Computational design of heterochiral peptides against a helical target

Journal of the American Chemical Society

Volumn 128, Issue 3, 2006, Pages 809-816

  Nanda, Vikas ^a,b   DeGrado, William F ^c  

^a RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTATION THEORY; CONFORMATIONS; MONTE CARLO METHODS; PROTEINS;

ENANTIOSELECTIVITY; HETEROCHIRAL INTERACTIONS; MOLECULAR RECOGNITION; PEPTIDE SCAFFOLDS;

POLYPEPTIDES;

AMINO ACID DERIVATIVE; PEPTIDE; POLYPEPTIDE;

ANALYTIC METHOD; ARTICLE; CHEMICAL STRUCTURE; CHIRALITY; COMPUTER AIDED DESIGN; ENANTIOSELECTIVITY; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; MONTE CARLO METHOD; PEPTIDE ANALYSIS; PROTEIN CONFORMATION; PROTEIN INTERACTION;

ALANINE; BIOMIMETIC MATERIALS; COMPUTER SIMULATION; DRUG DESIGN; MODELS, MOLECULAR; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; STEREOISOMERISM;

EID: 31444449249     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja054452t     Document Type: Article

References (71)

1. Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. Chem. Rev. 2001, 101, 3893-4011.
2. Aravinda, S.; Shamala, N.; Roy, R. S.; Balaram, P. Proc. Indian Acad. Sci., Chem. Sci. 2003, 115, 373-400.
3. Challis, G. L.; Naismith, J. H. Curr. Opin. Struct. Biol. 2004, 14, 748-756.
4. Finking, R.; Marahiel, M. A. Annu. Rev. Microbiol. 2004, 58, 453-488.
5. Wade, D.; Boman, A.; Wahlin, B.; Drain, C. M.; Andreu, D.; Boman, H. G.; Merrifield, R. B. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 4761-4765.
6. Oren, Z.; Hong, J.; Shai, Y. J. Biol. Chem. 1997, 272, 14643-14649.
7. Papo, N.; Shahar, M.; Eisenbach, L.; Shai, Y. J. Biol. Chem. 2003, 278, 21018-21023.
8. Van Regenmortel, M. H.; Muller, S. Curr. Opin. Biotechnol. 1998, 9, 377-382.
9. Shaw, J. P.; Petsko, G. A.; Ringe, D. Biochemistry 1997, 36, 1329-1342.
10. Watson, J. D.; Milner-White, E. J. J. Mol. Biol. 2002, 315, 183-191.
11. Chandrasekaran, R.; Ramachandran, G. N. In 2nd American Peptide Symposium, 1st ed.; Lande, S., Ed.; Gordon and Breach: Cleveland, OH, 1970; Vol. 2, pp 195-215.
12. Colonna-Cesari, F.; Premilat, S.; Heitz, F.; Spach, G.; Lotz, B. Macromolecules 1977, 10, 1284-1288.
13. Diblasio, B.; Benedetti, E.; Pavone, V.; Redone, C.; Gerber, C.; Lorenzi, G. P. Biopolymers 1989, 28, 203-214.
14. Heitz, F.; Detriche, G.; Vovelle, F.; Spach, G. Macromolecules 1981, 14, 47-50.
15. Hesselink, F. T.; Scheraga, H. A. Macromolecules 1972, 5, 455-463.
16. Lorenzi, G. P.; Gerber, C.; Jackle, H. Macromolecules 1985, 18, 154-159.
17. Lotan, N.; Hesselin, F. Th.; Benderly, H.; Van, J. F.; Schechter, I.; Berger, A.; Scheraga, H. A. Macromolecules 1973, 6, 447-453.
18. Ramachandran, G. N.; Ramakrishnan, C.; Sasisekharan, V. J. Mol. Biol. 1963, 7. 95 ff.
19. Rizzo, V.; Lorenzi, G. P. Macromolecules 1983, 16, 476-482.
20. Urry, D. W.; Goodall, M. C.; Glickson, J. D.; Mayers, D. F. Proc. Natl. Acad. Sci. U.S.A. 1971, 68, 1907 ff.
21. Veatch, W. R.; Fossel, E. T.; Blout, E. R. Biochemistry 1974, 13, 5249-5256.
22. Bamberg, E.; Apell, H. J.; Alpes, H. Proc. Natl. Acad. Sci. U.S.A. 1977, 74, 2402-2406.
23. Becker, N.; Oroudjev, E.; Mutz, S.; Cleveland, S. P.; Hansma, P. K.; Hayashi, C. Y.; Makarov, D. E.; Hansma, H. G. Nat. Mater. 2003, 2, 278-283.
24. Jourdan, F.; Lazzaroni, S.; Mendez, B. L.; Cantore, P. L.; Julio, M.; Amodeo, P.; Iacobellis, N. S.; Evidente, A.; Motta, A. Proteins: Struct., Funct., Genet. 2003, 52, 534-543.
25. Nutkins, J. C.; Mortishire-Smith, R. J.; Packman, L. C.; Brodey, C. L.; Rainey, P. B.; Johnstone, K.; Williams, D. H. J. Am. Chem. Soc. 1991, 113, 2621-2627.
26. Nanda, V.; DeGrado, W. F. J. Am. Chem. Soc. 2004, 126, 14459-14467.
27. Schellman, C. In Protein Folding; Jaenicke, R., Ed.; Elsevier/North- Holland: New York, 1980; pp 53-61.
28. Richardson, J. S.; Richardson, D. C. Science 1988, 240, 1648-1652.
29. Presta, L. G.; Rose, G. D. Science 1988, 240, 1632-1641.
30. Yin, H.; Hamilton, A. D. Angew. Chem. Int. Ed. 2005, 44, 4130-4163.
31. Orner, B. P.; Ernst, J. T.; Hamilton, A. D. J. Am. Chem. Soc. 2001, 123, 5382-5383.
32. Stephens, O. M.: Kim, S.; Welch, B. D.; Hodsdon, M. E.; Kay, M. S.; Schepartz, A. J. Am. Chem. Soc. 2005, 127, 13126-13127.
33. Gemperli, A. C.; Rutledge, S. E.; Maranda, A.; Schepartz, A. J. Am. Chem. Soc. 2005, 127, 1596-1597.
34. Kritzer, J. A.; Stephens, O. M.; Guarracino, D. A.; Reznik, S. K.; Schepartz, A. Bioorg. Med. Chem. 2005, 13, 11-16.
35. Benkirane, N.; Friede, M.; Guichard, G.; Briand, J. P.; Van Regenmortel, M. H.; Muller, S. J. Biol. Chem. 1993, 268, 26279-26285.
36. Chorev. M.; Goodman, M. Trends Biotechnol. 1995, 13, 438-445.
37. Gerber, D.; Shai, Y. J. Mol. Biol. 2002, 322, 491-495.
38. Sia, S. K.; Kim, P. S. Biochemistry 2001, 40, 8981-8989.
39. Sal-Man, N.; Gerber, D.; Shai, Y. J. Mol. Biol. 2004, 344, 855-864.
40. Chung, D. M.; Nowick, J. S. J. Am. Chem. Soc. 2004, 126, 3062-3063.
41. Hellinga, H. W.; Richards, F. M. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 5803-5807.
42. Kuhlman, B.; Baker, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 10383-10388.
43. Gordon, D. B.; Marshall, S. A.; Mayo, S. L. Curr. Opin. Struct. Biol. 1999, 9, 509-513.
44. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ohio, C.; Alagona, G.; Profeta, S. J.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765-784.
45. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. Chem. Phys. 1951, 21, 1087-1092.
46. Kumar, S.; Bansal, M. Biophys. J. 1998, 75, 1935-1944.
47. Bansal, M.; Kumar, S.; Velavan, R. J. Biomol. Struct. Dyn. 2000, 17, 811-819.
48. Lahr, S. J.; Engel, D. E.; Stayrook, S. E.; Maglio, O.; North, B.; Geremia, S.; Lombardi, A.; DeGrado, W. F. J. Mol. Biol. 2005, 346, 1441-1454.
49. Schneider, J. P.; DeGrado, W. F. J. Am. Chem. Soc. 1998, 120, 2764-2767.
50. Karle, I. L. Biopolymers 2001, 60, 351-365.
51. Aravinda, S.; Shamala, N.; Pramanik, A.; Das, C.; Balaram, P. Biochem. Biophys. Res. Commun. 2000, 273, 933-936.
52. Banerjee, A.; Raghothama, S. R.; Karle, I. L.; Balaram, P. Biopolymers 1996, 39, 279-285.
53. Chothia, C.; Levitt, M.; Richardson, D. J. Mol. Biol. 1981, 145, 215-250.
54. Kroon, J.; Kanters, J. A.; van Duijneveldt-van de Rijdt, J. G. C. M.; van Duijneveldt, F. B.; Vliegenthart, J. A. J. Mol. Struct. 1975, 24, 109-129.
55. Sibanda, B. L.; Blundell, T. L.; Thornton, J. M. J. Mol. Biol. 1989, 206, 759-777.
56. Sibanda, B. L.; Thornton, J. M. Nature 1985, 316, 170-174.
57. Gunasekaran, K.; Ramakrishnan, C.; Balaram, P. Protein Eng. 1997, 10, 1131-1141.
58. Golumbfskie, A. J.; Pande, V. S.; Chakraborty, A. K. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11707-11712.
59. Kriksin, Y. A.; Khalatur, P. G.; Khokhlov, A. R. J. Chem. Phys. 2005, 122, 114703.
60. Castells, V.; Yang, S. X.; Van Tassel, P. R. Phys. Rev. E 2002, 65, 031912.
61. Jayaraman, A.; Hall, C. K.; Genzer, J. Phys. Rev. Lett. 2005, 94, 078103.
62. Adams, P. D.; Arkin, I. T.; Engelman, D. M.; Brunger, A. T. Nat. Struct. Biol. 1995, 2, 154-162.
63. Torres, J.; Kukol, A.; Arkin, I. T. Biophys. J. 2001, 81, 2681-2692.
64. Li, H.; Tang, C.; Wingreen, N. S. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 4987-4990.
65. Emberly, E. G.; Winareen, N. S.; Tang, C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11163-11168.
66. Li, H.; Helling, R.; Tang, C.; Wingreen, N. Science 1996, 273, 666-669.
67. Saghatelian, A.; Yokobayashi, Y.; Soltani, K.; Ghadiri, M. R. Nature 2001, 409, 797-801.
68. Esler, W. P.; Stimson, E. R.; Fishman, J. B.; Ghilardi, J. R.; Vinters, H. V.; Mantyh, P. W.; Maggio, J. E. Biopolymers 1999, 49, 505-514.
69. Chalifour. R. J.; McLaughlin, R. W.; Lavoie, L.; Morissette, C.; Tremblay, N.; Boule, M.; Sarazin, P.; Stea, D.; Lacombe, D.; Tremblay, P.; Gervais, F. J. Biol. Chem. 2003, 278, 34874-34881.
70. Inai, Y.; Ousaka, N.; Okabe, T. J. Am. Chem. Soc. 2003, 125, 8151-8162.
71. Inai, Y.; Ishida, Y.; Tagawa, K.; Takasu, A.; Hirabayashi, T. J. Am. Chem. Soc. 2002, 124, 2466-2473.