peptide units. Biopolymers 6, 1425-1436.
8. C. Toniolo (1980). Intramolecularly hydrogen-bonded peptide conformations. CRC Crit. Rev. Biochem. 9, 1-44.
9. G. D. Rose, L. M. Gierasch and J. P. Smith (1985).Turns in peptides and proteins. Adv. Protein Chem. 37, 1-109.
10. 10-helix. TIBS 16, 350-353.
11. T. Srikrishnan, R. Srinivasan and R. Zand (1971). Studies in molecular structure, symmetry and conformation. I. Crystal and molecular structure of 1-aminocyclooctane carboxylic and hydrochloride. J. Cryst Mol. Struct 1, 199-212.
12. E. Benedetti, A. Santini, M. Saviano, B. Di Blasio, C. Pedone, V. Moretto, F. Formaggio, M. Crisma, G. M. Bonora, and C. Toniolo in: Peptides 1994, H.L.S. Maia (Ed.), ESCOM, Leiden 1995, 58-59.
13. F. A. Momany, R. F, McGuire, A. W. Burgess and H. A. Scheraga (1975). Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79, 2361-2381.
14. G. Nemethy, M. S. Pottle and H. A. Scheraga (1983). Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87, 1883-1887.
15. Insight/Discover Package, Biosym Technologies, San Diego, California.
16. S. Lifson, A. T. Hagler and P. Dauber (1979). Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 1. Carboxylic acids, amides and the C=O⋯H-hydrogen bonds. J. Am. chem. soc. 101, 5111-5121.
17. A. T. Hagler, S. Lifson and P. Dauber (1979). Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 2. A benchmark for the objective comparison of alternative force fields. J. Am. Chem. Soc. 101, 5122-5130.
18. A. T. Hagler, P. Dauber and S. Lifson (1979). Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 3. The C=O⋯H-hydrogen bond and the analysis of the energetics and packing of carboxylic acids. J. Am. Chem. Soc. 101, 5131-5141.
19. C. L. Brooks III, B. Montgomery Pettitt and M. Karplus: Proteins: A Theoretical Perspective of Dynamics. Structure and Thermodynamics, Wiley, New York 1988.
20. A. Altomare, G. Cascarano, G. Giacovazzo, A. Guagliardi, M. C. Burla, G. Polidori and M. Camalli (1992). SIR 92. A program for automatic solution of crystal structures by direct methods. J. Appl. Crystallogr. 27, 435.
21. B. A. Frenz and Associates, Inc., SDP Structure Determination Package, College Station, Texas, and Enraf-Nonius, Delft, The Netherlands 1985.
22. W. Dvouch, H. Fletcher III and H. E. Album (1964). Preparation of new amino acids and 2,5-oxazolidinediones. J. Org. Chem. 29, 2764-2765.
23. R J. W. Cremlyn, R M. Ellam and T. K. Mitra (1970). Synthesis of some 1-amino alicyclic carboxylic acids and their derivatives. Indian J. Chem. 8, 218-220.
24. J. W. Tsang, B. Schmied, R Nyfelder and M. Goodman (1984). Peptide sweeteners. Structural studies on the C-terminal amino acid of L-aspartyl dipeptide sweeteners. J. Med. Chem. 27, 1663-1668.
25. H. Th. Bücherer and V. A. Lieb (1934). Über die Bildung substituierter Hydantoine aus Aldehyden and Ketonen. Synthese von Hydantoinen. J. Prakt. Chem. 141, 5-43.
26. G. M. Bonora, C. Mapelli, C. Toniolo, R. R. Wilkening and E. S. Stevens (1984). Conformation analysis of linear peptides: 5. Spectroscopic characterization of β-turns in Aib-containing oligopeptides in chlorform. Int. J. Biol. Macromol. 6, 179-188.
27. G. Némethy and M. P. Printz (1972). The γ-turn, a possible folded conformation of the polypeptide chain. Comparison with the β-turn. Macromolecules 5, 755-758.
28. K. D. Kopple and M. Ohnishi (1969). Conformations of cyclic peptides. IV. Nuclear magnetic resonance studies of cyclopentaglycyl-L-leucyl and cyclodiglycyl-D-histidyldiglycyl-L-tyrosyl. Biochemistry 8, 4087-4095.
29. D. Martin and H. G. Hauthal in: Dimethyl Sulphoxide, Van Nostrand-Reinhold, Wokingham, UK 1975.
30. K. D. Kopple and T. J. Schamper (1972). Proton magnetic resonance line broadening produced by association with a nitroxide radical in studies of amide and peptide conformation. J. Am. Chem. Soc. 94, 3644-3646.
31. n. Macromolecules 26, 1980-1984.
32. C. Toniolo, M. Pantano, F. Formaggio, M. Crisma, G. M. Bonora, A. Aubry, D. Bayeul, A. Dautant, W. H. J. Boesten, H. E. Schoemaker and J. Kamphuis (1994). Onset of the fully extended conformation in (αMe)Leu derivatives and short peptides. Int J. Biol. Macromol. 16, 7-14.
33. 10-helical structure. Peptide Res. 8, 6-15.
34. IUPAC-IUB Commission on Biochemical Nomenclature (1970). Abbreviations and symbols for the description of the conformation of polypeptide chains. Biochemistry 9, 3471-3479.
35. E. Benedetti, C. Pedone, C. Toniolo, M. Dudek, G. Némethy and H. A. Scheraga (1983). Preferred conformation of the benzyloxycarbonyl-amino group in peptides. Int. J. Peptide Protein Res. 21, 163-181.
36. 10-helices at atomic resolution. J. Biomol. Struct. Dyn. 5, 803-817.
37. W. B. Schweizer and J. D. Dunitz (1982). Structural characteristics of the carboxylic ester group. Helv. Chim. Acta 65, 1547-1554.
38. E. Benedetti in: Chemistry and Biochemistry of Amino Acids, Peptides, and Proteins, B. Weinstein (Ed.), Vol. 6, p. 105-184, Dekker, New York 1982.
39. T. Ashida, Y. Tsunogae, I. Tanaka and T. Yamane (1987). Peptide chain structural parameters, bond angles and conformational angles from the Cambridge structural database. Acta Crystallogr. B43, 212-218.
40. M. Bixon and S. Lifson (1967). Potential functions and conformations in cycloalkanes. Tetrahedron 23, 769-784.
41. F. H. Allen, O. Kennard, D. G. Watson, L. Brammer, A. G. Orpen and R. Taylor (1987). Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds. J. Chem. Soc., Perkin Trans. 2, S1-S19.
42. Y. Paterson, S. M. Rumsey, E. Benedetti, G. Némethy and H. A. Scheraga (1981). Sensitivity of polypeptide conformation to geometry. Theoretical conformational analysis of oligomers of α-aminoisobutyric acid. J. Am. Chem. Soc. 103, 2947-2955.
43. C. Ramakrishnan and N. Prasad (1971). Study of hydrogen bonds in amino acids and peptides. Int J. Protein Res. 3, 209-231.
44. R. Taylor, O. Kennard and W. Versichel (1984). The geometry of the N-H⋯O=C hydrogen bond. 3. Hydrogen-bond distances and angles. Acta Crystallogr. B40, 280-288.
45. C. H. Görbitz (1989). Hydrogen-bond distances and angles in the structures of amino acids and peptides. Acta Crystallogr. B45, 390-395.
46. J. D. Dunitz in: JUPAC Symposium on Conformational Analysis, G. Chiurdoglou (Ed.), p. 495-508, Butterworths, London 1971.
47. F. P. L. Anet and J. Krane (1973). Strain energy calculation of conformations and conformational change in cyclooctane. Tetrahedron Lett., 5029-5032.
48. D. G. Evans and J. C. A. Boeyens (1988). Mapping the conformation of eight-membered rings. Acta Crystallogr. B44, 663-671.
49. J. P. Fitzgerald (1993). Cyclooctane conformational analysis via mechanical and computational methods. J. Chem. Edite. 70, 988-990.
50. F. H. Allen, J. A. K. Howard and N. A. Pitchford (1993). Symmetry-modified mapping and classification of seven-and eight-membered ring conformations using crystallographic data. Acta Crystallogr. B49, 195-196 (PS-06.06.14).
51. I. D. Brown (1976). On the geometry of O-H⋯O hydrogen bonds. Acta Crystallogr. A32, 24-31.
52. J. Mitra and C. Ramakrishnan (1977). Analysis of O-H-⋯O hydrogen bonds. Int. J. Peptide Protein Res. 9, 27-48.
53. R. Taylor, O. Kennard and W. Versichel (1984). Geometry of the N-H⋯O=C hydrogen bond. 2. Three-center ('bifurcated') and four-center ('trifurcated') bonds. J. Am. Chem. Soc. 106, 244-248.
54. C. H. Yang, J. N. Brown and K. D. Kopple (1979). Peptide-water association in peptide crystals. Int. J. Peptide Protein Res. 14, 12-20.
55. V. J. Hruby, F. Al-Obeidi and W. Kazmierski (1990). Emerging approaches in the molecular design of receptor-selective peptide ligands: conformational, topographical and dynamic considerations. Biochem. J. 268, 249-262.
56. C. Toniolo (1990). Conformationally restricted peptides through short-range cyclizations. Int. J. Peptide Protein Res. 35, 287-300.
57. G. Holzemann (1991). Peptide conformation mimetics. Kontakte (Darmstadt), 3-12 (part 1) and 55-63 (part 2).
58. A. Giannis and T. Kolter (1993). Peptidomimetics for receptor ligands. Discovery, development, and medical perspectives. Angew. Chem. Int. Ed. Engl. 32, 1244-1267.
59. A. E. P. Adang, P. H. H. Hermkens, J. T. M. Linders, H. C. J. Ottenheijm and C. J. van Staveren (1994). Case histories of peptidomimetics: progression from peptides to drugs. Recl. Trav. Chim. Pays-Bos 113, 63-78.
60. J. Gante (1994). Peptidomimetics: taylored enzyme Inhibitors. Angew. Chem. Int. Ed. Engl. 33, 1699-1720.
61. R. M. J. Liskamp (1994). Conformationally restricted amino acids and dipeptides, (non)peptidomimetics and secondary structure mimetics. Recl. Trav. Chim. Pays-Bas 113, 1-19.