Role of azaamino acid residue in β-turn formation and stability in designed peptide

Journal of Peptide Research

Volumn 56, Issue 1, 2000, Pages 35-46

  Lee, H J ^a   Ahn, I A ^a,b   Ro, S ^b   Choi, K H ^c   Choi, Y S ^c   Lee, Kang Bong ^a  

^a Korea Institute of Science and Technology   (South Korea)

^b LG Chemical Ltd   (South Korea)

^c Korea University   (South Korea)

Author keywords

turn; Ab initio calculation; Azapeptide; IR; Molecular dynamics; NMR

Indexed keywords

AMINO ACID; PEPTIDE;

AMINO ACID SUBSTITUTION; ARTICLE; CALCULATION; INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEAR OVERHAUSER EFFECT; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTON NUCLEAR MAGNETIC RESONANCE;

AZA COMPOUNDS; DIPEPTIDES; DRUG DESIGN; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; OLIGOPEPTIDES; PROTEIN STRUCTURE, SECONDARY; SOLVENTS; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; TEMPERATURE;

EID: 0033918938     PISSN: 1397002X     EISSN: None     Source Type: Journal    
DOI: 10.1034/j.1399-3011.2000.00717.x     Document Type: Article

References (38)

1. 1. Wolff, M.E., ed. (1995) Burger's Medicinal Chemistry and Drug Discovery, Vol. I: Principles and Practice, 5th edn. Wiley, New York, pp. 803-861.
2. 2. Maynard, A.J., Sharman, G.J. & Searle, M.S. (1998) Origin of β-hairpin stability in solution: structural and thermodynamic analysis of the folding of a model peptide supports hydrophobic stabilization in water. J. Am. Chem. Soc. 120, 1996-2007.
3. 3. Jiménez, A.I., Cativiela, C., Aubry, A. & Marraud, M. (1998) β-Turn preferences induced by 2,3-methanophyenylalanine chirality. J. Am. Chem. Soc. 120, 9452-9459.
4. 4. Lombardi, A., D'Auria, G., Maglio, O., Nastri, F., Quartara, L., Pedone, C. & Pavone, V. (1998) A novel rigid β-turn molecular scaffold. J. Am. Chem. Soc. 120, 5879-5886, and references cited therein.
5. 5. Jean, F., Buisine, E., Melnyk, O., Drobecq, H., Odaert, B., Hugues, M., Lippens, G. & Tartar, A. (1998) Synthesis and structural and functional evaluation of a protein modified with a β-turn mimic. J. Am. Chem. Soc. 120, 6076-6083.
6. 6. Fink, B.E., Kym, P.R. & Katzenellenbogen, J.A. (1998) Design, synthesis, and conformational analysis of a proposed type I β-turn mimic. J. Am. Chem. Soc. 120, 4334-4344.
7. 7. Kabsch, W. & Sanders, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
8. 8. Stanfield, R.L., Fieser, T.M., Lemer, R.A. & Wilson, I.A. (1990) Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 Å. Science 248, 712-719.
9. 9. Nikiforovich, G. & Marshall, G.R. (1993) Conformation-function relationships in LHRH analogs. I. Conformations of LHRH peptide backbone. Int. J. Peptide Protein Res. 42, 171-180.
10. 10. Sibanda, B.L. & Thornton, J.M. (1985) β-Hairpin families in globular proteins. Nature 316, 170-174.
11. 11. Venkatachalam, C.M. (1968) Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 6, 1425-1436.
12. 12. Gante, J. (1994) Peptidomimetics - tailored enzyme inhibitors. Angew. Chem. Int. ed. Engl. 33, 1699-1720.
13. 13. André, F., Boussard, G., Bayeul, D., Didierjean, C., Aubry, A. & Marraud, M. (1997) II. X-ray structures of aza-alanine and aza-asparagine-containing peptides. J. Peptide Res. 49, 556-562.
14. 14. André, F., Vicherat, A., Boussard, G., Aubry, A. & Marraud, M. (1997) Aza-peptides. III. Experimental structural analysis of aza-alanine and aza-asparagine-containing peptides. J. Peptide Res. 50, 372-381.
15. 15. Rose, G.D., Gierasch, L.M. & Smith, J.A. (1985) Turns in peptides and proteins. Adv. Protein Chem. 37, 1-109.
16. 16. Frishc, M.J. et al. (1950) Gaussian 94. Revision E1. Gaussian Inc, Pittsburgh, PA.
17. 17. Pietro, W.J., Francl, M.M., Hehre, W.J., Defrees, D.J., Pople, J.A. & Binkley, J.S. (1982) Self-consistent molecular orbital methods. 24. Supplemented small split-valence basis sets for second-row elements. J. Am. Chem. Soc. 104, 5039-5049.
18. 18. Petersson, G.A., Bennett, A., Tensfeldt, T.G., Al-Laharm, M.A., Shirley, W.A. & Mantzaris, J. (1988) A complete basis set model chemistry, 1. The total energies of closed-shell atoms and hydrides of first-row elements. J. Chem. Phys. 89, 2193-2218.
19. 19. Becke, A.D. (1993) Density-functional thermochemistry III. The role of exact exchange. J. Chem. Phys. 98, 5648-5652.
20. 20. Head-Gordon, T., Head-Gordon, M., Frisch, M.J., Brooks,C.L. III & Pople, J.A. (1991) Theoretical study of blocked glycine and alanine peptide analogues. J. Am. Chem. Soc. 113, 5989-5997.
21. 21. Brooks, C.L. III & Case, D.A. (1993) Simulations of peptide conformational dynamics and thermodynamics. Chem. Rev. 93, 2487-2502.
22. 2. J. Mol. Struct. (Theochem.) 391, 15-26.
23. 23. Oppenheimer, N.J. & James, T.L., eds. (1989) Methods in Enzymology, Vol. 177: Nuclear Magnetic Resonance Part B Structure and Mechanism. Academic Press, New York, p. 145.
24. 24. Bax, A.J. & Davis, D.G. (1985) Practical aspects of two-dimensional transverse NOE spcctroscopy. J. Magn. Reson. 65, 355-360.
25. 25. Jeener, J., Meier, B.H., Bachmann, P. & Ernst, R.R. (1979) Investigation of exchange processes by two-dimensional NMR spectroscopy. J. Chem. Phys. 71, 4546-4553.
26. 26. Craik, D.J., ed. (1996) NMR in Drug Design. CRC Press, New York, p. 163.
27. 27. Neuhaus, D. & Willimson, M. (1989) The Nuclear Overhauser Effect in Structural and Conformational Analysis. VCH, Weinheim, Germany.
28. 28. Mierke, D.F., Geyer, A. & Kessler, H. (1994) Coupling constants and hydrogen bonds as experimental restraints in a distance geometry refinement protocol. Int. J. Peptide Protein Res. 44, 325-331.
29. 3H nuclear magnetic resonance and distance geometry. J. Mol. Biol. 182, 295-315.
30. 30. Reynolds, C.H, & Hormann, R.E. (1996) Theoretical study of the structure and rotational flexibility of diacylhydrazines: implications for the structure of nonsteroidal ecdysone agonists and azapeptides. J. Am. Chem. Soc. 118, 9395-9401.
31. 31. Berliner, L.J. & Reuben, J., eds. (1980) Biological Magnetic Resonance, Vol. 2. Plenum Press, New York, pp. 243-344.
32. 32. Tsang, K.Y., Diaz, H., Graciani, N. & Kelly, J.W. (1994) Hydrophobic cluster formation is necessary for dibenzofuran-based amino acids to function as β-sheet nucleators. J. Am. Chem. Soc. 116, 3988-4055.
33. 33. Haushalter, K.A., Lau, J. & Roberts, J.D. (1996) An NMR investigation of the effect of hydrogen bonding on the rates of rotation about the C-N bonds in urea and thiourca. J. Am. Chem. Soc. 118, 8891-8896.
34. 34. Nowick, J.S., Abdi, M., Bellamo, K.A., Love, J.A., Martinez, E.J., Noronha, G., Smith, E.R. & Ziller, J.W. (1995) Molecular scaffolds. 2. Intramolecular hydrogen bonding in 1,2-diaminoethane diureas. J. Am. Chem. Soc. 117, 89-99.
35. α for identification of helical secondary structure. J. Mol. Biol. 180, 741-751.
36. 36. Bradley, E.K., Thomason, J.F., Cohen, F.E., Kosen, P.A. & Kuntz, I.D. (1990) Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance. J. Mol. Biol. 215, 607-622.
37. 37. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids. Wiley, New York.
38. 38. Ramírez-Alvarado, M., Kortemme, T., Blanco, F.J. & Serrano, L. (1999) β-Hairpin and β-sheet formation in designed linear peptides. Bioorganic Med. Chem. 7, 93-103.