A complete set of NMR chemical shifts and spin-spin coupling constants for L-alanyl-L-alanine zwitterion and analysis of its conformational behavior

Journal of the American Chemical Society

Volumn 127, Issue 48, 2005, Pages 17079-17089

  Bouř, Petr ^a   Buděšínský, Miloš ^a   Špirko, Vladimír ^a   Kapitán, Josef ^a   Šebestík, Jaroslav ^a   Sychrovský, Vladimír ^a  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; ISOTOPES; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; SPIN COATING;

CHEMICAL SHIFTS; COUPLING CONSTANTS; WAVE FUNCTION;

ORGANIC COMPOUNDS;

ALANINE; ALANYLALANINE; AMPHOLYTE; CARBON; CARBON 13; DIPEPTIDE; HYDROGEN; NITROGEN 15; SOLVENT; UNCLASSIFIED DRUG; WATER;

AQUEOUS SOLUTION; ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; DISPERSION; ENERGY; ISOTOPE LABELING; MOLECULAR DYNAMICS; NITROGEN NUCLEAR MAGNETIC RESONANCE; PEPTIDE SYNTHESIS; PROTEIN STRUCTURE; TEMPERATURE; VIBRATION; X RAY CRYSTALLOGRAPHY;

DIPEPTIDES; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; SOLUTIONS; SURFACE PROPERTIES; THERMODYNAMICS; WATER;

EID: 28944446881     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0552343     Document Type: Article

References (96)

1. Torii, H. J. Phys. Chem. A 2004, 108, 7272-7280.
2. Ham, S.; Kim, J. H.; Kochan, L.; Cho, M. J. Chem. Phys. 2003, 118, 3491-3498.
3. Park, S. W.; Ahn, D. S.; Lee, S. Chem. Phys. Lett. 2003, 371, 74-79.
4. Selvarengan, P.; Kolandaivel, P. THEOCHEM 2004, 671, 77-86.
5. Nandini, G.; Sathyanarayana, D. N. J. Phys. Chem. A 2003, 117, 11391-1140.
6. Xu, S.; Nilles, J. M.; Bowen, K. H. J. J. Chem. Phys. 2003, 119, 10696-10701.
7. Hudaky, I.; Hudaky, P.; Percel, A. J. Comput. Chem. 2004, 25 (12), 1522-1531.
8. Jalkanen, K. J.; Elstner, M.; Suhai, S. THEOCHEM 2004, 675 (1-3), 61-77.
9. Oboodi, M. R.; Alva, C.; Diem, M. J. Phys. Chem. 1984, 88 (3), 501-505.
10. Diem, M.; Oboodi, M. R.; Alva, C. Biopolymers 1984, 23, 1917-1930.
11. Lee, O.; Roberts, G. M.; Diem, M. Biopolymers 1989, 28, 1759-1770.
12. Mehta, M. A.; Fry, E. A.; Eddy, M. T.; Dedeo, M. T.; Anagnost, A. E.; Long, J. R. J. Phys. Chem. B 2004, 108, 2777-2780.
13. Jacob, R.; Fischer, G. J. Phys. Chem. A 2003, 107, 6136-6143.
14. Bouř, P.; Kapitán, J.; Baumruk, V. J. Phys. Chem. A 2001, 105, 6362-6368.
15. Knapp-Mohammady, M.; Jalkanen, K. J.; Nardi, F.; Wade, R. C.; Suhai, S. Chem. Phys. 1999, 240, 63-77.
16. Lucas, B.; Gregoire, H.; Maitre, P.; Ortega, J. M.; Rupenyan, A.; Reimann, B.; Scherman, J. P.; Desfrancois, C. Phys. Chem. Chem. Phys. 2004, 6, 2659-2663.
17. Diem, M.; Lee, O.; Roberts, G. M. J. Phys. Chem. 1992, 96, 548-554.
18. Jalkanen, K. J.; Nieminen, R. M.; Knapp-Mohammady, M.; Suhai, S. Int. J. Quantum Chem. 2003, 92 (2), 239-259.
19. Weir, A. F.; Lowrey, A. H.; Williams, R. W. Biopolymers 2001, 58, 577-591.
20. Zuk, W. M.; Freedman, T. B.; Nafie, L. A. Biopolymers 1989, 28, 2025-2044.
21. Peterson, J. R.; Bickford, L. C.; Morgan, D.; Kim, A. S.; Ouerfelli, O.; Kirschner, M. W.; Rosen, M. K. Nat. Struct. Mol. Biol. 2004, 11, 747-755.
22. Roberts, G. C. K. NMR of Macromolecules: IRL: Oxford, 1993.
23. Wüthrich, K. NMR of Proteins and Nucleic Acids; Wiley: New York, 1986.
24. Evans, J. N. S. Biomolecular NMR Spectroscopy. Oxford University Press: Oxford, 1995.
25. Dobson, C. M. NMR and Protein Folding: Studies of Lysozyme and alpha-Lactalbumin. Protein Conformation (CIBA Foundation Symposium 161); Wiley: Chichester, 1991; p 167.
26. Cavanagh, J.; Fairbrother, W. J.; Palmer, A. G., III: Skelton, N. J. Protein NMR Spectroscopy; Academic Press Inc.: San Diego, 1995.
27. Smith, L. J.; Dobson, C. M. Int. J. Quantum Chem. 1996, 59, 315-332.
28. Eberstadt, M.; Gemmecker, G.; Mierke, D. F.; Kessler, H. Angew. Chem., Int. Ed. Engl. 1996, 34 (16), 1671-1695.
29. Helgaker, T.; Jaszunski, M.; Ruud, K. Chem. Rev. 1999, 99(1), 293-352.
30. Malkina, O. L.; Malkin, V. G. Angew. Chem., Int. Ed. 2003, 42 (36), 4335-4338.
31. Sychrovský, V.; Gräfenstein, J.; Cremer, D. J. Chem. Phys. 2000, 113, 3530-3547.
32. Helgaker, T.; Watson, M.; Handy, N. C. J. Chem. Phys. 2000, 113 (21), 9402-9409.
33. Schreckenbach, G.; Ziegler, T. J. Phys. Chem. 1995, 99 (2), 606-611.
34. Tomena, C. F.; Rittner, R.; Contreras, R. H.; Peralta, J. E. J. Phys. Chem. A 2004, 108 (38), 7762-7768.
35. Barfield, M.; Dingley, A. J.; Feigon, J.; Grzesiek, S. J. Am. Chem. Soc. 2001, 123 (17), 4014-4022.
36. Šponer, J. E.; Sychrovský, V.; Hobza, P.; Šponer, J. Phys. Chem. Chem. Phys. 2004, 6 (10), 2772-2780.
37. Bernátková, M.; Dvǒáková, H.; Andrioletti, B.; Král, V.; Bouř, P. J. Phys. Chem. A 2005, 109, 5518-5526.
38. Jaszunski, M.; Ruud, K.; Helgaker, T. Mol. Phys. 2003, 101 (13), 1997-2002.
39. Haasnoot, C. A. G.; de Leeuw, F. A. A. M.; de Leeuw, H. P. M.; Altona, C. Org. Magn. Reson. 1981, 15, 43-52.
40. Miranker, A.; Radford, S. E.; Karplus, M.; Dobson, C. M. Nature 1991, 349, 633-636.
41. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: a theoretical perspective of dynamics, structure and thermodynamics. John Wiley & Sons: New York, 1988; Vol. LXXI.
42. Smith, L. J.; Bolin, K. A.; Schwalbe, H.; Macarthur, M. W.; Thornton, J. M.; Dobson, C. M. J. Mol. Biol. 1996, 255, 494-506.
43. Ratajczyk, T.; Pecul, M.; Sadlej, J.; Helgaker, T. J. Phys. Chem. A 2004, 108, 2758-2769.
44. Wu, A. N.; Cremer, D.; Auer, A. A.; Gauss, J. J. Phys. Chem. A 2002, 106, 657-667.
45. Hu, J. S.; Bax, A. J. Am. Chem. Soc. 1997, 119, 6360-6368.
46. Boǔ, P.; Raich, I.; Kaminský, J.; Hrabal, R.; Cejka, J.; Sychrovský, V. J. Phys. Chem. A 2004, 108, 6365-6372.
47. Sebastiani, D.; Rothlisberger, U. J. Phys. Chem. B 2004, 108, 2807-2815.
48. Bouř, P.; Sychrovský, V.; Maloň, P.; Hanzlíková, J.; Baumruk, V.; Pospíšek, J.; Buděšínský, M. J. Phys. Chem. A 2002, 106, 7321-7327.
49. Kamiya, N.; Watanabe, Y. S.; Ono, S.; Higo, J. Chem. Phys. Lett. 2005, 401, 312-317.
50. Sandstrom, J. Dynamic NMR Spectroscopy; Academic Press: London, 1982.
51. Cheng, L.; Goodwin, C. A.; Schully, M. F.; Kakkar, V. V. J. Med. Chem. 1992, 35 (18), 3364-3369.
52. Wünsch, E.; Wendlberger, G.; Deimer, K. H. Hoppe-Seyler's Z. Physiol. Chem. 1976, 357 (3), 447-458.
53. Stein, W. H.; Moore, S.; Bergmann, M. J. Biol. Chem. 1944, 154, 191-201.
54. Becke, A. D. Exchange-correlation approximations in density-functional theory. In Modern electronic structure theoy; Yarkony, D. R., Ed. World Scientific: Singapore, 1995; Vol. 2, pp 1022-1046.
55. Becke, A. Phys. Rev. A 1988, 38, 3098-3100.
56. Cammi, R.; Mennucci, B.; Tomasi, J. J. Phys. Chem. A 2000, 104, 5631-5637.
57. Klamt, A. J. Phys. Chem. 1995, 99, 2224-2235.
58. Klamt, A. COSMO and COSMO-RS. In The Encyclopedia of Computatinal Chemistry; Schleyer, P. R., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer, H. F., III, Schreiner, P. R., Eds. John Wiley & Sons: Chichester, 1998; Vol. 1, pp 604-615.
59. Frisch, M. J. at al. Gaussian 03; Gaussian, Inc.: Pittsburgh, PA, 2003.
60. Ponder, J. W. Tinker, version 3.8; Washington University School of Medecine: Saint Louis, MS, 2000.
61. Ditchfield, R. Mol. Phys. 1974, 27, 789-807.
62. Dodds, J. L.; McWeeny, R.; Sadlej, A. J. Mol. Phys. 1980, 41, 1419-1430.
63. Wolinski, K.; Hilton, J. F.; Pulay, P. J. Am. Chem. Soc. 1990, 112, 8251-8260.
64. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652.
65. Kutzelnigg, W.; Fleischer, U.; Schindler, M. NMR - Basis Principles and Progress; Springer: Heidelberg, 1990.
66. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; Debolt, S.; Ferguson, D. M.; Seibel, G.; Kollman, P. A. Comput. Phys. Commun. 1995, 91, 1-41.
67. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
68. Wang, J.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074.
69. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T. J. Comput. Chem. 2003, 24, 1999-2012.
70. Foloppe, N.; MacKerell, A. D. J. Comput. Chem. 2000, 21, 86-104.
71. Ren, P.; Ponder, W. J. Phys. Chem. B 2003, 107, 5933-5947.
72. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
73. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D. J. Chem. Phys. 1983, 79, 926-935.
74. Cejchan, A.; Špirko, V. J. Mol. Spectrosc. 2003, 217 (1), 142-145.
75. Ixaru, L. Numerical Methods for Differential Equations and Applications; Reidel: Dordrecht, 1984.
76. Fletterick, R. J.; Tsai, C.; Hughes, R. E. J. Phys. Chem. 1971, 75 (7), 918-922.
77. Gnanakaran, S.; Garcia, A. E. J. Phys. Chem. B 2003, 107, 12555-12557.
78. Hu, H.; Elstner, M.; Hermans, J. Proteins: Struct., Funct., Genet. 2003, 50, 451-463.
79. Papoušek, D.; Aliev, M. R. Molecular Vibrational/Rotational Spectra; Academia: Prague, 1982.
80. Špirko, V.; Piecuch, P.; Bludský, O. J. Chem. Phys. 2000, 112 (1), 189-202.
81. Fadda, E.; Casida, M. E.; Salahub, D. R. J. Phys. Chem. A 2003, 107, 9924-9930.
82. Soncini, A.; P., L. Chem. Phys. Lett. 2005, 409, 177-186.
83. Bystrov, V. F. Prog. NMR Spectrosc. 1976, 10, 41-81.
84. Pecul, M.; Sadlej, J. Chem. Phys. 1998, 234-119, 111.
85. Boǔ, P.; Michalík, D.; Kapitán; J. J. Chem. Phys. 2005, 122, 144501 1-9.
86. Bouř, P. J. Chem. Phys. 2004, 121 (16), 7545-7548.
87. Wishart, D. S.; Sykes, B. D. J. Biomol. NMR 1994, 4, 171-180.
88. Wagner, G.; Pardi, A.; Wuthrich, K. J. Am. Chem. Soc. 1983, 105 (18), 5948-5949.
89. Grzesiek, S.; Cordier, F.; Jaravine, V.; Darfield, M. Prog. NMR Spectrosc. 2004, 45 (3-4), 275-300.
90. Xu, X. P.; Case, D. A. J. Biomol. NMR 2001, 21, 321-333.
91. Plaxco, K. W.; Gross, M. Nature 1997, 386, 657.
92. Uversky, V. N. Proteins 2000, 41, 415-427.
93. Bouř, P.; Buděšínský, M. J. Chem. Phys. 1999, 110, 2836-2843.
94. Malkin, V. G.; Malkina, O. L.; Steinebrunner, G.; Huber, H. Chem.-Eur. J. 1996, 2, 452-457.
95. Pfrommer, B. G.; Mauri, F.; Louie, S. G. J. Am. Chem. Soc. 2000, 122, 123-129.
96. Pennanen, T. S.; Vaara, J.; Lantto, P.; Sillanpaa, A. J.; Laasonen, K.; Jokisaari, J. J. Am. Chem. Soc. 2004, 124, 11093-11102.