Rapid evaluation of the binding energies between peptide amide and DNA base

Journal of Computational Chemistry

Volumn 32, Issue 13, 2011, Pages 2765-2773

  Li, Yang ^a   Wang, Chang Sheng ^a  

^a LIAONING NORMAL UNIVERSITY   (China)

Author keywords

amide adenine dimers; amide cytosine dimers; amide guanine dimers; amide thymine dimers; analytic potential energy function; potential energy curve

Indexed keywords

AMIDE-ADENINE DIMERS; AMIDE-CYTOSINE DIMERS; AMIDE-GUANINE DIMERS; AMIDE-THYMINE DIMERS; ANALYTIC POTENTIAL ENERGY FUNCTION; POTENTIAL ENERGY CURVE;

AMIDES; AMINO ACIDS; DIMERS; DNA; FUNCTION EVALUATION; HYDROGEN; HYDROGEN BONDS; PEPTIDES; POSITIVE IONS; POTENTIAL ENERGY FUNCTIONS;

BINDING ENERGY;

ADENINE; AMIDE; CYTOSINE; DNA; GUANINE; PEPTIDE; THYMINE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DIMERIZATION; HYDROGEN BOND; METABOLISM; PROTEIN BINDING; THERMODYNAMICS;

ADENINE; AMIDES; CYTOSINE; DIMERIZATION; DNA; GUANINE; HYDROGEN BONDING; MODELS, MOLECULAR; PEPTIDES; PROTEIN BINDING; THERMODYNAMICS; THYMINE;

EID: 79960619107     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21856     Document Type: Article

References (47)

1. P. Hobza, J. Šponer, Chem Rev 1999, 99, 3247.
2. J. Šponer, J. Leszczynski, P. Hobza, Biopolymers 2002, 61, 3.
3. (a), R. Wieczorek, J. J. Dannenberg, J Am Chem Soc 2003, 125, 8124
4. (b), R. Wieczorek, J. J. Dannenberg, J Am Chem Soc 2003, 125, 14065
5. (c), R. Wieczorek, J. J. Dannenberg, J Am Chem Soc 2004, 126, 14198
6. (d), P. Salvador, N. Kobko, R. Wieczorek, J. J. Dannenberg, J Am Chem Soc 2004, 126, 14190.
7. (a), C.-S. Wang, Y. Zhang, K. Gao, Z.-Z. Yang, J Chem Phys 2005, 123, 024307
8. (b), Y. Zhang, C. -S. Wang, J Comput Chem 2009, 30, 1251
9. (c), Y. Zhang, C.-S. Wang, Z.-Z. Yang, J Theor Comput Chem 2009, 8, 279.
10. A. Mohajeri, F. F. Nobandegani, J Phys Chem A 2008, 112, 281.
11. H. Dong, W. J. Hua, S. H. Li, J Phys Chem A 2007, 111, 2941.
12. S. Jones, P. van Heyningen, H. M. Berman, J. M. Thornton, J Mol Biol 1999, 287, 877.
13. D. Lejeune, N. Delsaux, B. Charloteaux, A. Thomas, R. Brasseur, Protein Struct Funct Bioinform 2005, 61, 258.
14. S. Mukherjee, S. Majumdar, D. Bhattacharyya, J Phys Chem B 2005, 109, 10484.
15. J. Gu, J. Wang, J. Leszczynski, J Phys Chem B 2006, 110, 13590.
16. Z. Czyznikowska, L. Lipkowski, R. W. Góra, R. Zaleśny, A. C. Cheng, J Phys Chem B 2009, 113, 11511.
17. A. C. Cheng, W. W. Chen, C. N. Fuhrmann, A. D. Frankel, J Mol Biol 2003, 327, 781.
18. J. Allers, Y. Shamoo, J Mol Biol 2001, 311, 75.
19. C. O. Pabo, Ann Rev Biochem 1984, 53, 293.
20. R. Sathyapriya, S. Vishveshwara, Nucleic Acid Res 2004, 32, 4109.
21. M. M. Gromiha, J. G. Siebers, S. Selvaraj, H. Kono, A. Sarai, J Mol Biol 2004, 337, 285.
22. B. Contreras-Moreira, Nucleic Acids Res 2010, 38, D91.
23. S. Lee, T. L. Blundell, Bioinformatics 2009, 25, 1559.
24. M. Y. Tkachenko, O. P. Boryskina, A. V. Shestopalova, M. Y. Tolstorukov, Int J Quantum Chem 2010, 110, 230.
25. K. C. Hunter, A. L. Millen, S. D. Wetmore, J Phys Chem B 2007, 111, 1858.
26. E. Jeong, H. Kim, S.-W. Lee, K. Han, Mol Cells 2003, 16, 161.
27. A. C. Cheng, A. D. Frankel, J Am Chem Soc 2004, 126, 434.
28. P. Jurečka, P. Hobza, J Am Chem Soc 2003, 125, 15608.
29. I. Dabkowska, P. Jurečka, P. Hobza, J Chem Phys 2005, 122, 204322.
30. K. E. Riley, M. Pitoňák, J. Černý, P. Hobza, J Chem Theor Comput 2010, 6, 66.
31. J. Rejnek, P. Hobza, J Phys Chem B 2007, 111, 641.
32. T. H. Dunning, Jr. , J Phys Chem A 2000, 104, 9062.
33. R. Vargas, J. Garza, R. A. Friesner, H. Stern, B. P. Hay, D. A. Dixon, J Phys Chem A 2001, 105, 4963.
34. A. Asensio, N. Kobko, J. J. Dannenberg, J Phys Chem A 2003, 107, 6441.
35. S. Scheiner, J Phys Chem B 2005, 109, 16132.
36. W. Chin, F. Piuzzi, I. Dimicoli, M. Mons, Phys Chem Chem Phys 2006, 8, 1033.
37. C.-L. Sun, X.-N. Jiang, C.-S. Wang, J Comput Chem 2009, 30, 2567.
38. C.-S. Wang, C.-L. Sun, J Comput Chem 2010, 31, 1036.
39. X.-N. Jiang, C.-S. Wang, ChemPhysChem 2009, 10, 3330.
40. X.-N. Jiang, C.-L. Sun, C.-S. Wang, J Comput Chem 2010, 31, 1410.
41. Y. Li, X.-N. Jiang, C.-S. Wang, J Comput Chem 2011, 32, 953.
42. S. F. Boys, F. Bernardi, Mol Phys 1970, 19, 553.
43. S. Simon, M. Duran, J. J. Dannenberg, J Chem Phys 1996, 105, 11024.
44. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr. , R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. 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, A. D. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, 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. Johnson, W. Chem, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, J. A. Pople, Gaussian 03; Gaussian Inc.: Pittsburgh, PA, 2003.
45. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr. , D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, P. A. Kollman, J Am Chem Soc 1995, 117, 5179.
46. G. A. Kaminsky, R. A. Friesner, J. Tirado-Rives, W. L. Jorgensen, J Phys Chem B 2001, 105, 6474.
47. A. D. MacKerell, Jr. , D. Bashford, M. Bellott, R. L. Dunbrack, Jr. , J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus, J Phys Chem B 1998, 102, 2586.