Investigating diproline segments in proteins: Occurrences, conformation and classification

Biopolymers

Volumn 97, Issue 1, 2012, Pages 54-64

  Saha, Indranil ^a,b   Shamala, Narayanaswamy ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b SINCROTRONE TRIESTE   (Italy)

Author keywords

cis Pro Pro peptide bond; conformational states; diproline segments; flanking residue conformation; trans Pro Pro peptide bond

Indexed keywords

CONFORMATIONAL STATE; DIPROLINE SEGMENTS; FLANKING RESIDUE CONFORMATION; PEPTIDE BONDS; TRANS PRO-PRO PEPTIDE BOND;

AMINO ACIDS;

PEPTIDES;

PROLINE; PYRROLIDINE DERIVATIVE;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL BOND; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE;

ALGORITHMS; AMINO ACID MOTIFS; DIPEPTIDES; HYDROGEN BONDING; MODELS, MOLECULAR; PROLINE; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; STEREOISOMERISM;

EID: 80055052594     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.21703     Document Type: Article

References (59)

1. Chou, P. Y.,;, Fasman, G. D., J Mol Biol 1977, 115, 135-175.
2. Wilmot, C. M.,;, Thornton, J. M., J Mol Biol 1988, 203, 221-232.
3. Richardson, J. S.,;, Richardson, D. C., Prediction of Protein Conformation; Plenum: New York, 1989; pp 1-98.
4. Richardson, J. S.,;, Richardson, D. C., Trends Biochem Sci 1989, 14, 304-309.
5. Chatterjee, B.,;, Saha, I.,;, Raghothama, S.,;, Aravinda, S.,;, Rai, R.,;, Shamala, N.,;, Balaram, P., ChemâEur J 2008, 14, 6192-6204.
6. Saha, I.,;, Chatterjee, B.,;, Shamala, N.,;, Balaram, P., Biopolymers (Peptide Sci) 2008, 90, 537-543.
7. Levitt, M., J Mol Biol 1981, 145, 251-263.
8. MacArthur, M. W.,;, Thornton, J. M., J Mol Biol 1991, 218, 397-412.
9. Reimer, U.,;, Scherer, G.,;, Drewello, M.,;, Kruber, S.,;, Schutkowski, M,;, Fischer, G., J Mol Biol 1998, 279, 449-460.
10. Eyles, S. J.,;, Gierasch, L. M., J Mol Biol 2000, 301, 737-747.
11. Schimmel, P. R.,;, Flory, P. J., J Mol Biol 1968, 34, 105-120.
12. Chou, P. Y.,;, Fasman, G. D., Biochemistry 1974, 13, 211-222.
13. Chou, P. Y.,;, Fasman, G. D., Biochemistry 1974, 13, 222-245.
14. Anfinsen, C. B.,;, Scheraga, H. A., Adv Protein Chem 1975, 29, 205-300.
15. Robson, B.,;, Suzuki, E., J Mol Biol 1976, 107, 327-356.
16. Zimmerman, S. S.,;, Scheraga, H. A., Proc Natl Acad Sci USA 1977, 74, 4126-4129.
17. Richardson, J. S.,;, Richardson, D. C., Science 1988, 240, 1648-1652.
18. Smith, C. K.,;, Withka, J. M.,;, Regan, L., Biochemistry 1994, 33, 5510-5517.
19. Minor, D.L., Jr. ,;, Kim, P. S., Nature 1994, 367, 660-663.
20. Piela, L.,;, Nemethy, G.,;, Scheraga, H. A., Biopolymers 1987, 26, 1587-1600.
21. Presta, L. G.,;, Rose, G. D., Science 1988, 240, 1632-1641.
22. Yun, R. H.,;, Anderson, A. D.,;, Hermans, J., Proteins Struct Funct Genet 1991, 10, 219-228.
23. Adzhubei, A. A.,;, Sternberg, M. J. E., J Mol Biol 1993, 229, 472-493.
24. Aurora, R.,;, Rose, G. D., Protein Sci 1998, 7, 21-38.
25. Gunasekaran, K.,;, Gomathi, L.,;, Ramakrishnan, C.,;, Balaram, P., J Mol Biol 1998, 284, 1505-1516.
26. Viguera, A. R.,;, Serrano, L., Protein Sci 1999, 8, 1733-1742.
27. Kim, M. K.,;, Kang. Y. K., Protein Sci 1999, 8, 1492-1499.
28. Chakrabarti, P.,;, Chakrabarti, S., J Mol Biol 1998, 284, 867-873.
29. Searle, M. S.,;, Williams, D. H.,;, Packman, L. C., Nat Struct Biol 1995, 2, 999-1006.
30. Gunasekaran, K.,;, Ramakrishnan, C.,;, Balaram, P., Protein Eng 1997, 10, 1131-1141.
31. Simpson, E. R.,;, Meldrum, J. K.,;, Bofill, R.,;, Crespo, M. D,;, Holmes, E.,;, Searle, M. S., Angew Chem Int Ed Engl 2005, 44, 4939-4944.
32. Bofill, R,;, Simpson, E. R.,;, Platt, G. W.,;, Crespo, M. D.,;, Searle, M. S., J Mol Biol 2005, 349, 205-221.
33. Venkatachalapathi, Y. V.,;, Balaram, P., Nature 1979, 281, 83-84.
34. Smith, J. A.,;, Pease, L. G., CRC Crit Rev Biochem 1980, 8, 315-399.
35. Balaram, P., Proc Ind Acad Sci Chem Sci 1984, 93, 703-717.
36. Sibanda, B. L.,;, Thornton, J. M., Nature 1985, 316, 170-174.
37. Gellman, S. H., Curr Opin Chem Biol 1998, 2, 717-725.
38. Balaram, P., J Pept Res 1999, 54, 195-199.
39. Kaul, R.,;, Balaram, P., Bioorg Med Chem 1999, 7, 105-117.
40. Tanaka, S.,;, Scheraga, H. A., Macromolecules 1974, 7, 698-705.
41. Richardson, J. S., Adv Protein Chem 1981, 34, 167-339.
42. Hutchinson, E. G.,;, Thornton, J. M., Protein Sci 1994, 3, 2207-2216.
43. Brandts, J. F.,;, Halvorson, H. R.,;, Brennan, M., Biochemistry 1975, 14, 4953-4963.
44. Grathwohl, C.,;, Wuthrich, K., Biopolymers 1976, 15, 2025-2041.
45. Ramachandran, G. N.,;, Mitra, A. K., J Mol Biol 1976, 107, 85-92.
46. Pauling, L., J Am Chem Soc 1940, 62, 2643-2657.
47. Edsall, J. T., J Polym Sci 1954, 12, 253-280.
48. Toma, F.,;, Fermandjian, S.,;, Low, M.,;, Kisfaludy, L., Biochim Biophys Acta 1978, 534, 112-122.
49. Stewart, D. E.,;, Sarkar, A.,;, Wampler, J. E., J Mol Biol 1990, 214, 253-260.
50. Pal, D.,;, Chakrabarti, P., J Mol Biol 1999, 294, 271-288.
51. Wedemeyer, W. J.,;, Welker, E.,;, Scheraga, H. A., Biochemistry 2002, 41, 14637-14644.
52. Bernstein, F. C.,;, Koetzle, T. F.,;, Williams, G. J. B.,;, Meyer, E. F. Jr. ,;, Brice, M. D.,;, Rodgers, J. R.,;, Kennard, O.,;, Shimanouchi, T.,;, Tasumi M., J Mol Biol 1977, 112, 535-542.
53. Wang, G.,;, Dunbrack, R. L., Jr. , Bioinformatics 2003, 19, 1589-1591.
54. Creamer, T. P., Proteins Struct Funct Genet 1998, 33, 218-226.
55. Rai, R.,;, Aravinda, S.,;, Kanagarajadurai, K.,;, Raghothama, S.,;, Shamala, N.,;, Balaram, P., J Am Chem Soc 2006, 128, 7916-7928.
56. Couture, J. F.,;, Collazo, E.,;, Hauk, G.,;, Trievel, R. C., Nat Struct Mol Biol 2006, 13, 140-146.
57. Brown, G.,;, Singer, A.,;, Proudfoot, M.,;, Skarina, T.,;, Kim, Y.,;, Chang, C.,;, Dementieva, I.,;, Kuznetsova, E.,;, Gonzalez, C. F.,;, Joachimiak, A.,;, Savchenko, A.,;, Yakunin, A. F., Biochemistry 2008, 47, 5724-5735.
58. Huvent, I.,;, Belrhali, H.,;, Antoine, R.,;, Bompard, C.,;, Locht, C.,;, Dubuisson, F. J.,;, Villeret, V., J Mol Biol 2006, 356, 1014-1026.
59. Videau, L. L.,;, Arendall, W. B., III,;, Richardson, J. S., Proteins Struct Funct Bioinformatics 2004, 56, 298-309.