Effects of multiple occupancy and interparticle interactions on selective transport through narrow channels: Theory versus experiment

Biophysical Journal

Volumn 96, Issue 4, 2009, Pages 1235-1248

  Zilman, Anton ^a  

^a CENTER FOR NONLINEAR STUDIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL TRANSPORT; ENERGY; KINETICS; MOLECULAR INTERACTION; NANOTECHNOLOGY; THEORETICAL STUDY; ALGORITHM; BIOLOGICAL MODEL; CHEMICAL MODEL; METABOLISM; TRANSPORT AT THE CELLULAR LEVEL;

CARRIER PROTEIN; DNA;

ALGORITHMS; BIOLOGICAL TRANSPORT; DNA; KINETICS; MEMBRANE TRANSPORT PROTEINS; MODELS, BIOLOGICAL; MODELS, CHEMICAL;

EID: 62649117352     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2008.09.058     Document Type: Article

References (66)

1. Alberts, B., D. Bray, J. Lewis, M. Raff, K. Roberts, et al. 1994. Molecular Biology of the Cell. Garland Publishing, Boca Raton, FL.
2. Nestorovich, E. M., C. Danelon, M. Winterhalter, and S. M. Bezrukov. 2002. Designed to penetrate: time-resolved interaction of single antibiotic molecules with bacterial pores. Proc. Natl. Acad. Sci. USA. 99:9789-9794.
3. Bezrukov, S., L. Kullman, and M. Winterhalter. 2000. Probing sugar translocation through maltoporin at the single channel level. FEBS Lett. 476:224-228. (Pubitemid 30410822)
4. Lu, D., K. Schulten, and P. Grayson. 2003. Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF. Biophys. J. 85:2977-2987. (Pubitemid 37351013)
5. de Groot, B. L., and H. Grubmuller. 2001. Water permeation across biological membranes: mechanism and dynamics of Aquaporin-1 and GlpF. Science. 294:2353-2357.
6. Hohmann, S., S. Nielsen, and P. Agre. 2001. Aquaporins. Academic Press, San Diego, CA.
7. Borgnia, M. J., and P. Agre. 2001. Reconstitution and functional comparison of purified GlpF and AqpZ, the glycerol and water channels from Escherichia coli. Proc. Natl. Acad. Sci. USA. 98:2888-2893.
8. Rout, M. P., M. O. Magnasco, B. T. Chait, and J. D. Aitchison. 2003. Virtual gating and nuclear transport: the hole picture. Trends Cell Biol. 13:622-628.
9. Macara, I. 2001. Transport into and out of the nucleus. Microbiol. Mol. Biol. Rev. 65:570-594. (Pubitemid 33123518)
10. Tran, E. J., and S. R. Wente. 2006. Dynamic nuclear pore complexes: life on the edge. Cell. 125:1041-1053.
11. Lim, R. Y. H., U. Aebi, and B. Fahrenkrog. 2008. Towards reconciling structure and function of the nuclear pore complex. Histochem. Cell Biol. 129:105-116.
12. Stewart, M., R. Baker, R. Bayliss, L. Clayton, R. Grant, et al. 2001. Molecular mechanism of translocation through nuclear pore complexes during nuclear protein import. FEBS Lett. 498:145-149.
13. Caspi, Y., D. Zbaida, H. Cohen, and M. Elbaum. 2008. Facilitated diffusion inside nanopores: a chemical mimic of the nuclear pore complex. Nano Lett. 8:3728-3734.
14. Lee, S. B., D. T. Mitchell, L. Trofin, T. K. Nevanen, H. Soderlund, et al. 2002. Antibody-based bio-nanotube membranes for enantiomeric drug separations. Science. 296:2198-2200.
15. Jirage, K. B., J. C. Hulteen, and C. R. Martin. 1997. Nanotubule-based molecular-filtration membranes. Science. 278:655-658. (Pubitemid 27464957)
16. Kohli, P., C. C. Harrell, Z. Cao, R. Gasparac, W. Tan, et al. 2004. DNA-functionalized nanotube membranes with single-base mismatch selectivity. Science. 305:984-986.
17. Savariar, E., K. Krishnamoorty, and S. Thayumanavan. 2008. Molecular discrimination inside polymer nanotubules. Nature Nanotechnol. 3:112-117.
18. Iqbal, S., D. Akin, and R. Bashir. 2007. Solid-state nanopore channels with DNA selectivity. Nature Nanotechnol. 2:243-248. (Pubitemid 46739815)
19. Jovanovic-Talisman, T., J. Tetenbaum-Novatt, A. S. McKenney, A. Zilman, R. Peters, et al. 2008. Artificial nanopores that mimic the transport selectivity of the nuclear pore complex. Nature. In press.
20. Luedemann, S. K., V. R. E. Lounnas, and R. C. Wade. 2000. How do substrates enter and products exit the buried active site of Cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. J. Mol. Biol. 303:797-811.
21. Hille, B. 2001. Ionic Channels in Excitable Membranes. Sinauer Publishing, Sunderland, MA.
22. Miloshevsky, G. V., and P. C. Jordan. 2004. Permeation in ion channels: the interplay of structure and theory. Trends Neurosci. 27:308-314.
23. Corry, B., and S. Chung. 2006. Mechanisms of valence selectivity in biological ion channels. Cell. Mol. Life Sci. 63:301-315. (Pubitemid 43202312)
24. Boda, D., W. Nonner, M. Valisko, D. Henderson, B. Eisenberg, et al. 2007. Steric selectivity in Na channels arising from protein polarization and mobile side chains. Biophys. J. 93:1960-1980.
25. Smit, B., and R. Krishna. 2003. Molecular simulations in zeolitic process design. Chem. Eng. Sci. 58:557-568. (Pubitemid 36310112)
26. Berezhkovskii, A. M., S. M. Bezrukov, and M. A. Pustovoit. 2002. Channel-facilitated membrane transport: transit probability and interaction with the channel. J. Chem. Phys. 116:9952-9956.
27. Noble, R. D. 1992. Generalized microscopic mechanism of facilitated transport in fixed site carrier membranes. J. Membr. Sci. 75:121-129. (Pubitemid 23030401)
28. Noble, R. D. 1991. Facilitated transport with fixed-site carrier membranes. J. Chem. Soc., Faraday Trans. 87:2089-2092.
29. Keminer, O., and R. Peters. 1999. Permeability of single nuclear pores. Biophys. J. 77:217-228. (Pubitemid 29305222)
30. Yang, W., J. Gelles, and S. Musser. 2004. Imaging of single-molecule translocation through nuclear pore complexes. Proc. Natl. Acad. Sci. USA. 101:12887-12892. (Pubitemid 39167553)
31. Berezhkovskii, A. M., and S. M. Bezrukov. 2005. Channel-facilitated membrane transport: constructive role of particle attraction to the channel pore. Chem. Phys. 319:342-349.
32. Zilman, A., S. Di Talia, M. O. Magnasco, B. T. Chait, and M. P. Rout. 2007. Efficiency, selectivity and robustness of the nucleocytoplasmic transport. PLoS Comp Biol. 3:e125.
33. Bezrukov, S. M., A. M. Berezhkovskii, and A. Szabo. 2007. Diffusion model of solute dynamics in a membrane channel: mapping onto the two-site model and optimizing the flux. J. Chem. Phys. 127:115101.
34. Bauer, W. R., and W. Nadler. 2006. Molecular transport through channels and pores: effects of in-channel interactions and blocking. Proc. Natl. Acad. Sci. USA. 103:11446-11451.
35. 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.
36. Gardiner, M. 2003. Stochastic Processes in Physics, Chemistry and Biology. Springer-Verlag, New York.
37. Wyman, J. 1966. Facilitated diffusion and the possible role of myoglobin as a transport mechanism. J. Biol. Chem. 211:115-121.
38. Berezhkovskii, A., and S. Bezrukov. 2005. Optimizing transport of metabolites through large channels: molecular sieves with and without binding. Biophys. J. 88:L17-L19.
39. Kolomeisky, A. 2007. Channel-facilitated molecular transport across membranes: attraction, repulsion, and asymmetry. Phys. Rev. Lett. 98, 048105.
40. Chou, T. 1998. How fast do fluids squeeze through microscopic single-file pores? Phys. Rev. Lett. 80:85-88. (Pubitemid 128621455)
41. Schütz, G. M. 2003. Critical phenomena and universal dynamics in one-dimensional driven diffusive systems with two species of particles. J. Phys. Math. Gen. 36:R339-R379. (Pubitemid 37316754)
42. Lakatos, G., and T. Chou. 2003. Totally asymmetric exclusion processes with particles of arbitrary size. J. Phys. A. 36:2027-2041. (Pubitemid 37341312)
43. Schütz, G. 2005. Single-file diffusion far from equilibrium. Diffusion Fundamentals. 2:5.
44. Chou, T., and D. Lohse. 1999. Entropy-driven pumping in zeolites and biological channels. Phys. Rev. Lett. 82:3552-3555. (Pubitemid 129690002)
45. Derrida, B., E. Domany, and D. Mukamel. 1992. An exact solution of a one-dimensional asymmetric exclusion model with open boundaries. J. Stat. Phys. 69:667-687.
46. Berezhkovskii, A., and G. Hummer. 2002. Single-file transport of water molecules through a carbon nanotube. Phys. Rev. Lett. 89:064503.
47. Reguera, D., G. Schmid, P. Burada, J. Rubí, P. Reimann, et al. 2006. Entropic transport: kinetics, scaling, and control mechanisms. Phys. Rev. Lett. 96:130603.
48. Kubitscheck, U., D. Grünwald, A. Hoekstra, D. Rohleder, T. Kues, et al. 2005. Nuclear transport of single molecules: dwell times at the nuclear pore complex. J. Cell Biol. 168:233-243.
49. Yang, W., and S. Musser. 2006. Nuclear import time and transport efficiency depend on importin-α concentration. J. Cell Biol. 174:951-961.
50. Schuss, Z., B. Nadler, and R. S. Eisenberg. 2001. Derivation of Poisson and Nernst-Planck equations in a bath and channel from a molecular model. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 64:036116.
51. Berg, H. C. 1993. Random Walks in Biology. Princeton University Press, Princeton, NJ.
52. Redner, S. 2001. A Guide to First-Passage Processes. Cambridge University Press, Cambridge, UK.
53. Zhou, Y., J. E. Pearson, and A. Auerbach. 2005. F-value analysis of a linear, sequential reaction mechanism: theory and application to ion channel gating. Biophys. J. 89:3680-3685.
54. Ribbeck, K., and D. Görlich. 2001. Kinetic analysis of translocation through nuclear pore complexes. EMBO J. 20:1320-1330. (Pubitemid 32233972)
55. Sinitsyn, N., and I. Nemenman. 2007. Berry phase and pump effect in stochastic chemical kinetics. Europhys. Lett. 77:58001.
56. Kopito, R. B., and M. Elbaum. 2007. Reversibility in nucleocytoplasmic transport. Proc. Natl. Acad. Sci. USA. 104:12743-12748. (Pubitemid 47255225)
57. Timney, B., J. Tetenbaum-Novatt, D. Agate, R. Williams, W. Zhang, et al. 2006. Simple kinetic relationships and nonspecific competition govern nuclear import rates in vivo. J. Cell Biol. 175:579-593.
58. Cussler, E. L., R. Aris, and A. Bhown. 1989. On the limits of facilitated diffusion. J. Membr. Sci. 43:149-164.
59. Doi, M., and S. F. Edwards. 1998. The Theory of Polymer Dynamics. Clarendon Press, Oxford, UK.
60. Bezrukov, S. M., A. M. Berezhkovskii, M. A. Pustovoit, and A. Szabo. 2000. Particle number fluctuations in a membrane channel. J. Chem. Phys. 113:8206-8211.
61. Shaw, L. B. R., K. P. Zia, and K. H. Lee. 2003. Totally asymmetric exclusion process with extended objects: a model for protein synthesis. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 68:21910.
62. Schoenherr, G., and G. M. Schütz. 2004. Exclusion process for particles of arbitrary extension: hydrodynamic limit and algebraic properties. J. Phys. A. 37:8215-8231.
63. MacDonald, C. T., J. H. Gibbs, and A. C. Pipkin. 1968. Kinetics of biopolymerization on nucleic acid templates. Biopolymers. 6:1-5.
64. Zhou, H., S. Wlodek, and J. McCammon. 1998. Conformation gating as a mechanism for enzyme specificity. Proc. Natl. Acad. Sci. USA. 95:9280-9283. (Pubitemid 28506222)
65. McClean, M., A. Mody, J. Broach, and S. Ramanathan. 2007. Cross-talk and decision making in MAP kinase pathways. Nat. Genet. 39:409-414. (Pubitemid 46328483)
66. McKeithan, T. 1995. Kinetic proofreading in T-cell receptor signal transduction. Proc. Natl. Acad. Sci. USA. 92:5042-5046.