Characterization of β-turn and Asx-turns mimicry in a model peptide: Stabilization via C-H ⋯ O interaction

Biopolymers

Volumn 81, Issue 6, 2006, Pages 440-449

  Thakur, A K ^a   Kishore, R ^a  

^a INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

Author keywords

turn; Asx turns; Chemical synthesis; Mimicry; Peptide protein interaction; X ray diffraction

Indexed keywords

CONFORMATIONS; CRYSTALS; HYDROGEN BONDS; MOLECULAR STRUCTURE; PROTEINS; STABILIZATION; TOPOLOGY; X RAY DIFFRACTION;

BIOMACROMOLECULES; BIOORGANIC; C-TERMINAL RESIDUES; PEPTIDES;

BIOPOLYMERS;

AMIDE; PROTEIN TERT BUTOXYCARBONYLTHREONYLTHREONYLAMIDE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; CONFORMATION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; HYDROGEN BOND; MACROMOLECULE; MOLECULAR INTERACTION; MOLECULAR MIMICRY; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN STABILITY; PROTEIN STRUCTURE; SYNTHESIS; X RAY DIFFRACTION;

CARBON; HYDROGEN BONDING; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR MIMICRY; OXYGEN; PEPTIDES; PROTEIN STRUCTURE, SECONDARY;

EID: 33645770299     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20441     Document Type: Article

References (97)

1. Spatola, A. In Chemistry and Biochemistry of Amino-acids, Peptides and Proteins, Vol. 7; Weinstein, B., Ed.; Dekker: New York, 1983; pp 267-357.
2. Toniolo, C. Int J Peptide Protein Res 1990, 35, 287-300.
3. Marraud, M.; Aubry, A. Biopolymers (Peptide Sci) 1996, 40, 3-44.
4. Benedetti, E. Biopolymers (Peptide Sci) 1996, 40, 45-83.
5. Gellman, S. H. Curr Opin Chem Biol 1998, 2, 717-725.
6. Halab, L.; Gosselin, F.; Lubell, W. D. Biopolymers 2000, 55, 101-122.
7. Venkatraman, J.; Shankaramma, S. C.; Balaram, P. Chem Rev 2001, 101, 3131-3152.
8. Patch, J. A.; Barron, A. E. Curr Opin Chem Biol 2002, 6, 872-877.
9. Eguchi, M.; Kahn, M. Mini-Rev Med Chem 2002, 2, 447-462.
10. Matile, S.; Som, A.; Sorde, N. Tetrahedron 2004, 60, 6405-6435.
11. Padmanabhan, S.; Marquesse, S.; Ridgeway, T.; Laue, T. M.; Baldwin, R. L. Nature 1990, 344, 268-270.
12. Kim, C. A.; Berg, J. M. Nature 1993, 362, 267-270.
13. Minor, D. L., Jr.; Kim, P. S. Nature 1994, 367, 660-663.
14. Blanco, F.; Ramírez-Alvarado, M.; Serrano, L. Curr Opin Struct Biol 1998, 8, 107-111.
15. Serrano, L. Adv Protein Chem 2000, 53, 49-85.
16. Baltzer, L.; Nilsson, H.; Nilsson, J. Chem Rev 2001, 101, 3153-3163.
17. Toniolo, C. CRC Crit Rev Biochem 1980, 9, 1-44.
18. Prasad, B. V. V.; Balaram, P. CRC Crit Rev Biochem 1984, 16, 307-347.
19. Toniolo, C. Janssen, Janssen Chim Acta 1993, 11, 10-16.
20. Drechsel, H.; Jung, G. J. Peptide Sci 1998, 4, 147-181.
21. Vass, E.; Hollósi, M.; Besson, F.; Buchet, R. Chem Rev 2003, 103, 1917-1954
22. Komarov, I. V.; Grigorenko, A. O.; Turov, A. V.; Khilya, V. P. Russ Chem Rev 2004, 73, 785-810.
23. Janin, J.; Wodak, S.; Levitt, M.; Maigret, B. J Mol Biol 1978, 125, 357-386.
24. McGregor, M. J.; Islam, S. A.; Sternberg, M. J. E. J Mol Biol 1987, 198, 295-310.
25. Dunbrack, R. L., Jr.; Karplus, M. J Mol Biol 1993, 230, 543-574.
26. Swindells, M. B.; MacArthur, M. W.; Thornton, J. M. Nature Struct Biol 1995, 2, 596-603.
27. Hruby, V. J.; Li, G.; Haskell-Luevano, C.; Shenderovich, M. Biopolymers 1997, 43, 219-266.
28. Griffiths-Jones, S. R.; Sharman, G. J.; Maynard, A. J.; Searle, M. S. J Mol Biol 1998, 284, 1597-1609.
29. Baker, E. N.; Hubbard, R. E. Prog Biophys Mol Biol 1984, 44, 97-179.
30. Richardson, J. S.; Richardson, D. V. In Prediction of Protein Structure and the Principles of Protein Conformation; Fasman, G. D., Ed.; Plenum Press: New York, 1989; pp 1-98.
31. Wilson, D. R.; Finlay, B. B. Protein Eng 1997, 10, 519-529.
32. Wan, W.-Y.; Milner-White, E. J. J Mol Biol 1999, 286, 1651-1662.
33. Eswar, N.; Ramakrishnan, C. Protein Eng 1999, 12, 447-455.
34. Eswar, N.; Ramakrishnan, C. Protein Eng 2000 13, 227-238.
35. Duddy, W. J.; Nissink, J. W. M.; Allen, F. H.; Milner-White, E. J. Protein Sci 2004, 13, 3051-3055.
36. Zimm, B. H.; Bragg, J. K. J Chem Phys 1959, 31, 526-535.
37. Lewis, P. N.; Momany, F. A.; Scheraga, H. A. Isr J Chem 1973, 11, 121-153.
38. Zimmerman, S. S.; Pottle, M. S.; Némethy, G.; Scheraga, H. A. Macromolecules 1977, 10, 1-9.
39. Ashish; Kishore, R. Tetrahedron Lett. 1997, 37, 5747-5750.
40. Ashish; Kishore, R. FEBS Lett. 1997, 417, 97-100.
41. Banumathi, S.; Velmurugan, D.; Subramanian, E.; Ashish; Kishore, R. Acta Cryst 1999, C55, 78-79.
42. Thakur, A. K.; Ashish; Kishore, R. Chem Commun 1999, 1643-1644.
43. Thakur, A. K.; Kishore, R. Tetrahedron Lett 2001, 42, 4691-4694.
44. Royo, S.; De Borggraeve, W. M.; Peggion, C.; Formaggio, F.; Crisma, M.; Jiménez, A. I.; Cativiela, C.; Toniolo, C. J Am Chem Soc 2005, 127, 2036-2037.
45. Venkatachalam, C. M. Biopolymers 1968, 6, 1425-1436.
46. Chou, P. Y.; Fasman, G. D. J Mol Biol 1977, 115, 135-175.
47. Richardson, J. S. Adv Protein Chem 1981, 34, 167-339.
48. Rose, G. D.; Gierasch, L. M.; Smith, J. A. Adv Protein Chem 1985, 37, 1-109.
49. Wilmot, C. M.; Thornton, J. M. J Mol Biol 1988, 203, 221-232.
50. Gunasekaran, K.; Gomathi, L.; Ramakrishnan, C.; Chandrasekhar, J.; Balaram, P. J Mol Biol 1998, 284, 1505-1516.
51. Tainer, J. A.; Getzoff, E. D.; Beem, K. M.; Richardson, J. S.; Richardson, D. C. J Mol Biol 1982, 160, 181-217.
52. Rees, D. C.; Lewis, M.; Lipscomb, W. N. J Mol Biol 1983, 168, 367-387.
53. Abbadi, A.; Mcharfi, M.; Aubry, A.; Premilat, S.; Boussard, G.; Marraud, M. J Am Chem Soc 1991, 113, 2729-2735.
54. Duddy, W. J.; Nissink, J. W. M.; Allen, F.; Milner-White, E. J. Protein Sci 2004, 13, 3051-3055.
55. Taylor, R.; Kennard, O. J. Am. Chem. Soc. 1982, 104, 5063-5070.
56. Derewenda, Z. S.; Lee, L.; Derewenda, U. J Mol Biol 1995, 252, 248-262.
57. Desiraju, G. R. Angew Chem Int Ed Engl 1995, 34, 2311-2327.
58. Steiner, T. Chem Comm 1997, 727-734.
59. Musah, R. A.; Jensen, G. M.; Rosenfield, R. A.; McRee, D. E.; Goodin, D. B.; Bunte, S. W. J Am Chem Soc 1997, 119, 9083-9084.
60. Gu, Y.; Kar, T.; Scheiner, S. J Am Chem Soc 1999, 121, 4911-9422.
61. Desiraju, G. R.; Steiner, T. The Weak Hydrogen Bond in Structural Chemistry and Biology; Oxford University Press: Oxford, 1999.
62. Vargas, R.; Garza, J.; Dixon, D. A.; Hay, B. P. J Am Chem Soc 2000, 122, 4750-4755.
63. Scheiner, S.; Kar, T.; Gu, Y. J Biol Chem 2001, 276, 9832-9837.
64. Wüthrich, K. In NMR of Proteins and Nucleic Acids; John Wiley & Sons: New York, 1986.
65. Evans, J. N. S. In Biomolecular NMR Spectroscopy; Oxford University Press: Oxford, 1995.
66. Sheldrick, G. M. SHELXS-97: Program for the Solution and the Refinement of Crystal Structures from X-Ray Diffraction Data; University of Göttingen, Germany, 1997.
67. Benadetti, E.; Morelli, G.; Nemethy, G.; Scheraga, H. A. Int J Peptide Protein Res 1983, 22, 1-15.
68. Bella, J.; Berman, H. M. J Mol Biol 1996, 264, 734-742.
69. Wahl, M. C.; Sundaralingam, M. TIBS 1997, 22, 97-102.
70. Y.; Margalit, H.; Jernigan, R. L.; Zhurkin, V. B. J Mol Biol 1998, 277, 1129-1140.
71. Ghosh, A.; Bansal, M. J Mol Biol 1999, 294, 1149-1158.
72. Ho, B. K.; Curmi, P. M. G. J Mol Biol 2002, 317, 291-308.
73. Babu, M. M.; Singh, S. K.; Balaram, P. J Mol Biol 2002, 322, 871-880.
74. Klaholz, B. P.; Moras, D. Structure 2002, 10, 1197-1204.
75. Singh, S. K.; Babu, M. M.; Balaram, P. Proteins Struct Funct Genet 2003, 51, 167-171.
76. Loll, B.; Raszewski, G.; Saenger, W.; Biesiadka, J. J Mol Biol 2003, 328,737-747.
77. Manikandan, K.; Ramakumar, S. Proteins Struct Funct Bioinforrm 2004, 56, 768-781.
78. Derewenda, Z. S.; Derewenda, U.; Kobos, P. M. J Mol Biol 1994, 241, 83-93.
79. Chakrabarti, P.; Chakrabarti, S. J Mol Biol 1998, 284, 867-873.
80. Steiner, T.; Saenger, W. J Am Chem Soc 1993, 115, 4540-4547.
81. Thomas, K. T.; Smith, G. M.; Thomas, T. B.; Feldmann, R. J. Proc Natl Acad Sci USA 1982, 79, 4843-4847.
82. Gellman, S. H.; Powell, D. R.; Desper, J. M. Tetrahedron Lett 1992, 33, 1963-1964.
83. Thakur, A. K.; Venugopalan, P.; Kishore, R. J. Peptide Res 2000, 56, 55-58.
84. Crisma, M.; Formaggio, F.; Toniolo, C.; Yoshikawa, T.; Wakamiya, T. J Am Chem Soc 1999, 121, 3272-3278.
85. Aravinda, S.; Shamala, N.; Pramanik, A.; Das, C.; Balaram, P. Biochem Biophys Res Commun 2000, 273, 933-936.
86. Thakur, A. K.; Kishore, R. Biopolymers 2000, 53, 447-454.
87. Cheung, E. Y.; McCabe, E. E.; Harris, K. D. M.; Johnston, R. L.; Tedesco, E.; Raja, K. M. P.; Balaram, P. Angew Chem Int Ed Engl 2002, 41, 494-496.
88. Aubry, A.; Marraud, M. Acta Crystallogr 1985, C41, 65-67.
89. Wolf, W. M.; Stasiak, M.; Leplawy, M. T.; Bianco, A.; Formaggio, F.; Crisma, M.; Toniolo, C. J Am Chem Soc 1998, 120, 11558-11566.
90. Pert, C. B.; Hill, J. M.; Ruff, M. R.; Berman, R. M.; Robey, W. G.; Arthur, L. O.; Ruscetti, F. W.; Farrar, W. L. Proc Natl Acad Sci USA 1986, 83, 9254-9258.
91. Picone, D.; Temussi, P. A.; Marastoni, M.; Tomatis, R.; Motta, A. FEBS Lett 1988, 231, 159-163.
92. Toniolo, C.; Biano, A.; Maggini, M.; Scorrano, G.; Prato, M.; Marastoni, M.; Tomatis, R.; Spisani, S.; Palú, G.; Blair, E. D. J Med Chem 1994, 37, 4558-4562.
93. Picone, D.; Rivieccio, A.; Crescenzi, O.; Caliendo, G.; Santagada, V.; Perissutti, E.; Spisani, S.; Traniello, S.; Temussi, P. A. J Peptide Sci 2001, 7, 197-207.
94. Briskin, M. J.; McEvoy, L. M.; Butcher, E. C. Nature 1993, 363, 461-464.
95. Imperiali, B. Acc Chem Res 1997, 30, 452-457.
96. Imperiali, B.; O'Connor, S. E.; Hendrickson, T.; Kellenberger, C. Pure Appl Chem 1999, 1, 777-787.
97. Wu. W.; Pasternack, L.; Huang, D.; Koeller, M. K.; Lin, C. C.; Seitz, O.; Wong, C. J Am Chem Soc 1999, 121, 2409-2417.