The folding of acetyl(Ala)28NH2 and acetyl(Ala) 40NH2 extended strand peptides into antiparallel β-sheets. a density functional theory study of β-sheets with β-turns

Journal of Physical Chemistry B

Volumn 116, Issue 48, 2012, Pages 14017-14022

  Ali Torres, Jorge ^a   Dannenberg, J J ^a  

^a CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AQUEOUS SOLVATION; FOLDED STRUCTURES; OPTIMIZED STRUCTURES; SHEET FORMATION;

PHYSICAL CHEMISTRY; PHYSICS;

DENSITY FUNCTIONAL THEORY;

PEPTIDE; POLYALANINE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; HYDROGEN BOND; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

HYDROGEN BONDING; MODELS, MOLECULAR; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

EID: 84870775815     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp3094947     Document Type: Article

References (40)

1. Plumley, J. A.; Dannenberg, J. J. J. Phys. Chem. B 2011, 115, 10560
2. Plumley, J. A.; Tsai, M. I.-H.; Dannenberg, J. J. J. Phys. Chem. B 2011, 115, 1562
3. Viswanathan, R.; Asensio, A.; Dannenberg, J. J. J. Phys. Chem. A 2004, 108, 9205
4. Zhao, Y.-L.; Wu, Y.-D. J. Am. Chem. Soc. 2002, 124, 1570
5. Suhai, S. Int. J. Quantum Chem. 1991, 40, 559
6. Perczel, A.; Gaspari, Z.; Csizmadia, I. G. J. Comput. Chem. 2005, 26, 1155
7. Scheiner, S. J. Phys. Chem. B 2006, 110, 18670-18679
8. Wang, C.-S.; Sun, C.-L. J. Comput. Chem. 2010, 31, 1036
9. Ireta, J. J. Chem. Theory Comput. 2011, 7, 2630
10. Morokuma, K. Bull. Korean Chem. Soc. 2003, 24, 797
11. Vreven, T.; Morokuma, K. J. Chem. Phys. 2000, 113, 2969
12. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A. Gaussian 09, revision A.2.; Gaussian, Inc.: Wallingford CT, 2009.
13. Becke, A. D. J. Chem. Phys. 1993, 98, 5648
14. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785
15. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902
16. Turi, L.; Dannenberg, J. J. J. Phys. Chem. 1993, 97, 2488
17. Simon, S.; Duran, M.; Dannenberg, J. J. J. Chem. Phys. 1996, 105, 11024
18. Wieczorek, R.; Dannenberg, J. J. J. Am. Chem. Soc. 2003, 125, 8124
19. Wieczorek, R.; Dannenberg, J. J. J. Am. Chem. Soc. 2004, 126, 14198
20. Marianski, M.; Asensio, A.; Dannenberg, J. J. J. Chem. Phys. 2012, 137, 044109
21. Roy, D.; Marianski, M.; Maitra, N.; Dannenberg, J. J. J. Chem. Phys. 2012, 137, 134109
22. Plumley, J. A.; Dannenberg, J. J. J. Comput. Chem. 2011, 32, 1519
23. Simon, S.; Duran, M.; Dannenberg, J. J. J. Phys. Chem. A 1999, 103, 1640
24. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 1998, 102, 3257
25. Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102, 1995
26. Cossi, M.; Rega, N.; Scalmani, G.; Barone, V. J. Comput. Chem. 2003, 24, 669
27. Besler, B. H.; Merz, K. M.; Kollman, P. A. J. Comput. Chem. 1990, 11, 431
28. AMPAC, 8.16 ed.; Semichem, Inc.: Shawnee, KS.
29. Marianski, M.; Dannenberg, J. J. J. Phys. Chem. B 2012, 116, 1437
30. Tsai, M. I.-H.; Xu, Y.; Dannenberg, J. J. J. Phys. Chem. B 2009, 113, 309
31. Salvador, P.; Asensio, A.; Dannenberg, J. J. J. Phys. Chem. B 2007, 111, 7462
32. Lewis, P. N.; Momany, F. A.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1971, 68, 2293
33. Rose, G. D.; Glerasch, L. M.; Smith, J. A. Adv. Protein Chem. 1985, 37, 1
34. Kuo-Chen, C. Anal. Biohem. 2000, 286, 1
35. Venkatachalam, C. M. Biopolymers 1968, 6, 1425
36. Roy, D.; Pohl, G.; Ali-Torres, J.; Marianski, M.; Dannenberg, J. J. Biochemistry 2012, 51, 5387
37. Plumley, J. A.; Dannenberg, J. J. J. Am. Chem. Soc. 2010, 132, 1758-1759
38. Roy, D.; Dannenberg, J. J. Chem. Phys. Lett. 2011, 512, 255
39. Sikorski, P.; Atkins, E. Biomacromolecules 2005, 6, 425
40. Perutz, M. F.; Johnson, T.; Suzuki, M.; Finch, J. T. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 5355