Molecular recognition explored by a statistical-mechanics theory of liquids

Current Pharmaceutical Design

Volumn 17, Issue 17, 2011, Pages 1740-1757

  Phongphanphanee, Saree ^a   Yoshida, Norio ^a   Hirata, Fumio ^a  

^a INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

Author keywords

3d RISM; Aquaporin; M2 channel; Molecular recognition; Proton channel

Indexed keywords

AQUAGLYCEROPORIN; AQUAPORIN; LIGAND; PROTEIN M2; PROTON;

CELLULAR DISTRIBUTION; CHANNEL GATING; CONDUCTANCE; LIQUID; MECHANICS; MEMBRANE PERMEABILITY; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROKARYOTE; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTON TRANSPORT; REVIEW; THEORETICAL MODEL; THREE DIMENSIONAL REFERENCE INTERACTION SITE MODEL THEORY; WATER SUPPLY;

AQUAPORINS; LIGANDS; MODELS, MOLECULAR; MODELS, THEORETICAL; PROBABILITY; PROTEIN CONFORMATION; WATER;

EID: 79960307353     PISSN: 13816128     EISSN: 18734286     Source Type: Journal    
DOI: 10.2174/138161211796355100     Document Type: Review

References (84)

1. Michaelis L, Menten ML. Die Kinetik der Invertinwirkung, Bio-Chem Z 1913; 49: pp. 333-369.
2. Lehn JM. Supramolecular Chemistry, Willy-VCH, Weinheim 1995.
3. Gellman SG. Introduction: Molecular Recognition, Chem Rev 1997; 97: pp. 1231-1232.
4. Sotriffer C, Klebe G. Identification and mapping of small-molecule binding sites in proteins: Computational tools for structure-based drug design, Il Farmaco, 2002; 57: pp. 243-251.
5. Gohlke H, Klebe G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors, Angew. Chem Int Ed. 2002; 41, pp. 2644-2676.
6. Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics, J Am Chem Soc 1990; 112: pp. 6127-6129.
7. Gilson MK, Honig B. Energetics of charge - charge interactions in proteins, Proteins: Struct. Funct. Genet. 1988; 3: pp. 32-52.
8. Kato M, Warshel A. Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels, J Phys Chem B 2005; 109: pp. 19516-19522.
9. Zhu F, Tajkhorshid E, Schulten K. Theory and Simulation of Water Permeation in Aquaporin-1, BioPhys J 2004; 86: pp. 50-57.
10. Hirata F., ed. Molecular Theory of Solvation, Springer-Kluwer, Dordrecht, Netherlands 2003.
11. Kovalenko A, Hirata F. Three-dimensional density profiles of water in contact with a solute of arbitrary shape: A RISM approach, Chem Phys Lett. 1998; 290: pp. 237-244.
12. Beglov D, Roux B. An integral equation to describe the salvation of polar molecules in liquid water, J Phys Chem B, 1997; 101: pp. 7821-7826.
13. Hansen JP, McDonald IR. Theory of Simple Liquids, 3rd edn. Academic, London. 2006.
14. Blum L, Torruella AJ. Invariant expansion for two-body correlations: Thermodynamic functions, scattering, and the ornsteinzernike equation, J Chem Phys 1972; 56: pp. 303-310.
15. Imai T, Kovalenko A, Hirata F. Solvation thermodynamics of protein studied by the 3D-RISM theory, Chem Phys Lett. 2004; 395: pp. 1-6.
16. Imai T, Hiraoka R, Kovalenko A, Hirata F. Water molecules in a protein cavity detected by a statistical-mechanical theory, J Am Chem Soc. 2005; 127: pp. 15334-15335.
17. Chandler D, Andersen HC. Optimized Cluster Expansions for Classical Fluids. II. Theory of Molecular Liquids, J Chem Phys 1972; 57: pp. 1930-1937.
18. Cortis CM, Rossky PJ, Friesner RA. A three-dimensional reduction of the Ornstein-Zernicke equation for molecular liquids, J Chem Phys 1997; 107: pp. 6400-6414.
19. Kovalenko A, Hirata F. Self-consistent description of a metal-water interface by the Kohn-Sham density functional theory and the three-dimensional reference interaction site model, J Chem Phys 1999; 110: pp. 10095-10112.
20. Singer SJ, Chandler D. Free energy functions in the extended RISM approximation, Mol. Phys 1985; 55: pp. 621-625.
21. Kirkwood JG, Buff FD. The statistical mechanical theory of solutions. I, J Chem Phys 1951; 19: pp. 774-777.
22. Imai T, Kinoshita M, Hirata F. Theoretical study for partial molar volume of amino acids in aqueous solution: implication of ideal fluctuation volume, J Chem Phys 2000; 112: pp. 9469-9478.
23. Harano Y, Imai T, Kovalenko A, Hirata F. Theoretical study for partial molar volume of amino acids and polypeptides by the threedimensional reference interaction site model, J Chem Phys 2001; 114: pp. 9506-9511.
24. Borgnia M, Neilsen S, Engel A, Agre P. Cellular and molecular biology of the aquaporin water channels, Annu. Rev BioChem 1999; 68: pp. 425-458.
25. Kruse E, Uehlein N, Kaldenhoff R. 2006; The aquaporins, Genome Biol 7: pp 206.
26. Johansson I, Karlsson M, Johanson U, Larsson C, Kjellbom P. The role of aquaporins in cellular and whole plant water balance, Biochimica et Biophysica Acta 2000; 1465: pp 324-342.
27. Agre P, King LS, Yasui M, et al. Aquaporin water channels-from atomic structure to clinical medicine. J Physiol. 2002; 542: pp 3-16.
28. Jiang J, Daniels BV, Fu D. Crystal Structure of AqpZ Tetramer Reveals Two Distinct Arg-189 Conformations associated with water permeation through the narrowest constriction of the waterconducting channel, J Biol Chem 2006; 281: pp 454-460.
29. Smart OS, Goodfellow JM, Wallace BA. The pore dimensions of gramicidin A, BioPhys J 1993; 65: pp 2455-2460.
30. Wu B, Beitz, E. Aquaporins with selectivity for unconventional permeants, Cell. Mol Life Sci 2007; 64: pp 2413-2421.
31. Nakhoul NL, Davis BA, Romero MF, Boron WF. Effect of expressing the water channel aquaporin-1 on the CO2 permeability of Xenopus oocytes, Am J Physiol Cell Physio. 1998; 274: pp C543-C548.
32. Endeward V, Musa-Aziz R, Cooper GJ, et al. Evidence that aquaporin 1 is a major pathway for CO2 transport across the human erythrocyte membrane, FASEB J 2006; 20: pp 1974-1981.
33. Prasad GVR, Coury LA, Finn F, Zeidel ML. Reconstitute aquaporin 1 water channels transport CO2 across membranes, J Biol Chem, 1998; 273: pp 33123-33126.
34. + in oocytes expressing aquaporin-1, Am J Physiol Renal Physiol. 2001; 281: pp F255-F263.
35. Ripoche P, Goossens D, Devuyst O, et al. Role of RhAG and AQP1 in NH3 and CO2 gas transport in red cell ghosts: a stoppedflow analysis, Transf. Clin. Biol 2006; 13: pp 117-122.
36. Yang B, Fukuda N, Van Hoek A, Mathay MA, Ma T. Verkman AS. Carbon dioxide permeability of aquaporin-1 measured in erythrocytes and lung of aquaporin-1 null mice and in reconstitute proteoliposomes, J Biol Chem 2000; 275: pp 2686-2692.
37. Fang X, Yang B, Matthay MA, Verkman AS. Evidence agains aquaporin-1-dependent CO2 permeability in lung and kidney, J Physiol. 2002; 542: pp 63-69.
38. Beitz E, Wu B, Holm LM, Schultz J E, Zeuthen T. Point mutations in the aromatic/arginine region in aquaorin 1 allow passage of urea, glycerol, ammonia and protons, Proc Natl Acad Sci USA 2006; 103: pp 269-274.
39. + permeability in aquaporin-expressing Xenopus oocytes, Eur. J Physiol. 2005; 450: pp 415-428.
40. Callam CS, Singer SJ, Lowary TL, Hadad CM. Computational analysis of the potential energy surfaces of glycerol in the gas and aqueous phases: Effect of level of theory, basis set, and salvation on strongly intramolecularly hydrogen-bonded system, J Am Chem Soc. 2001; 123: 11743-11754.
41. Hub, JS, de Groot, BL. Mechanism of selectivity in aquaporins and aquaglyceroporins, Proc Natl Acad Sci USA 2008; 105: pp 1198-1203.
42. Wang Y, Schulten K, Tajkhorshid E. What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF, Structure 2005; 13: 1107-1118.
43. Jensen MØ, Park S, Tajkhorshid E, Schulten K. Energetics of glycerol conduction through aquaglyceroporin GlpF, Proc Natl Acad Sci USA 2002; 99: 6731-6736.
44. Heller KB, Lin ECC, Wilson TH. Substrate specificity and transport properties of the glycerol facilitator of Escherichia coli, J Bacteriol. 1980; 144: 274-278.
45. Preston GM, Carroll TP, Guggino WB, Agre P. Appearance of water channels in Xenopus oocytes expressing red cell CHIP28 protein, Science 1992; 256: pp 385-387.
46. Zeidel ML, Ambudkar SV, Smith BL, Agre P. Reconstitution of functional water channels in liposomes containing purified red cell CHIP28 protein, Biochemistry 1992; 31: pp 7436-7440.
47. Saparov SM, Tsunoda SP, Pohl P. Proton exclusion by an aquaglyceroprotein: a voltage clamp study, Biol Cell, 2005; 97: pp 545-550.
48. de Groot BL, Grubmüller H. Water Permeation across Biological membranes: mechanism and dynamics of aquaporin-1 and GlpF, Science, 2001; 294: pp 2353-2357.
49. Agre P, Lee MD, Devidas LS, Guggino WB. Aquaporin and ion conductance, Science 1997; 275: pp 1490-1492.
50. de Groot BL, Grubmüller H. The dynamics and energetics of water permeation and proton exclusion in aquaporins, Curr. Opin. Struct. Biol 2005; 15: pp. 176-183.
51. Tajkhorshid E, Nollert P, Jensen MØ, et al. Control of the selectivity of the aquaporin water channel family by global orientational tuning, Science 2002; 296: pp. 525-530.
52. Jensen MØ, Tajkhorshid E, Schulten K. Electrostatic Tuning of Permeation and Selectivity in Aquaporin Water Channels, BioPhys J 2003; 85: pp. 2884-2899.
53. Ilan B, Tajkhorshid E, Schulten K, Voth GA. The Mechanism of Proton Exclusion in Aquaporin Channels, Protein 2004; 55: pp. 223-228.
54. Chen H, Ilan B, Wu Y, Zhu F, Schulten K, Voth GA. Charge delocalization in proton channels, I: The aquaporin channels and proton blockage, BioPhys J 2007; 92: pp. 46-60.
55. Burykin A, Warshel A. What Really Prevents Proton Transport through Aquaporin? Charge Self-Energy versus Proton Wire Proposals, BioPhys J 2003; 85: pp. 3969-3706.
56. Burykin A, Warshel A. On the origin of the electrostatic barrier for proton transport in aquaporin, FEBS Letter 2004; 570: pp. 41-46.
57. Chakrabarti N, Roux B, Pomès R. Structural determinants of proton blockage in aquaporins, J Mol Biol 2004; 343: pp. 493-510.
58. Chakrabarti N, Tajkhorshid E, Roux B, Pomès R. Molecular Basis of Proton Blockage in Aquaporins, Structure 2004; 12: pp. 65-74.
59. Kato M, Pisliakov AV, Warshel A. The barrier for proton transport in aquaporins as a challenge for electrostatic models: The role of protein relaxation in mutational calculations, Proteins 2006; 64: pp. 829-844.
60. von Grotthuss CJ D. Sur la décomposition de l'eau et des corps qu'elle tient en dissolution à l'aide de l'électricité galvanique, Ann. Chim., 58 1806; pp. 54-73.
61. Agmon N. The Grotthuss mechanism, Chem Phys Lett. 1995; 244, pp. 456-462.
62. Kovalenko A, Hirata F. Potential of mean force between two molecular ions in a polar molecular solvent: A study by the three dimensional reference interaction site model, J Phys Chem B. 1999; 103: pp. 7942-7957.
63. Yoshida N, Phongphanphanee S, Maruyama Y, Imai T, Hirata F. Selective ion-binding by protein probed with the 3D-RISM theory, J Am Chem Soc. 2006; 128: pp. 12042-12043.
64. Yoshida N, Phongphanphanee S, Hirata F. Selective ion binding by protein probed with the statistical mechanical integral equation theory, J Phys Chem B. 2007; 111: pp. 4588-4595.
65. Imai T, Hiraoka R, Kovalenko A, Hirata F. Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation, Protein, 2007; 66: pp. 804-813.
66. Phongphanphanee S, Yoshida N, Hirata F. The statisticalmechanics study for the distribution of water molecules in aquaporin, Chem Phys Lett. 2007; 449: pp. 196-201.
67. Phongphanphanee S, Yoshida N, Hirata F. On the proton exclusion of aquaporins: A statistical mechanics study, J Am Chem Soc. 2008; 130: pp. 1540-1541.
68. Phongphanphanee S, Yoshida N, Hirata F. The potential of mean force of water and ions in aquaporin channels investigated by the 3D-RISM method, J Mol Liquid 2009; 147: pp. 107-111.
69. Lamb RA, Holsinger LJ, Pinto LH. In Receptor-mediated Virus Entry into Cells (Wimmer, E., ed), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1994; pp. 303-321.
70. Helenius A. Unpacking the incoming influenza virus, Cell 1992; 69: pp. 577-578.
71. Pinto LH, Holsinger LJ, Lamb RA. Influenza virus M2 protein has ion channel activity, Cell 1992; 69: pp. 517-528.
72. Lear JD. Proton conduction through the M2 protein of the influenza A virus; a quantitative, mechanistic analysis of experimental data, FEBS Letters, 2003; 552: pp. 17-22.
73. Mould JA, Li H, Dunlak CS, et al. Mechanism for proton conduction of the M2 ion channel of influenza A virus, J Biol Chem 2000; 275: pp. 8592-8599.
74. Mould JA, Drury JE, Frings SM, et al. Permeation and activation of the M2 ion channel of influenza A virus, J Biol Chem 2000; 275: pp. 31038-31050.
75. Chizhmakov IV, Geraghty FM, Ogden DC, Hayhurst A, Antoniou M, Hay AJ. Selective proton permeability and pH regulation of the influenza virus M2 channel expressed in mouse erythroleukaemia cells, J Physiol. 1996; 494: pp. 329-336.
76. Vijayvergiya V, Wilson R, Chorak A, Gao PF, Cross TA, Busath DD. Proton conductance of influenza virus M2 protein in planar lipid bilayers, BioPhys J 2004; 87: pp. 1697-1704.
77. Venkataraman P, Lamb RA, Pinto LH. Chemical rescue of histidine selectivity filter mutants of the M2 ion channel of influenza A virus, J Biol Chem 2005; 280: pp. 21463-21472.
78. Hu J, Fu R, Nishimura K, et al. Histidines, heart of the hydrogen ion channel from influenza A virus: Toward an understanding of conductance and proton selectivity, Proc Natl Acad Sci USA 2006; 103: pp. 6856-6870.
79. Tang Y, Zaitseva F, Lamb RA, Pinto LH. The gate of the influenza virus M2 proton channel is formed by a single tryptophan residue, J Biol Chem 2002; 277: pp. 39880-39886.
80. Okada A, Miura T, Takeuchi H. Protonation of histidine and histidine- tryptophan interaction in the activation of the M2 ion channel from influenza A virus, Biochemistry 2001; 40: pp. 6053-6060.
81. Takeuchi H, Okada A, Miura T. Roles of the histidine and tryptophan side chains in the M2 proton channel from influenza A virus, FEBS Lett. 2003; 552: pp. 35-38.
82. Intharathep P, Laohpongspaisan C, Rungrotmongkol T, et al. How amantadine and rimantadine inhibit proton transport in the M2 protein channel, J Mol Graph. Model. 2008; 27: pp. 342-348.
83. Kass I, Arkin T. How pH opens a H+ channel: The gating mechanism of influenza A M2, Structure 2005; 13: pp. 1789-1798.
84. Chen H, Wu Y, Voth GA. Proton transport behavior through the influenza A M2 channel: Insights from molecular simulation, Bio-Phys J 2007; 93: pp. 3470-3479.