Intrinsically Stable Secondary Structure Elements of Proteins: A Comprehensive Study of Folding Units of Proteins by Computation and by Analysis of Data Determined by X-ray Crystallography

Chemistry - A European Journal

Volumn 9, Issue 21, 2003, Pages 5332-5342

  Perczel, András ^a   Jákli, Imre ^a   Csizmadia, Imre G ^a,b  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Ab initio calculations; Peptides; Protein structures; Secondary structure elements; Structure energy correlations

Indexed keywords

AMINO ACIDS; CONFORMATIONS; MOLECULAR STRUCTURE; OLIGOMERS; X RAY CRYSTALLOGRAPHY;

AB INITIO PROCESSES; HETEROCONFORMATIONS; HOMOCONFORMATIONS;

PROTEINS;

ALANINE DERIVATIVE; GLYCINE DERIVATIVE; OLIGOPEPTIDE; PROTEIN;

ADDITION REACTION; AQUEOUS SOLUTION; ARTICLE; CHIRALITY; CONFORMATIONAL TRANSITION; CRYSTALLIZATION; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN DETERMINATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; REACTION OPTIMIZATION; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

COMPUTERS, MOLECULAR; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; OLIGOPEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0344065556     PISSN: 09476539     EISSN: None     Source Type: Journal    
DOI: 10.1002/chem.200304843     Document Type: Article

References (38)

1. Gaussian 98 (Revision A. 7), M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, Ö. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komáromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M. W. Gill, B. G. Johnson, W. Chen, M. W. Wong, J. L. Andres, M. Head-Gordon, E. S. Replogle, J. A. Pople, Gaussian, Inc., Pittsburgh, PA, 1998.
2. Ö. Farkas, H. Bernhard Schlegel, J. Chem. Phys. 2003, in press.
3. P. Pulay, Chem. Phys. Lett. 1980, 73, 393-398.
4. P. Pulay, J. Comp. Chem. 1982, 3, 556-560.
5. P. Császár, P. Pulay, J. Mol. Struct. (Theochem) 1984, 114, 31-34.
6. G. Endrédi, A. Perczel, Ö. Farkas, M. A. McAllister, G. I. Csonka, J. Ladik, I. G. Csizmadia, J. Mol. Struct. (Theochem) 1997, 391, 15-26.
7. K. Möhle, H.-J. Hoffman, J. Mol. Model. 1998, 4, 53-60.
8. A. Perczel, Ö. Farkas, I. Jákli, I. A. Topol, unpublished results.
9. U. Hobohm, M. Charf, R. Schneider, C. Sander, Prot. Sci. 1992, 1, 409-417.
10. U. Hobohm, C. Sander, Prot. Sci. 1994, 3, 522-524.
11. C. Ramakrishnan, G. N. Ramachandran, Biophys. J. 1965, 5, 909.
12. A. Perczel, J. G. Angyán, M. Kajtár, W. Viviani, J.-L. Rivail, J.-F. Marcoccia, I. G. Csizmadia, J. Am. Chem. Soc. 1991, 113, 6256-6265.
13. IUPAC/IUB Commission on Biochemical Nomenclature, Abbreviations and symbols for description of conformation of polypeptide chains-Tentative rules: Biochemistry 1969, 9, 3471.
14. I. Simon, L. Glasser, H. A. Scheraga, Proc. Natl. Acad. Sci. USA 1991, 88, 3661-3665.
15. I. L. Shamovsky, G. M. Ross, R. J. Riopelle, J. Phys. Chem. B 2000, 104, 11296-11307.
16. C. Park, W. A. Goddard III, J. Phys. Chem. B. 2000, 104, 7784-7789.
17. M. D. Beachy, D. Chasman, R. B. Murphy, T. A. Halgren, R. A. Friesner, J. Am. Chem. Soc. 1997, 119, 5908-5920.
18. P. Derreumaux, Theor. Chem. Acc. 2000, 104, 1-6.
19. F. Forcellino, P. Derreumaux, Struct. Funct. Genet. 2001, 45, 159-166.
20. G. Némethy, H. A. Scheraga, Biopolymers 1965, 3, 155.
21. F. A. Momany, R. F. McGuire, A. W. Burgess, H. A. Scheraga, J. Phys. Chem. 1975, 79, 2361-2381.
22. S. J. Leach, G. Nemethy, H. A. Scheraga, Biopolymers 1966, 4, 369.
23. J. C. Howard, A. Ali, H. A. Scheraga, F. A. Momany, Macromolecules 1975, 8, 607-622.
24. S. S. Zimmerman, M. A. Pottle, G. Nemethy, H. A. Scheraga, Macromolecules 1977, 10, 1-9.
25. J. N. Scarsdale, C. Van Alsenoy, V. J. Klimkowski, L. Schäfer, F. A. Momany, J. Am. Chem. Soc. 1983, 105, 3438-3445.
26. L. Schäfer, C. Van Alsenoy, J. N. Scharsdale, J. Chem. Phys. 1982, 76, 1439-1444.
27. L. Schäfer, V. J. Kimkowski, F. A. Momany, H. Chuman, C. Van Alsenoy, Biopolymers 1984, 23, 2335-2347.
28. L. Schäfer, S. Q. Newton, M. Cao, A. Peeters, C. Van Alsenoy, K. Wolinski, F. A. Momany, J. Am. Chem. Soc. 1993, 115, 272-280.
29. A. M. Sapse, B. S. Schweitzer, A. P. Dicker, J. R. Bertino, V. Frecer, Int. J. Pept. Prot. Res. 1992, 39, 18-23.
30. A. Perczel, I. G. Csizmadia, The amide linkage, structural significance in chemistry, biochemistry and materials sciences (Eds.: A. Greenberg, C. M. Breneman, J. F. Liebman), Wiley, New York, 2000, pp. 409-463.
31. A. G. Császár, A. Perczel, Progr. Biophys. Mol. Biol. 1999, 71, 243-309.
32. M. A. Berg, G. A. Chasse, E. Deretey, A. K. Füzéry, B. M. Fung, D. Y. K. Fung, H. Henry-Riyad, A. C. Lin, M. L. Mak, A. Mantas, I. V. Repyakh, M. Staikova, S. J. Salpietro, T. H. Tang, J. C. Vank, A. Perczel, G. I. Csonka, Ö. Farkas, L. L. Torday, Z. Székey, I. G. Csizmadia, J. Mol. Struct. (THEOCHEM) 2000, 500, 5-59.
33. A. Perczel, M. A. McAllister, P. Császár, I. G. Csizmadia, J. Am. Chem. Soc. 1993, 115, 4849-4858.
34. M. A. McAllister, A. Perczel, P. Császár, I. G. Csizmadia, J. Mol. Struct. (THEOCHEM) 1993, 290, 181-198.
35. A. Perczel, M. A. McAllister, P. Császár, I. G. Csizmadia, Can. J. Chem. 1994, 72, 2050-2070.
36. C.-H. Yu, L. Schafer, M. Ramek, J. Phys. Chem. A. 1999, 103, 8337-8345.
37. A. Perczel, G. Endrédi, M. A. McAllister, Ö. Farkas, P. Császár, J. Ladik, I. G. Csizmadia, J. Mol. Struct. (THEOCHEM) 1994, 331, 5-10.
38. I. A. Topol, S. K. Burt, E. Deretey, T.-H. Tang, A. Perczel, A. Rashin, I. G. Csizmadia, J. Am. Chem. Soc. 2001, 123, 6054-6060.