Permeation through the calcium release channel of cardiac muscle

Biophysical Journal

Volumn 73, Issue 3, 1997, Pages 1337-1354

  Chen, Duan ^a   Xu, Le ^b   Tripathy, Ashutosh ^b   Meissner, Gerhard ^b   Eisenberg, Bob ^a  

^a RUSH MEDICAL COLLEGE   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RYANODINE; RYANODINE RECEPTOR;

ARTICLE; DIFFUSION; DIFFUSION COEFFICIENT; HEART MUSCLE; IONIZATION; MEMBRANE CURRENT; MEMBRANE PERMEABILITY; SARCOPLASMIC RETICULUM;

EID: 0030799617     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78167-0     Document Type: Article

References (127)

1. Alvarez, O., A. Villaroel, and G. Eisenman. 1992. Calculations of ion currents from energy profiles and energy profiles from ion currents in multibarrier, multisite, multioccupancy channel model. Methods Enzymol. 207:816-854.
2. Andersen, O. S., and R. E. Koeppe. 1992. Molecular determinants of channel function. Physiol. Rev. 72:S89-S157.
3. Ashcroft, N. W., and N. D. Mermin. 1976. Solid State Physics. Harcourt Brace College Publishers, New York.
4. Balian, R. 1992. From Microphysics to Macrophysics. Springer Verlag, New York.
5. Barcilon, V., D.-P. Chen, R. S. Eisenberg, and J. W. Jerome. 1997. Qualitative properties of steady-state Poisson-Nernst-Planck systems: perturbation and simulation study. SIAM J. Appl. Math. 57:631-648.
6. Barcilon, V., D. Chen, R. Eisenberg, and M. Ratner. 1993. Barrier crossing with concentration boundary conditions in biological channels and chemical reactions. J. Chem. Phys. 98:1193-1211.
7. Barkai, E., R. S. Eisenberg, and Z. Schuss. 1996. A bidirectional shot noise in a singly occupied channel. Phys. Rev. E. 54:1161-1175.
8. Bek, S., and E. Jakobsson. 1994. Brownian dynamics study of a multiply-occupied cation channel: application to understanding permeation in potassium channels. Biophys. J. 66:1028-1038.
9. Berne, B. J., M. Borkovec, and J. E. Straub. 1988. Classical and modern methods in reaction rate theory. J. Phys. Chem. 92:3711-3725.
10. Berry, S. R., S. A. Rice, and J. Ross. 1980. Physical Chemistry. John Wiley and Sons, New York.
11. Bird, G. A. 1994. Molecular Gas Dynamics and the Direct Simulation of Gas Flows. Clarendon Press, Oxford.
12. Booth, M. J., A. C. Eaton, and D. J. Haymet. 1995. Electrolytes at charged interfaces: integral equation theory for 2-2 and 1-1 model electrolytes. J. Chem. Phys 103:417-431.
13. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 4:187-217.
14. Brooks, C. L., M. Karplus, and B. M. Pettitt. 1988. Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics. John Wiley and Sons, New York.
15. Cercignani, C., R. Illner, and M. Pulvirenti. 1994. The Mathematical Theory of Dilute Gases. Springer Verlag, New York.
16. Chandler, D. 1978. Statistical mechanics of isomerization dynamics in liquids and the transition state approximation. J. Chem. Phys. 68: 2959-2970.
17. Chandler, D. 1987. Introduction to Modern Statistical Mechanics. Oxford University Press, New York.
18. Chen, D. P., V. Barcilon, and R. S. Eisenberg. 1992. Constant field and constant gradients in open ionic channels. Biophys. J. 61:1372-1393.
19. Chen, D. P., and R. S. Eisenberg. 1993a. Charges, currents and potentials in ionic channels of one conformation. Biophys. J. 64:1405-1421.
20. Chen, D. P., and R. S. Eisenberg. 1993b. Flux, coupling, and selectivity in ionic channels of one conformation. Biophys. J. 65:727-746.
21. Chen, D., R. Eisenberg, J. Jerome, and C. Shu. 1995a. Hydrodynamic model of temperature change in open ionic channels. Biophys. J. 69: 2304-2322.
22. Chen, D. P., J. Lear, and R. S. Eisenberg. 1997. Permeation through an open channel. Poisson-Nernst-Planck theory of a synthetic ionic channel. Biophys. J. 72:97-116.
23. Chen, D. P., W. Nonner, and R. S. Eisenberg. 1995b. PNP theory fits current-voltage (IV) relations of a neuronal anion channel in 13 solutions. Biophys. J. 68:A370.
24. Chiu, S. W., and E. Jakobsson. 1989. Stochastic theory of singly occupied ion channels. II. Effects of access resistance and potential gradients extending into the bath. Biophys. J. 55:147-157.
25. Conley, E. C. 1996a. The Ion Channel Facts Book. I. Extracellular Ligand-Gated Channels. Academic Press, New York.
26. Conley, E. C. 1996b. The Ion Channel Facts Book. II. Intracellular Ligand-Gated Channels. Academic Press, New York.
27. Conley, E. C. 1997. The Ion Channel Facts Book. III. Inward Rectifier and Intercellular Channels. Academic Press, New York.
28. Cooper, K. E., P. Y. Gates, and R. S. Eisenberg. 1988a. Diffusion theory and discrete rate constants in ion permeation. J. Membr. Biol. 109: 95-105.
29. Cooper, K. E., P. Y. Gates, and R. S. Eisenberg. 1988b. Surmounting barriers in ionic channels. Q. Rev. Biophys. 21:331-364.
30. Cooper, K., E. Jakobsson, and P. Wolynes. 1985. The theory of ion transport through membrane channels. Prog. Biophys. Mol. Biol. 46: 51-96.
31. Coronado, R., J. Morrissette, M. Sukhareva, and D. M. Vaughan. 1994. Structure and function of ryanodine receptors. Am. J. Physiol. 266: C1485-C1504.
32. Crouzy, S., T. B. Woolf, and B. Roux. 1994. A molecular dynamics study of gating in dioxolane-linked gramicidin A channels. Biophys. J. 67: 1370-1386.
33. Dani, J. A., and D. G. Levitt. 1981. Water transport and ion-water interaction in the gramicidin channel. Biophys. J. 35:501-508.
34. Davis, M. E., and J. A. McCammon. 1990. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 90:509-521.
35. Eisenberg, R. S. 1990. Channels as enzymes. J. Membr. Biol. 115:1-12.
36. Eisenberg, R. S. 1996. Computing the field in proteins and channels. J. Membr. Biol. 150:1-25.
37. Eisenman, G., and R. Horn. 1983. Ionic selectivity revisited: the role of kinetic and equilibrium processes in ion permeation through channels. J. Membr. Biol. 76:197-225.
38. Eisenberg, R. S., M. M. Klosek, and Z. Schuss. 1995. Diffusion as a chemical reaction: stochastic trajectories between fixed concentrations. J. Chem. Phys. 102:1767-1780.
39. Elber, R. 1996. Reaction path studies of biological molecules. In Recent Developments in Theoretical Studies of Proteins. R. Elber, editor. World Scientific, River Edge, NJ. 65-136.
40. Elber, R., A. Roitberg, C. Simmerling, R. Goldstein, G. Verkhivker, H. Li, and A. Ulitsky, editors. 1993. MOIL: a molecular dynamics program with emphasis on conformational searches and reaction path calculations. In Statistical Mechanics, Protein Structure and Protein-Substrate Interactions. Plenum Press, New York.
41. Ennis, J., R. Kjellander, and D. J. Mitchel. 1995. Dressed ion theory for bulk symmetric electrolytes in the restricted primitive model. J. Chem. Phys. 102:975-991.
42. Fabiato, A. 1983. Calcium-induced release of calcium from the cardiac sarcoplasmic reticulum. Am. J. Physiol. 245:C1-C14.
43. Feller, W. 1957. An Introduction to Probability Theory and Its Application. John Wiley and Sons, New York.
44. Feller, W. 1971. An Introduction to Probability Theory and its Applications. John Wiley and Sons, New York.
45. Fleming, G. R., S. H. Courtney, and M. W. Balk. 1986. Activated barrier crossing: comparison of experiment and theory. J. Statist. Phys. 42: 83-104.
46. Fleming, G., and P. Hänggi, editors. 1993. Activated Barrier Crossing: Applications in Physics, Chemistry and Biology. World Scientific, River Edge, NJ.
47. Friedman, H. L. 1985. A Course in Statistical Mechanics. Prentice Hall, Englewood Cliffs, NJ.
48. Gardiner, C. W. 1985. Handbook of Stochastic Methods: For Physics, Chemistry and the Natural Sciences. Springer Verlag, New York.
49. Garrod, C. 1995. Statistical Mechanics and Thermodynamics. Oxford University Press, New York.
50. Goldman, D. E. 1943. Potential, impedance and rectification in membranes. J. Gen. Physiol. 27:37-60.
51. Haile, J. M. 1992. Molecular Dynamics Simulation. John Wiley and Sons, New York.
52. Hall, J. E., C. A. Mead, and G. Szabo. 1973. A barrier model for current flow in lipid bilayer membranes. J. Membr. Biol. 11:75-97.
53. Hänggi, P., P. Talkner, and M. Borokovec. 1990. Reaction-rate theory: fifty years after Kramers. Rev. Modern Phys. 62:251-341.
54. Hill, T. L. 1977. Free Energy Transduction in Biology. Academic Press, New York.
55. Hill, T. L. 1985. Cooperativity Theory in Biochemistry. Springer Verlag, New York.
56. Hille, B. 1975. Ionic Selectivity, saturation, and block in sodium channels. A four barrier model. J. Gen. Physiol. 66:535-560.
57. Hille, B. 1992. Ionic Channels of Excitable Membranes. Sinauer Associates, Sunderland, MA.
58. Hille, E., and W. Schwartz. 1978. Potassium channels as multi-ion single-file pores. J. Gen. Physiol. 72:409-442.
59. Hodgkin, A. L., and B. Katz. 1949. The effect of sodium ions on the electrical activity of the giant axon of the squid. J. Physiol. (Lond.). 108:37-77.
60. Honig, B., and A. Nichols. 1995. Classical electrostatics in biology and chemistry. Science. 268:1144-1149.
61. Hummer, G., L. R. Pratt, and A. E. Garcia. 1996. Free energy of ionic hydration. J. Phys. Chem. 100:1206-1215.
62. Hynes, J. T. 1985. Chemical reaction dynamics in solution. Annu. Rev. Phys. Chem. 36:573-597.
63. Hynes, J. T. 1986. The theory of reactions in solution. In Theory of Chemical Reactions, Vol. 4. M. Baer, editor. Boca Raton, FL. 171-234.
64. Jerome, J. W. 1995. Mathematical Theory and Approximation of Semiconductor Models. Springer Verlag, New York.
65. Johnson, F. H., H. Eyring, and B. J. Stover. 1974. The Theory of Rate Processes in Biology and Medicine. John Wiley, New York.
66. Kalko, S. G., G. Sese, and J. A. Padro. 1996. On the effects of truncating the electrostatic interactions: free energies of ion hydration. J. Chem. Phys. 104:9578-9585.
67. Karlin, S., and H. M. Taylor. 1975. A First Course in Stochastic Processes. Academic Press, New York.
68. Karlin, S., and H. M. Taylor. 1981. A Second Course in Stochastic Processes. Academic Press, New York.
69. Keizer, J. 1987. Statistical Thermodynamics of Nonequilibrium Processes. Springer-Verlag, New York.
70. Kevorkian, J., and J. D. Cole. 1996. Multiple Scale and Singular Perturbation Methods. Springer Verlag, New York.
71. Kjellander, R. 1995. Modified Debye-Huckel approximation with effective charges: an application of dressed ion theory for electrolyte solutions. J. Phys. Chem. 99:10392-10407.
72. Kjellander, R., and D. J. Mitchell. 1994. Dressed ion theory for electrolyte solutions: a Debye-Huckel-like reformulation of the exact theory for the primitive model. J. Chem. Phys. 101:603-626.
73. Kramers, H. A. 1940. Brownian motion in a field of force and the diffusion model of chemical reactions. Physica. 7:284-304.
74. Krukowski, A., H. S. Chan, and K. A. Dill. 1995. An exact lattice model of complex solutions: chemical potential depend on solute and solvent shape. J. Chem. Phys. 103:10675-10688.
75. Laidler, K. J., and M. C. King. 1983. The development of transition state theory. J. Phys. Chem. 87:2657-2664.
76. Läuger, P. 1991. Electrogenic Ion Pump. Sinauer Associates, Sunderland, MA.
77. Lee, S. H., and J. C. Rasaiah. 1994. Molecular dynamics simulation of ionic mobility. I. Alkali metal cations in water at 25°C. J. Chem. Phys. 101:6964-6974.
78. Levine, R. D., and R. B. Bernstein. 1987. Molecular Reaction Dynamics and Chemical Reactivity. Oxford University Press, New York.
79. Levitt, D. G. 1982. Comparison of Nernst-Planck and reaction-rate models for multiply occupied channels. Biophys. J. 37:575-587.
80. Levitt, D. G. 1984. Kinetics of movement in narrow channels. Curr. Top. Membr. Transp. 21:181-198.
81. Levitt, D. G. 1985. Strong electrolyte continuum theory solution for equilibrium profiles, diffusion limitation, and conductance in charged ion channels. Biophys. J. 52:575-587.
82. Levitt, D. G. 1986. Interpretation of biological ion channel flux data. Reaction rate versus continuum theory. Annu. Rev. Biophys. Biophys. Chem. 15:29-57.
83. Levitt, D. G. 1987. Exact continuum solution for a channel that can be occupied by two ions. Biophys. J. 52:455-466.
84. Lundstrom, M. 1992. Fundamentals of Carrier Transport. Addison-Wesley, New York.
85. Ma, S. K. 1985. Statistical Mechanics. World Scientific, Philadelphia.
86. Mahan, G. D. 1993. Many Particle Physics. Plenum, New York.
87. Mason, E., and E. McDaniel. 1988. Transport Properties of Ions in Gases. John Wiley and Sons, New York.
88. McCammon, J. A., and S. C. Harvey. 1987. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, New York.
89. McLaughlin, S. 1989. The electrostatic properties of membranes. Annu. Rev. Biophys. Biophys. Chem. 18:113-136.
90. McLaughlin, S., N. Mulrine, T. Gresalfi, G. Vaio, and A. McLaughlin. 1981. Absorption of divalent cations to bilayer membranes containing phosphatidylserine. J. Gen. Physiol. 77:445-473.
91. McQuarrie, D. A. 1976. Statistical Mechanics. Harper and Row, New York.
92. Mehler, E. L. 1996. Self-consistent free energy based approximation to calculate pH dependent electrostatic effects in proteins. J. Phys. Chem. 100:16006-16018.
93. 2+ release channel of sarcoplasmic reticulum. J. Biol. Chem. 261:6300-6306.
94. 2+ release channels and their regulation by endogenous effectors. Annu. Rev. Physiol. 56:485-508.
95. 2+ ions in excitation-contraction coupling of skeletal muscle fibres. Biochim. Biophys. Acta. 1241:59-116.
96. Moczydlowski, E. 1986. Single-channel enzymology. In Ion Channel Reconstitution. C. Miller, editor. Plenum Press, New York.
97. Naeh, T., M. M. Klosek, B. J. Matkowsky, and Z. Schuss. 1990. A direct approach to the exit problem. Siam J. Appl. Math. 50:595-627.
98. Onsager, L., and S. Machlup. 1953. Fluctuations and irreversible processes. Phys. Rev. 91:1505-1512.
99. Pechukas, P. 1976. Statistical approximations in collision theory. In Dynamics of Molecular Collisions. Part B. W. H. Miller, editor. Plenum Press, New York. 269-322.
100. Rios, E., and G. Pizzaro. 1991. Voltage sensor of excitation contraction coupling in skeletal muscle. Physiol. Rev. 71:849-908.
101. Robinson, P. J., and K. A. Holbrook. 1972. Unimolecular Reactions. John Wiley, New York.
102. Rouston, D. J. 1990. Bipolar Semiconductor Devices. McGraw-Hill Publishing Company, New York.
103. Roux, B., and M. Karplus. 1991. Ion transport in a gramicidin-like channel: dynamics and mobility. J. Phys. Chem. 95:4856-4868.
104. Schneider, M. F. 1994. Control of calcium release in functioning skeletal muscle fibers. Annu. Rev. Physiol. 56:463-484.
105. Schönert, H. 1994. Debye-Hückel theory for hydrated ions. 6. Thermodynamic properties of aqueous solutions of 1:1 chlorides between 273 and 523 K. J. Phys. Chem. 98:643-653.
106. Schroeder, J., and J. Troe. 1993. Solvent effects in the dynamics of dissociation, recombination, and isomerization reactions. In Activated Barrier Crossing: Applications in Physics, Chemistry and Biology. G. Fleming and P. Hänggi, editors. World Scientific Publishing. River Edge, NJ. 206-240.
107. Schuss, Z. 1980. Theory and Applications of Stochastic Differential Equations. John Wiley and Sons, New York.
108. Selberherr, S. 1984. Analysis and Simulation of Semiconductor Devices. Springer Verlag, New York.
109. Smith, H., and H. Jensen. 1989. Transport Phenomena. Clarendon Press, Oxford University Press, New York. 1-427.
110. Smith, J., T. Imagawa, J. Ma, M. Fill, K. Campbell, and R. Coronado. 1988. Purified ryanodine receptor from rabbit skeletal muscle is the calcium-release channel of sarcoplasmic reticulum. J. Gen. Physiol. 92:1-26.
111. Spohn, H. 1991. Large Scale Dynamics of Interacting Particles. Springer Verlag, New York.
112. Steinfeld, J. I., J. S. Francisco, and W. L. N. J. Hase. 1989. Chemical Kinetics and Dynamics. Prentice Hall, Englewood Cliffs, NJ.
113. Stryer, L. 1995. Biochemistry. W. H. Freeman, New York.
114. Syganow, A., and E. von Kitzing. 1995. Integral weak diffusion and diffusion approximations applied to ion transport through biological ion channels. J. Phys. Chem. 99:12030-12040.
115. Sze, S. M. 1981. Physics of Semiconductor Devices. John Wiley and Sons, New York.
116. Tang, J., D. Chen, N. Saint, J. Rosenbusch, and R. Eisenberg. 1997. Permeation through porin and its mutant G119D. Biophys. J. 72:A108.
117. Tinker, A., A. R. G. Lindsay, and A. J. Williams. 1992. A model for ionic conduction in the ryanodine receptor channel of sheep cardiac muscle sarcoplasmic reticulum. J. Gen. Physiol. 100:495-517.
118. Tinker, A., and A. Williams. 1995. Measuring the length of the pore of the sheep cardiac sarcoplasmic reticulum calcium-release channel using related trimethylammonium ions as molecular calipers. Biophys. J. 68: 111-120.
119. 2+ release channel. Biophys. J. 70:2600-2615.
120. 2+ release channel. Biophys. J. 67:2280-2285.
121. Tyrrell, H. J. V., and K. R. Harris. 1984. Diffusion in Liquids. Butterworths, Boston, MA.
122. Vlad, M. O., and J. Ross. 1995. Fluctuation-dissipation relations for chemical systems far from equilibrium. J. Chem. Phys. 100:7268-7278.
123. Walsh, C. 1979. Enzymatic Reaction Mechanisms. W. H. Freeman, San Francisco.
124. Warshel, A., and S. T. Russell. 1984. Calculations of electrostatic interactions in biological systems and in solutions. Q. Rev. Biophys. 17: 283-422.
125. 2+ in mammalian ventricle: dynamic control by cellular processes. Annu. Rev. Physiol. 52:467-485.
126. Williams, A. 1992. Ionic conduction and discrimination in the sarcoplasmic reticulum ryanodine receptor/calcium release channel. J. Muscle Res. Cell Motil. 13:7-26.
127. 2+, and adenine nucleotides under normal and simulated ischemic conditions. Circ. Res. 79:1100-1109.