Structures and stability of salt-bridge in aqueous solution

Biophysical Chemistry

Volumn 117, Issue 2, 2005, Pages 119-140

  Sagarik, Kritsana ^a   Chaiyapongs, Supaporn ^b  

^a SURANAREE UNIVERSITY OF TECHNOLOGY   (Thailand)

^b RAMKHAMHAENG UNIVERSITY   (Thailand)

Author keywords

Formate; Guanidinium; Hydration; Ion pair; Salt bridge

Indexed keywords

FORMIC ACID; GUANIDINE; SODIUM CHLORIDE; WATER;

AQUEOUS SOLUTION; ARTICLE; CHEMICAL STRUCTURE; HYDRATION; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR STABILITY; PRIORITY JOURNAL; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING; WATER STRUCTURE;

CRYSTALLOGRAPHY, X-RAY; FORMIC ACIDS; GUANIDINE; HYDROGEN BONDING; MODELS, CHEMICAL; MODELS, MOLECULAR; THERMODYNAMICS; WATER;

EID: 23944439902     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2005.04.012     Document Type: Article

References (60)

1. D. Gandini, L. Gogioso, M. Bolognesi, and D. Bordo Pattern of ionizable sidechains interactions in protein structures Proteins: Struct., Funct., Genet. 24 1996 439 449
2. D.J. Barlow, and J.M. Thornton Ion-pairs in proteins J. Mol. Biol. 168 1983 867 885
3. J.F. Riordan, K.D. McElvany, and C.L. Borders Jr. Arginyl residues: anion recognition sites in enzymes Science 195 1977 884 886
4. J.F. Kirsch, G. Eichcle, G.C. Ford, M.G. Vincent, J.N. Jansonius, H. Gehring, and P. Christen Mechanism of action of aspartate aminotransferase proposed on the basis of its spatial structure J. Mol. Biol. 174 1984 497 525
5. J. Tormo, D. Blaas, N.R. Parry, D. Rowlands, D. Stuart, and I. Fita Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2 EMBO J. 13 1994 2247 2256
6. J. Singh, J.M. Thornton, M. Snarey, and S.F. Campbell The geometries of interacting arginine-carboxyls in proteins FEBS Lett. 224 1987 161 171
7. M.P. Fülscher, and E.L. Mehler Ab initio interaction potentials of guanidine-formic acid in neutral and charged states J. Mol. Struct., Theochem 165 1988 319 327
8. Y.-J. Zheng, and R.L. Ornstein What happens to salt-bridges in nonaqueous environments: insights from quantum mechanics calculations J. Am. Chem. Soc. 118 1996 11237 11243
9. X. Barril, C. Alemán, M. Orozco, and F.J. Luque Salt bridge interactions: stability of the ionic and neutral complexes in the gas phase, in solution, and in proteins Proteins: Struct., Funct., Genet. 32 1998 67 79
10. A. Melo, M.J. Ramos, W.B. Floriano, J.A.N.F. Gomes, J.F.R. Leão, A.L. Magalhães, B. Maigret, M.C. Nascimento, and N. Reuter Theoretical study of arginine-carboxylate interactions J. Mol. Struct., Theochem 463 1999 81 90
11. J.B.O. Mitchell, J.M. Thornton, J. Singh, and S.L. Price Towards an understanding of the arginine-aspartate interaction J. Mol. Biol. 226 1992 251 262
12. J.A. Ippolito, R.S. Alexander, and D.W. Christainson Hydrogen bond stereochemistry in protein structure and function J. Mol. Biol. 215 1990 457 471
13. S. Saigal, and J. Pranata Monte Carlo simulations of guanidinium acetate and methylammonium acetate ion pairs in water Bioorg. Chem. 25 1997 11 21
14. X. Rozanska, and C. Chipot Modeling ion-ion interaction in proteins: a molecular dynamics free energy calculation of the guanidinium-acetate association J. Chem. Phys. 112 2000 9691 9694
15. T.A. Keith, and M.J. Frisch D.A. Smith Inclusion of Explicit Solvent Molecules in a Self-Consistent-Reaction Field Model of Solvation Modeling the Hydrogen Bond, ACS Symposium Series vol. 569 1994 American Chemical Society Washington 22
16. K. Sagarik, and S. Dokmaisrijan A theoretical study on hydration of alanine zwitterions J. Mol. Struct., Theochem 718 2005 31 47
17. H.J. Böhm, and R. Ahlrichs A study of short-range repulsions J. Chem. Phys. 77 1982 2028 2034
18. J. Hoinkis, R. Ahlrichs, and H.J. Böhm A simple treatment of intermolecular interactions: synthesis of ab initio calculations and combination rules Int. J. Quant. Chem. 23 1983 821 834
19. 2 J. Chem. Phys. 81 1984 1389 1395
20. 3 with new pair potentials Mol. Phys. 54 1985 1261 1274
21. E. Clementi Computational aspects for large chemical systems Lecture Notes in Chemistry vol. 19 1980 Springer-Verlag Berlin
22. 2 with a test-particle model potential Chem. Phys. Lett. 131 1986 74 81
23. K.P. Sagarik, R. Ahlrichs, and S. Brode Intermolecular potentials for ammonia based on the test particle model and the coupled pair functional method Mol. Phys. 57 1986 1247 1264
24. K.P. Sagarik, and R. Ahlrichs A test particle model potential for formamide and molecular dynamics simulations of the liquid J. Chem. Phys. 86 1987 5117 5126
25. 3, guanine and cytosine Chem. Phys. 156 1991 439 456
26. K. Sagarik, and E. Spohr Statistical mechanical simulations on properties of liquid pyridine Chem. Phys. 199 1995 73 82
27. K. Sagarik, and P. Asawakun Intermolecular potential for phenol based on the test particle model Chem. Phys. 219 1997 173 191
28. K. Sagarik Theoretical studies on hydrogen bonding in hydroxylamine clusters and liquid J. Mol. Struct., Theochem 465 1999 141 155
29. K. Sagarik, and B.M. Rode Intermolecular potential for benzoic acid-water based on the test-particle model and statistical mechanical simulations of benzoic acid in aqueous solutions Chem. Phys. 260 2000 159 182
30. K. Sagarik, S. Chaiwongwattana, and P. Sisot A theoretical study on clusters of benzoic acid-water in benzene solutions Chem. Phys. 306 2004 1 12
31. C.M. Breneman, and K.B. Wiberg Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis J. Comput. Chem. 11 1990 361 373
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, B.B. Stefanov, G. Lui, 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.G. Johnson, W. Chen, M.W. Wong, J.L. Andres, M. Head-Gordon, E.S. Replogle, and J.A. Pople Gaussian vol. 98 1998 Gaussian Inc. Pittsburgh
33. P.L. Cummins, and J.E. Gready The electrostatic potential in the semiempirical molecular orbital approximation Chem. Phys. Lett. 225 1994 11 17
34. S.F. Boys, and F. Bernardi The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors Mol. Phys. 19 1970 553 566
35. Y. Su, and E. Gallicchio The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions Biophys. Chem. 109 2004 251 260
36. K. Sagarik, and S. Chaiyapongs Structures and stability of model salt-bridge interaction in aqueous solution Proceedings of the 8th Annual National Symposium on Computational Science and Engineering (ANSCSE-8) 2004 Suranaree University of Technology Nakhon Ratchasima, Thailand 9
37. SURFER for Window, Version 6.04 1997 Golden Software Inc. USA
38. K. Wüthrich K. Wüthrich Hydration of Biological Macromolecules in Solution: Surface Structure and Molecular Recognition NMR in Structural Biology, World Scientific Series in 20th Century Chemistry vol. 5 1995 World Scientific Singapore 647
39. M. Odelius, and A. Laaksonen P.B. Balbuena J.M. Seminario Combined MD Simulation-NMR Relaxation Studies of Molecular Motion and Intermolecular Interactions Molecular Dynamics from Classical to Quantum Methods, Theoretical and Computational Chemistry vol. 7 1999 Elsevier Amsterdam 281
40. R.M. Brunne, E. Liepinsh, G. Otting, K. Wüthrich, and W.F. van Gunsteren Hydration of proteins: a comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations J. Mol. Biol. 231 1993 1040 1048
41. R.W. Impey, P.A. Madden, and I.R. McDonald Hydration and mobility of ions in solution J. Phys. Chem. 87 1983 5071 5083
42. D.E. Smith, and L.X. Dang Computer simulations of NaCl association in polarizable water J. Chem. Phys. 100 1994 3757 3766
43. D.A. Case, D.A. Pearlman, J.W. Caldwell, T.E. Cheatham III, W.S. Ross, C. Simmerling, T. Darden, K.M. Merz, R.V. Stanton, A. Cheng, J.J. Vincent, M. Crowley, V. Tsui, R. Radmer, Y. Duan, J. Pitera, I. Massova, G.L. Seibel, U.C. Singh, P. Weiner, and P.A. Kollman AMBER, Version 6 1999 University of California San Francisco
44. W.L. Jorgensen, and J. Tirado-Rives The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin J. Am. Chem. Soc. 110 1988 1657 1666
45. J. Gao D.A. Smith Computation of Intermolecular Interactions with a Combined Quantum Mechanical and Classical Approach Modeling the Hydrogen Bond, ACS Symposium Series vol. 569 1994 American Chemical Society Washington 8
46. M.J. Field, P.A. Bash, and M. Karplus A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations J. Comput. Chem. 11 1990 700 733
47. I. Lukovits, A. Karpfen, H. Lischka, and P. Schuster Ab initio LCMO studies on the hydration of formate ion Chem. Phys. Lett. 63 1979 151 154
48. W.L. Jorgensen, and J. Gao Monte Carlo simulations of the hydration of ammonium and carboxylate ions J. Phys. Chem. 90 1986 2174 2182
49. J. Gao, D.S. Garner, and W.L. Jorgensen Ab initio study of structures and binding energies for anion-water complexes J. Am. Chem. Soc. 108 1986 4784 4790
50. F.J. Luque, N. Reuter, A. Cartier, and M.F. Ruiz-López Calibration of the quantum/classical Hamiltonian in semiempirical QM/MM AM1 and PM3 methods J. Phys. Chem., A 104 2000 10923 10931
51. 2(8) graph set J. Phys. Chem. 100 1996 2957 2967
52. H.G. Hertz F. Franks Water A Comprehensive Treatise vol. 3 1973 Plenum Press New York
53. F. Brugè, E. Parisi, and S.L. Fornili Effects of simple model solutes on water dynamics: residence time analysis Chem. Phys. Lett. 250 1996 443 449
54. I. Muegge, and E.W. Knapp Residence times and lateral diffusion of water at protein surfaces: application to BPTI J. Phys. Chem. 99 1995 1371 1374
55. B. Linton, and A.D. Hamilton Calorimetric investigation of guanidinium-carboxylate interactions Tetrahedron 55 1999 6027 6038
56. E. Fan, S.A. Van Arman, S. Kincaid, and A.D. Hamilton Molecular recognition: hydrogen-bonding receptors that function in highly competitive solvents J. Am. Chem. Soc. 115 1993 369 370
57. D. Laria, and R. Fernández-Prini Molecular dynamics study of water clusters containing ion pairs: from contact to dissociation J. Chem. Phys. 102 1995 7664 7673
58. C. Chipot, B. Maigret, D.A. Pearlman, and P.A. Kollman Molecular dynamics potential of mean force calculations: a study of the toluene-ammonium π-cation interactions J. Am. Chem. Soc. 118 1996 2998 3005
59. P. Kollman Free energy calculations: applications to chemical and biological phenomena Chem. Rev. 93 1993 2395 2417
60. A.R. Leach Molecular Modelling: Principles and Applications 1996 Longman Singapore