Interplay of hydrogen bonds and n →π* interactions in proteins

Journal of the American Chemical Society

Volumn 135, Issue 49, 2013, Pages 18682-18688

  Bartlett, Gail J ^a   Newberry, Robert W ^b   Vanveller, Brett ^b   Raines, Ronald T ^b   Woolfson, Derek N ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTRON DELOCALIZATION; ELECTROSTATIC EFFECT; HYDROPHOBIC EFFECT; NATURAL BOND ORBITAL ANALYSIS; PROTEIN STABILITY; PROTEIN STRUCTURES; VAN DER WAALS INTERACTIONS; WEAK INTERACTIONS;

AMINO ACIDS; CHAINS; OXYGEN; PROTEINS; VAN DER WAALS FORCES;

HYDROGEN BONDS;

ASPARAGINE; CARBONYL DERIVATIVE; HYDROGEN; OXYGEN;

ARTICLE; CRYSTAL STRUCTURE; HYDROGEN BOND; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE;

ASPARAGINE; HYDROGEN BONDING; PROTEINS; STATIC ELECTRICITY;

EID: 84890509133     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja4106122     Document Type: Article

References (36)

1. Anfinsen, C. B. Science 1973, 181, 223
2. Dill, K. Biochemistry 1990, 29, 7133
3. Hinderaker, M. P.; Raines, R. T. Protein Sci. 2003, 12, 1188
4. Choudhary, A.; Raines, R. T. Protein Sci. 2011, 20, 1077
5. Raines, R. T.; Choudhary, A.; Gandla, D.; Krow, G. R. J. Am. Chem. Soc. 2009, 131, 7244
6. Bartlett, G. J.; Choudhary, A.; Raines, R. T.; Woolfson, D. N. Nat. Chem. Biol. 2010, 6, 615
7. Alabugin, I. V.; Manoharan, M.; Peabody, S.; Weinhold, F. J. Am. Chem. Soc. 2003, 125, 5973
8. Newberry, R. W.; VanVeller, B.; Guzei, I.; Raines, R. T. J. Am. Chem. Soc. 2013, 135, 7843
9. Creighton, T. E. Proteins: Structures and Molecular Properties; 2 nd ed.; Freeman: New York, 1993.
10. Der, B.; Jha, R. Proteins 2013, 81, 1245
11. Stranges, P. B.; Kuhlman, B. Protein Sci. 2013, 22, 74
12. Shoulders, M. D.; Kotch, F. W.; Choudhary, A.; Guzei, I. A.; Raines, R. T. J. Am. Chem. Soc. 2010, 132, 10857
13. Erdmann, R. S.; Wennemers, H. Angew. Chem., Int. Ed. 2011, 50, 6835
14. Erdmann, R. S.; Wennemers, H. J. Am. Chem. Soc. 2012, 134, 17117
15. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235
16. Deane, C. M.; Allen, F. H.; Taylor, R.; Blundell, T. L. Protein Eng. 1999, 12, 1025
17. Pal, T. K.; Sankararamakrishnan, R. J. Mol. Graphics Modell. 2008, 27, 20
18. Pal, T. K.; Sankararamakrishnan, R. J. Phys. Chem. B 2010, 114, 1038
19. Vasudev, P. G.; Banerjee, M.; Ramakrishnan, C.; Balaram, P. Proteins 2012, 80, 991
20. Morozov, A. V.; Kortemme, T.; Tsemekhman, K.; Baker, D. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 6946
21. Baker, D.; Kortemme, T.; Morozov, A. V. J. Mol. Biol. 2003, 326, 1239
22. Kuhlman, B.; Dantas, G.; Ireton, G. C.; Varani, G.; Stoddard, B. L.; Baker, D. Science 2003, 302, 1364
23. Röthlisberger, D.; Khersonsky, O.; Wollacott, A. M.; Jiang, L.; DeChancie, J.; Betker, J.; Gallaher, J. L.; Althoff, E.; Zanghellini, A.; Dym, O.; Albeck, S.; Houk, K. N.; Tawfik, D. S.; Baker, D. Nature 2008, 453, 190
24. Jiang, L.; Althoff, E.; Clemente, F. R.; Doyle, L.; Röthlisberger, D.; Zanghellini, A.; Gallaher, J. L.; Betker, J. L.; Tanaka, F.; Barbas, C. F., III; Hilvert, D.; Houk, K. N.; Stoddard, B. L.; Baker, D. Science 2008, 319, 1387
25. Das, R. PLoS One 2011, 6 e20044
26. Gorske, B. C.; Stringer, J. R.; Bastian, B. L.; Fowler, S. A.; Blackwell, H. E. J. Am. Chem. Soc. 2009, 131, 16555
27. Gillespie, R. J.; Robinson, E. A. Chem. Soc. Rev. 2005, 34, 396
28. O'Meara, M. Hydrogen Bond Energy Term. https://www.rosettacommons.org/ manuals/archive/rosetta3.5-user-guide/db/daf/hbonds.html (accessed Nov 22, 2013).
29. Wang, G.; Dunbrack, R. L. Bioinformatics 2003, 19, 1589
30. McDonald, I.; Thornton, J. J. Mol. Biol. 1994, 238, 777
31. Baker, E. N.; Hubbard, R. E. Prog. Biophys. Mol. Biol. 1984, 44, 97
32. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577
33. Hutchinson, E.; Thornton, J. Protein Sci. 1996, 5, 212
34. Reed, A. E.; Curtiss, L.; Weinhold, F. Chem. Rev. 1988, 88, 899
35. Glendening, E. D.; Reed, A. E.; Carpenter, J. E.; Weinhold, F. NBO, version 3.1.
36. 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.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, Ö.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian 09, revision B.01; Gaussian, Inc.: Wallingford, CT, 2009.