Simulated evolution of emergent chiral structures in polyalanine

Journal of the American Chemical Society

Volumn 126, Issue 44, 2004, Pages 14459-14467

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

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYMERS; PROTEINS; STEREOCHEMISTRY;

CHIRAL STRUCTURES; PROTEIN FOLDING;

MONOMERS;

ALANINE; MONOMER; POLYALANINE; POLYMER; POLYPEPTIDE; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CHEMICAL STRUCTURE; CHIRALITY; EPIMERIZATION; HOMOCHIRALITY; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STEREOCHEMISTRY; STEREOISOMERISM; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; PEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; STEREOISOMERISM; THERMODYNAMICS;

EID: 7744230016     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0461825     Document Type: Article

References (84)

1. Kuhlman, B.; Dantas, G.; Ireton, G. C.; Varani, G.; Stoddard, B. L.; Baker, D. Science 2003, 302, 1364-1368.
2. Harbury, P. B.; Plecs, J. J.; Tidor, B.; Alber, T.; Kim, P. S. Science 1998, 282, 1462-1467.
3. Walsh, S. T.; Cheng, H.; Bryson, J. W.; Roder, H.; DeGrado, W. F. Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 5486-5491.
4. Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. Chem. Rev. 2001, 101, 3893-4011.
5. Nakano, T.; Okamoto, Y. Chem. Rev. 2001, 101, 4013-4038.
6. Aravinda, S.; Shamala, N.; Roy, R. S.; Balaram, P. P. Natl. Acad. Sci. U. S. A. 2003, 115, 373-400.
7. Pauling, L.; Corey, R. B.; Branson, H. R. P. Natl. Acad. Sci. U. S. A. 1951, 37, 205-211.
8. Ramachandran, G. N.; Ramakrishnan, C.; Sasisekharan, V. J. Mol. Biol. 1963, 7, 95-99.
9. Chandras, R.; Lakshmin, Av; Pandya, U. V.; Ramachan. Gn Biochim. Biophys. Acta 1973, 303, 14-27.
10. Milton, R. C.; Milton, S. C.; Kent, S. B. Science 1992, 256, 1445-1448.
11. Hermans, J.; Andersen, A. G.; Yun, R. H. Biochemistry 1992, 31, 5646-5653.
12. Soares, T. A.; Lins, R. D.; Longo, R.; Garratt, R.; Ferreira, R. Z. Naturforsch., C. Biosci. 1997, 52c, 89-96.
13. Wald, G. Ann. N.Y. Acad. Sci. 1957, 69, 352-368.
14. Krause, E.; Bienert, M.; Schmieder, P.; Wenschuh, H. J. Am. Chem. Soc. 2000, 122, 4865-4870.
15. Fairman, R.; Anthony-Cahill, S. J.; DeGrado, W. F. J. Am. Chem. Soc. 1992, 114, 5458-5459.
16. Green, M. M.; Peterson, N. C.; Sato, T.; Teramoto, A.; Cook, R.; Lifson, S. Science 1995, 268, 1860-1866.
17. Lifson, S.; Andreola, C.; Peterson, N. C.; Green, M. M. J. Am. Chem. Soc. 1989, 111, 8850-8858.
18. Green, M. M.; Garetz, B. A.; Munoz, B.; Chang, H. P. J. Am. Chem. Soc. 1995, 117, 4181-4182.
19. Selinger, J. V.; Selinger, R. L. B. Phys. Rev. Lett. 1996, 76, 58-61.
20. Teramoto, A. Prog. Polym. Science 2001, 26, 667-720.
21. Zimm, B. H.; Bragg, J. K. J. Chem. Phys. 1959, 31, 526-535.
22. Young, J. A.; Cook, R. C. Macromolecules 2001, 34, 3646-3653.
23. Lifson, S.; Felder, C. E.; Green, M. M. Macromolecules 1992, 25, 4142-4148.
24. Rizzo, V.; Lorenzi, G. P. Macromolecules 1983, 16, 476-482.
25. Colonnacesari, F.; Premilat, S.; Heitz, F.; Spach, G.; Lotz, B. Macromolecules 1977, 10, 1284-1288.
26. Heitz, F.; Detriche, G.; Vovelle, F.; Spach, G. Macromolecules 1981, 14, 47-50.
27. Hesselin, Ft; Scheraga, H. A. Macromolecules 1972, 5, 455-462.
28. Urry, D. W. P. Natl. Acad. Sci. U. S. A. 1971, 68, 672-76.
29. Veatch, W. R.; Fossel, E. T.; Blout, E. R. Biochemistry-US 1974, 13, 5249-5256.
30. Bamberg, E.; Apell, H. J.; Alpes, H. P. Natl. Acad. Sci. U. S. A. 1977, 74, 2402-2406.
31. Becker, N.; Oroudjev, E.; Mutz, S.; Cleveland, J. P.; Hansma, P. K.; Hayashi, C. Y.; Makarov, D. E.; Hansma, H. G. Nat. Mater. 2003, 2, 278-283.
32. Hellinga, H. W.; Richards, F. M. P. Natl. Acad. Sci. U. S. A. 1994, 91, 5803-5807.
33. Hansmann, U. H. E.; Okamoto, Y. Curr. Opin. Struc. Biol. 1999, 9, 177-183.
34. Shakhnovich, E. I.; Gutin, A. M. P. Natl. Acad. Sci. U. S. A. 1993, 90, 7195-7199.
35. Shakhnovich, E. I.; Gutin, A. M. Protein Eng. 1993, 6, 793-800.
36. Shakhnovich, E. I.; Gutin, A. M. Biophys. Chem. 1989, 34, 187-199.
37. Shakhnovich, E. I.; Gutin, A. M. Nature 1990, 346, 773-775.
38. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. Chem. Phys. 1951, 21, 1087-1092.
39. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. Science 1983, 220, 671-680.
40. Smythe, M. L.; Huston, S. E.; Marshall, G. R. J. Am. Chem. Soc. 1995, 117, 5445-5452.
41. Dahiyat, B. I.; Mayo, S. L. P. Natl. Acad. Sci. U. S. A. 1997, 94, 10172-10177.
42. Kuhlman, B.; Baker, D. P. Natl. Acad. Sci. U. S. A. 2000, 97, 10383-10388.
43. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S. J.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765-784.
44. Gordon, D. B.; Marshall, S. A.; Mayo, S. L. Curr. Opin. Struc. Biol. 1999, 9, 509-513.
45. Clustering was performed using kclust (http://mmstb.scripps.edu) with a mean angular devation cutoff of 60° within structure families.
46. Karle, I. L.; Balaram, P. Biochemistry-Us 1990, 29, 6747-6756.
47. Barlow, D. J.; Thornton, J. M. J. Mol. Biol. 1988, 201, 601-619.
48. Takano, M.; Yamato, T.; Higo, J.; Suyama, A.; Nagayama, K. J. Am. Ghent. Soc. 1999, 121, 605-612.
49. Miick, S. M.; Martinez, G. V.; Fiori, W. R.; Todd, A. P.; Millhauser, G. L. Nature 1992, 359, 653-655.
50. Armen, R.; Alonso, D. O. V.; Daggett, V. Protein Sci. 2003, 12, 1145-1157.
51. Karpen, M. E.; Dehaseth, P. L.; Neet, K. E. Protein Sci. 1992, 1, 1333-1342.
52. Goodman, M.; Verdini, A. S.; Toniolo, C.; Phillips, W. D.; Bovey, F. A. P. Natl. Acad. Sci. U. S. A. 1969, 64, 444-450.
53. Lifson, S.; Roig, A. J. Chem. Phys. 1961, 34, 1963-1974.
54. Brooks, C. L. J. Phys. Chem-Us 1996, 100, 2546-2549.
55. Young, W. S.; Brooks, C. L. J. Mol. Biol. 1996, 259, 560-572.
56. Rohl, C. A.; Scholtz, J. M.; York, E. J.; Stewart, J. M.; Baldwin, R. L. Biochemistry-Us 1992, 31, 1263-1269.
57. Daggett, V.; Kollman, P. A.; Kuntz, I. D. Biopolymers 1991, 31, 1115-1134.
58. Sibanda, B. L.; Blundell, T. L.; Thornton, J. M. J. Mol. Biol. 1989, 206, 759-777.
59. Sibanda, B. L.; Thornton, J. M. Nature 1985, 316, 170-174.
60. Rajashankar, K. R.; Ramakumar, S. Protein Sci. 1995, 5, 932-946.
61. Gunasekaran, K.; Ramakrishnan, C.; Balaram, P. Protein Eng. 1997, 10, 1131-1141.
62. Schellman, C. In Protein Folding; Jaenicke, R., Ed.; Elsevier/North- Holland: New York, 1980; pp 53-61.
63. Presta, L. G.; Rose, G. D. Science 1988, 240, 1632-1641.
64. Richardson, J. S.; Richardson, D. C. Science 1988, 240, 1648-1652.
65. Aurora, R.; Rose, G. D. Protein. Sci. 1998, 7, 21-38.
66. Chou, K. C.; Scheraga, H. A. P. Natl. Acad. Sci. U. S. A. 1982, 79, 7047-7051.
67. Hesselink, F. T.; Scheraga, H. A. Macromolecules 1972, 5, 455-463.
68. Chandrasekaran, R.; Ramachandran, G. N. In 2nd American Peptide Symposium, First ed.; Lande, S., Ed.; Gordon and Breach; Cleveland, OH, 1970; Vol. 2. pp 195-215.
69. Dill, K. A. Biochemistry-Us 1990, 29, 7133-7155.
70. Kolinski, A.; Skolnick, J. J. Chem. Phys. 1992, 97, 9412-9426.
71. Pappu, R. V.; Srinivasan, R.; Rose, G. D. P. Natl. Acad. Sci. U. S. A. 2000, 97, 12565-12570.
72. Aravinda, S.; Shamala, N.; Pramanik, A.; Das, C.; Balaram, P. Biochem. Biophys. Res. Comm. 2000, 273, 933-936.
73. Aravinda, S.; Shamala, N.; Bandyopadhyay, A.; Balaram, P. J. Am. Chem. Soc. 2003, 125, 15065-15075.
74. Schneider, J. P.; DeGrado, W. F. J. Am. Chem. Soc. 1998, 120, 2764-2767.
75. Inai, Y.; Ishida, Y.; Tagawa, K.; Takasu, A.; Hirabayashi, T. J. Am. Chem. Soc. 2002, 124, 2466-2473.
76. Shamala, N.; Nagaraj, R.; Balaram, P. J. Chem. Soc. Chem. Comm. 1978, 996-997.
77. Inai, Y.; Kurokuwa, Y.; Kojima, N. J. Chem. Soc.. Perkin Transactions 2: Phys. Org. Chem. 2002, 1850-1857.
78. Karle, I. L. Biopolymers 2001, 60, 351-365.
79. Karle, I. L.; Banerjee, A.; Balaram, P. Folding & Design 1997, 2, 203-210.
80. Vriend, G. J. Mol. Graph. 1990, 8, 52-56.
81. Shaw, J. P.; Petsko, G. A.; Ringe, D. Biochemistry 1997,36, 1329-1342.
82. 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.
83. Elofsson, A.; Legrand, S. M.; Eisenberg, D. Proteins, Struct. Funct. Genet. 1995, 23, 73-82.
84. Navarro, E.; Fenude, E.; Celda, B. Biopolymers 2002, 64, 198-209.