A theoretical study of potassium cation binding to prolylglycine (PG) and glycylproline (GP) dipeptide

Journal of Molecular Structure: THEOCHEM

Volumn 729, Issue 3, 2005, Pages 193-202

  Abirami, Seduraman ^a,b   Wong, Carrie Hoi Shan ^c   Tsang, Chun Wai ^c   Ma, Ngai Ling ^a,d   Goh, Ngoh Khang ^b  

^a INSTITUTE OF HIGH PERFORMANCE COMPUTING   (Singapore)

^b NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^c HONG KONG POLYTECHNIC UNIVERSITY   (Hong Kong)

^d NOVARTIS INSTITUTE FOR TROPICAL DISEASES   (Singapore)

Author keywords

Density functional calculations; Metal ligand interactions; Peptides; Potassium ion; Zwitterions

Indexed keywords

EID: 24944450365     PISSN: 01661280     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.theochem.2005.05.029     Document Type: Article

References (56)

1. D.L. Nelson, and M.M. Cox Principles of Biochemistry third ed. 2000 W.H. Freeman and Company New York
2. A.G. Harrison Mass Spectrom. Rev. 16 1997 201
3. T. Marino, N. Russo, E. Tocci, and M. Toscano Int. J. Quant. Chem. 84 2001 64
4. S.P. Mirza, S. Prabhakar, and M. Vairamani Rapid Commun. Mass Spectrom. 15 2001 957
5. C. Pepe, S. Rochut, J.-P. Paumard, and J.-C. Tabet Rapid Commun. Mass Spectrom. 18 2004 307
6. T. Marino, N. Russo, E. Tocci, and M. Toscano J. Mass Spectrom. 36 2001 301
7. S.S. Zimmerman, and H.A. Scheraga Proc. Natl Acad. Sci. USA 74 1977 4126
8. E.G. Hutchinson, and J.M. Thornton Protein Sci. 3 1994 2207
9. C. Branden, and J. Tooze Introduction to Protein Structure second ed. 1999 Garland Pub. New York
10. G.A. Petsko, and D. Ringe Protein Structure and Function 2004 New Science Press Oxford
11. C.L. Jenkins, and T. Raines Nat. Prod. Rep. 19 2002 49
12. B.K. Kay, M.P. Williamson, and M. Sudol FASEB J. 14 2000 231
13. M. Kohtani, B.S. Kinnear, and M.F. Jarrold J. Am. Chem. Soc. 122 2000 12377
14. R. Sudha, M. Panda, J. Chandrasekhar, and P. Balaram Chem. Eur. J. 8 2002 4980
15. M. Kohtani, M.F. Jarrold, S. Wee, and R.A.J. O'Hair J. Phy. Chem. B 108 2004 6093
16. S.J. Lippard, and J.M. Berg Principles of Bioinorganic Chemistry 1994 University Science Books Mill Valley, California
17. L. Stryer Biochemistry fourth ed. 1995 W.H. Freeman New York
18. D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A.L. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, and R. Mackinnon Science 280 1998 69
19. Y. Jiang, A. Lee, J. Chen, V. Ruta, M. Cadene, B.T. Chait, and R. Mackinnon Nature 423 2003 33
20. Y.F. Zhou, and R. Mackinnon J. Mol. Biol. 333 2003 965
21. C. Miller Science 261 1993 1692
22. W.Y. Feng, S. Gronert, K.A. Fletcher, A. Warres, and C.B. Lebrilla Int. J. Mass Spectrom. 222 2003 117
23. S. Hoyau, K. Norrman, T.B. McMahon, and G. Ohanessian J. Am. Chem. Soc. 121 1999 8864
24. T. Marino, N. Russo, and M. Toscano J. Phys. Chem. B 107 2003 2588
25. N.P. Ewing, X. Zhang, and C.J. Cassady J. Mass Spectrom. 31 1996 1345
26. M. Kohtani, G.A. Breaux, and M.F. Jarrold J. Am. Chem. Soc. 126 2004 1206
27. C.H.S. Wong, N.L. Ma, and C.W. Tsang Chem. Eur. J. 8 2002 4909
28. Sybyl 6.7 Tripos Inc.: 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA.
29. T.A. Halgren J. Comput. Chem. 17 1996 616
30. T.A. Halgren J. Comput. Chem. 20 1999 720
31. T.A. Halgren J. Comput. Chem. 20 1999 730
32. 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, 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.G. 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, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, J.L. Andres, C. Gonzalez, M. Head-Gordon, E.S. Replogle, J.A. Pople, in Gaussian 98, Revision A.6, Gaussian, Inc., Pittsburgh, PA, 1998.
33. A.P. Scott, and L. Radom J. Phys. Chem. 100 1996 16502
34. J.K.-C. Lau, C.H.S. Wong, P.S. Ng, F.M. Siu, N.L. Ma, and C.W. Tsang Chem. Eur. J. 9 2003 3383
35. J.E. Del Bene, H.D. Mettee, M.J. Frisch, B.T. Luke, and J.A. Pople J. Phys. Chem. 87 1983 3279
36. C.H.S. Wong, F.M. Siu, N.L. Ma, and C.W. Tsang J. Mol. Struct. (THEOCHEM) 588 2002 9
37. C. Liebecq Biochemical Nomenclature and Related Documents second ed. 1992 Portland Press London
38. S. Fischer, R.L. Dunbrack, and M. Karplus J. Am. Chem. Soc. 116 1994 11931
39. D.Q. McDonald, and W.C. Still J. Org. Chem. 61 1996 1385
40. R. Improta, C. Benzi, and V. Barone J. Am. Chem. Soc. 123 2001 12568
41. C. Benzi, R. Improta, G. Scalmani, and V. Barone J. Comput. Chem. 23 2002 341
42. Y.K. Kang J. Mol. Struct. (THEOCHEM) 675 2004 37
43. O. Antohi, F. Naider, and A.-M. Sapse J. Mol. Struct. (THEOCHEM) 360 1996 99
44. -1 for free proline in Ref. [4]), we do not expect puckering would alter the relative stability of conformers/isomers reported here.
45. J.C. Kong, S. Abirami, P.S. Ng, F.M. Siu, N.K. Goh, manuscript under preparation.
46. J. Tortajada, E. Leon, J.-P. Morizur, A. Luna, O. Mo, and M. Yanez J. Phys. Chem. 99 1995 13890
47. M. Remko Mol. Phys. 91 1997 929
48. B.A. Cerda, S. Hoyau, G. Ohanessian, and C. Wesdemiotis J. Am. Chem. Soc. 120 1998 2437
49. 2) is less negative by at least ∼0.1 e (estimated by natural charge obtained at the B3-LYP/6-31G(d) level).
50. A. Luna, B. Amekraz, J. Tortajada, J.P. Morizur, M. Alcami, O. Mo, and M. Yanez J. Am. Chem. Soc. 120 1998 5411
51. Y. Tsang, F.M. Siu, C.S. Ho, N.L. Ma, and C.W. Tsang Rapid Commun. Mass Spectrom. 18 2004 345
52. -1is the energy difference between the exo and the twist form.
53. Y. Tsang, 2003. PhD Thesis, Hong Kong Polytechnic University.
54. C.H.S. Wong, unpublished work.
55. Z.B. Maksic, and B. Kovacevic Chem. Phys. Lett. 307 1999 497
56. +-GG.