Potentials of mean force and permeabilities for carbon dioxide, ammonia, and water flux across a Rhesus protein channel and lipid membranes

Journal of the American Chemical Society

Volumn 132, Issue 38, 2010, Pages 13251-13263

  Hub, Jochen S ^a   Winkler, Fritz K ^b   Merrick, Mike ^c   De Groot, Bert L ^d  

^a UPPSALA UNIVERSITY   (Sweden)

^b PAUL SCHERRER INSTITUTE   (Switzerland)

^c JOHN INNES CENTRE   (United Kingdom)

^d MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA AND CARBON DIOXIDE; AQUAPORINS; CHOLESTEROL CONTENT; CONFORMATIONAL CHANGE; DENSE MEMBRANE; LIPID MEMBRANES; MEMBRANE PROTEINS; MOLECULAR DYNAMICS SIMULATIONS; NITROSOMONAS EUROPAEA; POTENTIALS OF MEAN FORCES; RHESUS PROTEINS; WATER FLUX; WATER PERMEATION;

AMMONIA; AMMONIUM COMPOUNDS; BIOLOGICAL MEMBRANES; CARBON DIOXIDE; CHOLESTEROL; LIPIDS; MOLECULAR DYNAMICS; PROTEINS;

PERMEATION;

AMMONIA; AQUAPORIN; CARBON DIOXIDE; CHOLESTEROL; LIPID; MEMBRANE PROTEIN; METHYLAMINE; RHESUS PROTEIN CHANNEL; UNCLASSIFIED DRUG; WATER;

ARTICLE; BACTERIAL MEMBRANE; CONFORMATIONAL TRANSITION; CRYSTALLOGRAPHY; FORCE; LIPID MEMBRANE; MEMBRANE PERMEABILITY; MOLECULAR DYNAMICS; MOLECULAR MODEL; NITROSOMONAS EUROPAEA; PROTEIN FUNCTION; REGULATORY MECHANISM; SIMULATION; WATER PERMEABILITY;

AMMONIA; CARBON DIOXIDE; MEMBRANE LIPIDS; MEMBRANE PROTEINS; WATER;

EID: 77957110065     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja102133x     Document Type: Article

References (80)

1. Huang, C.-H. and Peng, J. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 15512-15517
2. Marini, A. M., Urrestarazu, A., Beauwens, R., and André, B. Trends Biochem. Sci. 1997, 22, 460-461
3. Marini, A. M., Matassi, G., Raynal, V., André, B., Cartron, J. P., and Chérif-Zahar, B. Nat. Genet. 2000, 26, 341-344
4. Westhoff, C. M. Transfusion 2004, 44, 1663-1673
5. Biver, S., Belge, H., Bourgeois, S., Vooren, P. V., Nowik, M., Scohy, S., Houillier, P., Szpirer, J., Szpirer, C., Wagner, C. A., Devuyst, O., and Marini, A. M. Nature 2008, 456, 339-343
6. Ripoche, P., Bertrand, O., Gane, P., Birkenmeier, C., Colin, Y., and Cartron, J.-P. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 17222-17227
7. Kustu, S. and Inwood, W. Transfus. Clin. Biol. 2006, 13, 103-110
8. Peng, J. and Huang, C. H. Transfus. Clin. Biol. 2006, 13, 85-94
9. Soupene, E., Inwood, W., and Kustu, S. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7787-7792
10. Endeward, V., Cartron, J.-P., Ripoche, P., and Gros, G. FASEB J. 2008, 22, 64-73
11. Khademi, S., O'Connell, J., Remis, J., Robles-Colmenares, Y., Miercke, L. J. W., and Stroud, R. M. Science 2004, 305, 1587-1594
12. Zheng, L., Kostrewa, D., Berneche, S., Winkler, F. K., and Li, X.-D. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 17090-17095
13. Andrade, S. L. A., Dickmanns, A., Ficner, R., and Einsle, O. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 14994-14999
14. Lupo, D., Li, X.-D., Durand, A., Tomizaki, T., Cherif-Zahar, B., Matassi, G., Merrick, M., and Winkler, F. K. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 19303-19308
15. Li, X., Jayachandran, S., Nguyen, H.-H. T., and Chan, M. K. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 19279-19284
16. Gruswitz, F., Chaudhary, S., Ho, J. D., Schlessinger, A., Pezeshki, B., Ho, C.-M., Sali, A., Westhoff, C. M., and Stroud, R. M. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 9638-9643
17. Zidi-Yahiaoui, N., Mouro-Chanteloup, I., D'Ambrosio, A.-M., Lopez, C., Gane, P., van Kim, C. L., Cartron, J.-P., Colin, Y., and Ripoche, P. Biochem. J. 2005, 391, 33-40
18. Zidi-Yahiaoui, N., Callebaut, I., Genetet, S., Kim, C. L. V., Cartron, J.-P., Colin, Y., Ripoche, P., and Mouro-Chanteloup, I. Am. J. Physiol. 2009, 297, C537-C547
19. Fong, R. N., Kim, K.-S., Yoshihara, C., Inwood, W. B., and Kustu, S. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 18706-18711
20. Javelle, A., Lupo, D., Ripoche, P., Fulford, T., Merrick, M., and Winkler, F. K. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 5040-5045
21. Mayer, M., Schaaf, G., Mouro, I., Lopez, C., Colin, Y., Neumann, P., Cartron, J.-P., and Ludewig, U. J. Gen. Physiol. 2006, 127, 133-144
22. Neuhäuser, B., Dynowski, M., and Ludewig, U. FEBS Lett. 2009, 583, 2833-2838
23. Walter, B., Küspert, M., Ansorge, D., Krämer, R., and Burkovski, A. J. Bacteriol. 2008, 190, 2611-2614
24. Endeward, V. and Gros, G. J. Physiol. 2009, 587, 1153-1167
25. Missner, A., Kügler, P., Saparov, S. M., Sommer, K., Mathai, J. C., Zeidel, M. L., and Pohl, P. J. Biol. Chem. 2008, 283, 25340-25347
26. Missner, A. and Pohl, P. ChemPhysChem 2009, 10, 1405-1414
27. Lande, M. B., Donovan, J. M., and Zeidel, M. L. J. Gen. Physiol. 1995, 106, 67-84
28. Prasad, G. V. R., Coury, L. A., Finn, F., and Zeidel, M. L. J. Biol. Chem. 1998, 273, 33123-33126
29. Hub, J. S. and de Groot, B. L. Biophys. J. 2006, 91, 842-848
30. Kikeri, D., Sun, A., Zeidel, M. L., and Hebert, S. C. Nature 1989, 339, 478-480
31. Waisbren, S. J., Geibel, J. P., Modlin, I. M., and Boron, W. F. Nature 1994, 368, 332-335
32. Hub, J. S. and de Groot, B. L. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1198-1203
33. Luzhkov, V. B., Almlöf, M., Nervall, M., and Åqvist, J. Biochemistry 2006, 45, 10807-10814
34. Nygaard, T. P., Rovira, C., Peters, G. H., and Jensen, M. Ø. Biophys. J. 2006, 91, 4401-4412
35. Lin, Y., Cao, Z., and Mo, Y. J. Am. Chem. Soc. 2006, 128, 10876-10884
36. Yang, H., Xu, Y., Zhu, W., Chen, K., and Jiang, H. Biophys. J. 2007, 92, 877-885
37. Cao, Z., Mo, Y., and Thiel, W. Angew. Chem., Int. Ed. 2007, 46, 6811-6815
38. Bostick, D. L. and Brooks, C. L. PLoS Comput. Biol. 2007, 3 e22
39. Bostick, D. L. and Brooks, C. L. Biophys. J. 2007, 92, L103-L105
40. Ishikita, H. and Knapp, E.-W. J. Am. Chem. Soc. 2007, 129, 1210-1215
41. Lamoureux, G., Klein, M. L., and Berneche, S. Biophys. J. 2007, 92, L82-L84
42. Mathai, J. C., Tristram-Nagle, S., Nagle, J. F., and Zeidel, M. L. J. Gen. Physiol. 2008, 131, 69-76
43. Subczynski, W. K., Hyde, J. S., and Kusumi, A. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 4474-4478
44. Welander, P. V., Hunter, R. C., Zhang, L., Sessions, A. L., Summons, R. E., and Newman, D. K. J. Bacteriol. 2009, 191, 6145-6156
45. Cherif-Zahar, B., Durand, A., Schmidt, I., Hamdaoui, N., Matic, I., Merrick, M., and Matassi, G. J. Bacteriol. 2007, 189, 9090-9100
46. Weidinger, K., Neuhäuser, B., Gilch, S., Ludewig, U., Meyer, O., and Schmidt, I. FEMS Microbiol. Lett. 2007, 273, 260-267
47. Walter, A. and Gutknecht, J. J. Membr. Biol. 1986, 90, 207-217
48. Antonenko, Y. N., Pohl, P., and Denisov, G. A. Biophys. J. 1997, 72, 2187-2195
49. Yang, B., Fukuda, N., van Hoek, A., Matthay, M. A., Ma, T., and Verkman, A. S. J. Biol. Chem. 2000, 275, 2686-2692
50. Hub, J. S., Grubmüller, H., and de Groot, B. L. Handb. Exp. Pharmacol. 2009, 190, 57-76
51. Endeward, V., Musa-Aziz, R., Cooper, G. J., Chen, L.-M., Pelletier, M. F., Virkki, L. V., Supuran, C. T., King, L. S., Boron, W. F., and Gros, G. FASEB J. 2006, 20, 1974-1981
52. Musa-Aziz, R., Chen, L.-M., Pelletier, M. F., and Boron, W. F. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 5406-5411
53. Mouro-Chanteloup, I., Cochet, S., Chami, M., Genetet, S., Zidi-Yahiaoui, N., Engel, A., Colin, Y., Bertrand, O., and Ripoche, P. PLoS One 2010, 5 e8921
54. Gutknecht, J., Bisson, M. A., and Tosteson, F. C. J. Gen. Physiol. 1977, 69, 779-794
55. Rattray, J. E., van de Vossenberg, J., Hopmans, E. C., Kartal, B., van Niftrik, L., Rijpstra, W. I. C., Strous, M., Jetten, M. S. M., Schouten, S., and Damsté, J. S. S. Arch. Microbiol. 2008, 190, 51-66
56. Khoo, K. H., Culberson, C. H., and Bates, R. G. J. Solution Chem. 1977, 6, 281-290
57. Saparov, S. M., Liu, K., Agre, P., and Pohl, P. J. Biol. Chem. 2007, 282, 5296-5301
58. Beitz, E., Wu, B., Holm, L. M., Schultz, J. E., and Zeuthen, T. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 269-274
59. Vriend, G. J. Mol. Graphics 1990, 8, 52-56
60. Faraldo-Gómez, J. D., Smith, G. R., and Sansom, M. S. P. Eur. Biophys. J. 2002, 31, 217-227
61. Van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., and Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 701-1719
62. Hess, B., Kutzner, C., van der Spoel, D., and Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-447
63. Jorgensen, W. L., Maxwell, D. S., and Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236
64. Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., and Jorgensen, W. L. J. Phys. Chem. B 2001, 105, 6474-6487
65. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
66. Berger, O., Edholm, O., and Jähnig, F. Biophys. J. 1997, 72, 2002-2013
67. Zhao, W., Róg, T., Gurtovenko, A. A., Vattulainen, I., and Karttunen, M. Biophys. J. 2007, 92 (4) 1114-1124
68. Darden, T., York, D., and Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092
69. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8592
70. Miyamoto, S. and Kollman, P. A. J. Comput. Chem. 1992, 13, 952-962
71. Hess, B. J. Chem. Theory Comput. 2008, 4, 116-122
72. Nosé, S. Mol. Phys. 1984, 52, 255-268
73. Hoover, W. G. Phys. Rev. A 1985, 31, 1695-1697
74. Parrinello, M. and Rahman, A. J. Appl. Phys. 1981, 52, 7182-7190
75. Espinosa, E., Molins, E., and Lecomte, C. Chem. Phys. Lett. 1998, 285, 170-173
76. Höltje, M., Förster, T., Brandt, B., Engels, T., von Rybinski, W., and Höltje, H. D. Biochim. Biophys. Acta 2001, 1511, 156-167
77. Smart, O. S., Neduvelil, J. G., Wang, X., Wallace, B. A., and Sansom, M. S. P. J. Mol. Graphics 1996, 14, 354-360
78. Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A., and Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021
79. Allen, T. W., Andersen, O. S., and Roux, B. Biophys. Chem. 2006, 124, 251-267
80. Finkelstein, A. Water movement through lipid bilayers, pores, and plasma membranes.: Wiley & Sons: 1987.