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166 Benoft RouxThis chapter demonstrates that modern computational methods and moleculardynamics techniques provide powerful tools to study ion transport in complexbiological systems. Already, macromolecular modeling with atomic models is increasinglyused, in combination with experimental studies, in the rational design andsynthesis of artificial channels [104- 1061. As their three-dimensional structures willbecome available, it is hoped that the theoretical methods outlined in this chapterwill provide a “roadmapyy in studying the function of biological channels.AcknowledgementsThe support of the Medical Research Council fo Canada is gratefully acknowledged.References[l] Hille, B., Ionic Channels of Excitable Membranes, Sinauer, Sunderland, MA, 1984.[2] Parsegian, A., Nature 1969, 221, 844-846.[3] Neher, E., Sackmann, B., Sci. Am. 1992, 266, 44-51.[4] Catterall, W. A., Science 1988, 242, 50-61.[5] Heineman, S. H., Terlau, H., Stuhmer, W., Imoto, K., Numa, S., Nature 1992, 356,441 -443.[6] Galzi, J. L., Devillers-Thiery A., Hussy, N., Bertrand, S., Changeux, J. P., Bertrand, D.,Nature 1992, 359, 500.[7] Guy, H. R., Seetharamulu, P., Proc. Natl. Acad. Sci. USA 1986, 83, 508-512.[8] Guy, H. R., Conti, F,, TINS 1990, 13, 201-206.[9] Durrel, S. R., Guy, H. R., Biophys. 1 1992, 62, 238-250.[lo] Boxer, A., Bogusz, S., Busath, D., Protein Eng. 1992, 5, 285-293.[ll] Bogusz, S., Busath D., Biophys. 1 1992, 62, 19-21.[12] Deisenhofer, J., Epp, O., Miki, K., Huber, R., Michel, H., Nature 1985, 328, 618-624.[13] Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckmann, E., Downing,K. H., L Mol. Biol. 1990, 213, 899-929.[14] Weiss, M. S., Wacker, T., Weckesser, J., Welte, W., Schultz, G. E., FEBSLett. 1990,267,269-272.[15] Cowan, S. W., Schirmer, T., Rummel, G., Steirt, M., Ghosh, R., Paupit, R. A., Jan-sonius J. N., Rosenbusch, J. P., Nature 1992, 358, 727-733.[16] Brisson A., Unwin, P. N. T., Nature 1985, 315, 474-477.[17] Demin, V. V., Grishinand, E. V., Kovalenko, V. A., Spadar, S. N., in: Chemistry ofpeptides andproteins, Vol. 3, Ovchinnikov, Y. A., Voelter, W., Bayer, E., Ivanov, V. T.,(eds.), W. de Gruyter and Co., Berlin, Germany, 1986, pp. 363-370.[18] Chappel, J. B., Crofts, A. R., Biochem. L 1965, 95, 393-402.[19] Pressman, B. C., Proc. Natl. Acad. Sci. USA 1965, 53, 1076-1080.[20] Hladky, S. B., Haydon, D. A., Biochim. Biophys. Acta 1972, 274, 294-312.[21] Hladky, S. B., Haydon, D. A., Curr. Top. Membr. l’kansp. 1984, 21, 327-372.
6 Theory of Thansport in Ion Channels 167[22] Dani, J. A., Levitt, D., Biophys. J. 1981, 35, 501-508.[23] Rosenberg, P. A., Finkelstein, A., J. Gen. Physiol. 1978, 72, 327-340.[24] Finkelstein, A., Andersen, 0. S., J. Membr. Biol. 1981, 59, 155-171.[25] Andersen, 0. S., Annu. Rev. Physiol. 1984, 46, 531-548.[26] Andersen, 0. S., Procopio, J., Acta Physiol. Suppl. 1980, 481, 27-35.[27] Becker, M. D., Koeppe 11, R. E., Andersen, 0. S., Biophys. J. 1992, 62, 25-27.[28] Mackay, D. H., Berens, P. H., Wilson, K. R., Biophys. J. 1983, 46, 229-248.[29] Kim, K. S., Clementi, E., J Am. Chem. SOC. 1985, 107, 5504-5513.[30] Urry, D. W., Venkatachalam, C. M., J. Comp. Chem. 1983, 4, 461-469.[31] Chiu, S. W., Subramaniam, S., Jakobsson, E., McCammon, J. A., Biophys. J. 1989, 56,253 -261.[32] Chiu, S. W., Jakobsson, E., Subramaniam, S., McCammon, J. A., Biophys. J. 1991, 60,273-285.[33] Etchebest, C., Pullman, A., J. Biomol. Struct. &Dun. 1986, 3, 805-825.[34] Pullman, A., Q. Rev. Biophys. 1987, 20, 173-200.[35] Jordan, P. C., Transport through membranes: Carriers, channels andpumps, A. Pullmanet al. (eds.), Kluwer Academic Publisher, 1988, pp. 237-251.[36] Aqvist, J., Warshel, A., Biophys. J. 1989, 56, 171-182.[37] Roux, B., Karplus, M., Biophys. J. 1988, 53, 297-309.[38] Roux, B., Karplus, M., Biophys. .I 1991, 59, 961-981.[39] Roux, B., Karplus, M., J. Phys. Chem. 1991, 95, 4856-4868.[40] Roux, B., Karplus, M., J. Am. Chem. SOC. 1993, 115, 3250-3262.[41] Urry, D. W., Proc. Natl. Acad. Sci. USA 1971, 68, 672-676.[42] Urry, D. W., Walker, J. T., Trapane, T. L., L Membr. Biol. 1982, 69, 225-231.[43] Urry, D. W., Prasad, K. U., Trapane, T. L., Proc. Natl. Acad. Sci. USA 1982, 79,390- 394.[44] Urry, D. W., Trapane, T. L., Prasad, K. U., Science 1983, 221, 1064-1067.[45] Arseniev, A. S., Bystrov, V. F., Ivanov, T. V., Ovchinnikov, Y. A., FEBS Lett. 1985, 186,168- 174.[46] Bystrov, V. F., Arseniev, A. S., Tetrahedron 1988, 44, 925-940.[47] Cornell, B. A., Separovic, F., Baldassi, A. J., Smith, R., Biophys. J. 1988, 53, 67-76.[48] Smith, R., Thomas, D. E., Separovic, F., Atkins, A. R., Cornell, B. A., Biophys. J; 1989,56, 307-314.[49] Nicholson, L. K., LoGrasso, P. V., Cross T, A., J. Am. Chem SOC. 1989, Ill, 400-401.[50] Nicholson, L. K., Cross, T. A., Biochem. 1989, 28, 9379-9385.[51] Wooley, G. A., Wallace, B. A., J. Membr. Biol. 1992, 129, 109-136.[52] Lauger, P., Biochim. Biophys. Acta 1973, 311, 423-441.[53] Levitt, D. G., Ann. Rev. Biophys. Chem. 1987, IS, 29-57.[54] Furois-Corbin S., Pullman, A., Biochim. Biophys. Acta 1989, 984, 339-350.[55] Furois-Corbin, S., Pullman, A., Biophys. Chem. 1991, 39, 153 - 159.[56] Brooks 111, C. L., Karplus, M., Pettitt, B. M., Advances in Chemical Physics Vol. LXXI,Prigogine, J., Rice, S. A. (eds.), John Wiley & Sons, New York, 1988.[57] Helfand, E., Phys. Rev. 1960, 119, 1-9.[58] Cooper, K. E., Jakobsson, E., Wolynes, P. G., Prog. Biophys. Mol. Biol. 1985,46, 51-96.[59] The net charge per unit area, Qhet, necessary to generate the transmembrane potential isAIJ/E~/M, where cM and AX are the dielectric constant and the thickness of thehydrocarbon region. For a typical potential of 100 millivolts the net charge per area isapproximately one unit charge per square of (25 nm)2. The charge imbalance is distributedwithin a distance comparable to the Debye length from the membrane, i. e., on theorder of (- 0.9 nm). Since a physiological concentration of KC1 (150 mM) represents ap-
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Computer Modellingin Molecular Biol
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Professor Julia M. GoodfellowDepart
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ContentsColour Illustrations ......
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XContributorsBenoit RouxGroupe de R
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Colour IllustrationsXI11Figure 4-4.
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XVIColour IllustrationsFigure 7-18.
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2 Julia M. Goodfellow and Mark A. W
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Computer Modelling in Molecular Bio
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2 Modellinn Protein Structures 11su
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2 Modelling Protein Structures 13St
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2 Modelling Protein Structures 271.
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2.3.3 Available Modelling Programs2
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2 Modelling Protein Structures 31sp
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2 Modellina Protein Structures 33Ac
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2 Modelling Protein Structures 35[8
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38 D. J Osmthorue and I? K. C Paul3
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4 Molecular Dynamics and Free Energ
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4 Molecular Dvnamics and Free Enera
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5 Modelling Nucleic Acids 105and it
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5 Modelling Nucleic Acids 107of the
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5 Modelling Nucleic Acids 109ElFigu
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5 Modellinn Nucleic Acids 1135.7 Ch
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Page 144 and 145: 134 Benoft Roux6.1 IntroductionThe
Page 146 and 147: 136 Benoit Roux[18-201. The gramici
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Page 152 and 153: 142 Benoft RouxTable 6-1. Interacti
Page 154 and 155: 144 Benoit RouxFigure 6-2. Solvated
Page 156 and 157: 146 Benoit Rouxwater box equilibrat
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Page 162 and 163: 152 Benoit RouxOne advantage of thi
Page 164 and 165: 154 Benoft Roux-.3.-15-c 10 -h5 5 -
Page 166 and 167: 156 Benoft Rouxwhere x and v are th
Page 168 and 169: 158 Benoit RouxReactant to ProductO
Page 170 and 171: 160 Benoit Rouxremain in close cont
Page 172 and 173: 162 Benoit Rouxis the deviation of
Page 174 and 175: 164 Benoft RouxTable 6-3. Pre-expon
Page 178 and 179: 168 Benoft Rouxproximately one Kf c
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218 Oliver S. Smartvolving large mo
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220 Oliver S. Smart8.2 TheoryConsid
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222 Oliver S. Smart(8-2)and applyin
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224 Oliver S. SmartThe repulsion te
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226 Oliver S. Smart8.4 Applications
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228 Oliver S. Smartrigid-body penal
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230 Oliver S. Smart216 252 200 324
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232 Oliver S. SmartrbFigure 8-5. A
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234 Oliver S. Smartlink the eoc and
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236 Oliver S. Smarttermediates mark
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240 Oliver S. Smart[39] Halgren, T.
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242 IndexGGramicidin A 134- NMR dat
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