×

A spatial model of cellular molecular trafficking including active transport along microtubules. (English) Zbl 1414.92132

Summary: We consider models of Ran-driven nuclear transport of molecules such as proteins in living cells. The mathematical model presented is the first to take into account for the active transport of molecules along the cytoplasmic microtubules. All parameters entering the models are thoroughly discussed. The model is tested by numerical simulations based on discontinuous Galerkin finite element methods. The numerical experiments are compared to the behavior observed experimentally.

MSC:

92C37 Cell biology
92C45 Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.)
35Q92 PDEs in connection with biology, chemistry and other natural sciences

Software:

deal.ii

References:

[1] Agutter, P. S.; Malone, P. C.; Wheatley, D. N., Intracellular transport mechanisms: a critique of diffusion theory, J. Theor. Biol., 176, 2, 261-272 (1995)
[2] Alberts, B.; Johnson, A.; Lewis, J.; Raff, M.; Roberts, K.; Walter, P., Molecular Biology of the Cell (2008), Garland Science
[3] Arnold, D. N., An interior penalty finite element method with discontinuous elements, SIAM J. Numer. Anal., 19, 4, 742-760 (1982) · Zbl 0482.65060
[4] Axelrod, D.; Koppel, D. E.; Schlessinger, J.; Elson, E.; Webb, W. W., Mobility measurement by analysis of fluorescence photobleaching recovery kinetics, Biophys. J., 16, 9, 1055-1069 (1976)
[5] Bangerth, W., Hartmann, R., Kanschat, G., deal.II. Differential equations analysis library. Technical Reference, \( \langle\) http://www.dealii.org \(\rangle \).; Bangerth, W., Hartmann, R., Kanschat, G., deal.II. Differential equations analysis library. Technical Reference, \( \langle\) http://www.dealii.org \(\rangle \). · Zbl 1365.65248
[6] Bangerth, W.; Hartmann, R.; Kanschat, G., deal.II—A general-purpose object-oriented finite element library, ACM Trans. Math. Software, 33, 4 (2007) · Zbl 1365.65248
[7] Becskei, A.; Mattaj, I., Quantitative models of nuclear transport, Curr. Opin. Cell Biol., 17, 1, 27-34 (2005)
[8] Berezhkovskii, A. M.; Makhnovskii, Y. A.; Monine, M. I.; Zitserman, V. Y.; Shvartsman, S. Y., Boundary homogenization for trapping by patchy surfaces, J. Chem. Phys., 121, 22, 11390-11394 (2004)
[9] Briggs, G.; Haldane, J., A note on the kinetics of enzyme action, Biochem. J., 197, 338-339 (1925)
[10] Calabrò, F.; Zunino, P., Global existence of strong solutions of parabolic problems on partitioned domains with nonlinear conditions at the interface. Applications to mass transfer processes through semi-permeable membranes, Math. Models Methods Appl. Sci., 16, 479-501 (2006) · Zbl 1101.35044
[11] Campbell, E. M.; Hope, T. J., Role of the cytoskeleton in nuclear import, Adv Drug Delivery Rev., 55, 6, 761-771 (2003)
[12] Cangiani, A., Georgoulis, E.H., Jensen, M., in preparation. Discontinuous Galerkin methods for mass transfer through semi-permeable membranes, in preparation.; Cangiani, A., Georgoulis, E.H., Jensen, M., in preparation. Discontinuous Galerkin methods for mass transfer through semi-permeable membranes, in preparation. · Zbl 1336.65162
[13] Caudron, M.; Bunt, G.; Bastiaens, P.; Karsenti, E., Spatial coordination of spindle assembly by chromosome-mediated signaling gradients, Science, 309, 1373-1376 (2005)
[14] Cockburn, B., Karniadakis, G., Shu, C.-W. (Eds.), Discontinuous Galerkin Methods. Theory, Computation and Applications, vol. 11 of DGMref. Springer, 2000.; Cockburn, B., Karniadakis, G., Shu, C.-W. (Eds.), Discontinuous Galerkin Methods. Theory, Computation and Applications, vol. 11 of DGMref. Springer, 2000.
[15] de Vries, G., Hillen, T., Lewis, M., Mller, J., Schnfisch, B., 2006. A Course in Mathematical Biology: Quantitative Modeling with Mathematical and Computational Methods. SIAM.; de Vries, G., Hillen, T., Lewis, M., Mller, J., Schnfisch, B., 2006. A Course in Mathematical Biology: Quantitative Modeling with Mathematical and Computational Methods. SIAM. · Zbl 1105.92002
[16] Dinh, A.-T.; Pangarkar, C.; Theofanous, T.; Mitragotri, S., Theory of spatial patterns of intracellular organelles, Biophys. J., 90, 10, 67-69 (2006)
[17] Dinh, A.-T.; Theofanous, T.; Mitragotri, S., A model for intracellular trafficking of adenoviral vectors, Biophys. J., 89, 3, 1574-1588 (2005)
[18] Eungdamrong, N. J.; Iyengar, R., Modeling cell signaling networks, Biol. Cell, 96, 5, 355-362 (2004)
[19] Fahrenkrog, B.; Aebi, U., The nuclear pore complex: nucleocytoplasmic transport and beyond, Nat. Rev. Mol. Cell Biol., 4, 10, 757-766 (2003)
[20] Fushimi, K.; Verkman, A., Low viscosity in the aqueous domain of cell cytoplasm measured by picosecond polarization microfluorimetry, J. Cell Biol., 112, 4, 719-725 (1991)
[21] Giannakakou, P.; Nakano, M.; Nicolaou, K. C.; O’Brate, A.; Yu, J.; Blagosklonny, M. V.; Greber, U. F.; Fojo, T., Enhanced microtubule-dependent trafficking and p53 nuclear accumulation by suppression of microtubule dynamics, Proc. Natl. Acad. Sci. U.S.A., 99, 16, 10855-10860 (2002)
[22] Giannakakou, P.; Sackett, D. L.; Ward, Y.; Webster, K. R.; Blagosklonny, M. V.; Fojo, T., p53 is associated with cellular microtubules and is transported to the nucleus by dynein, Nat. Cell Biol., 2, 709-717 (2000)
[23] Görlich, D.; Seewald, M.; Ribbeck, K., Characterization of Ran-driven cargo transport and the RanGTPase system by kinetic measurements and computer simulation, EMBO J., 22, 1088-1100 (2003)
[24] Gundersen, G. G.; Cook, T. A., Microtubules and signal transduction, Curr. Opin. Cell Biol., 11, 1, 81-94 (1999)
[25] Harding, A.; Tian, T.; Westbury, E.; Frische, E.; Hancock, J., Subcellular localization determines map kinase signal output, Curr. Biol., 15, 9, 869-873 (2005)
[26] Houston, P.; Schwab, C.; Süli, E., Discontinuous hp-finite element methods for advection-diffusion-reaction problems, SIAM J. Numer. Anal., 39, 6, 2133-2163 (2002), (electronic) · Zbl 1015.65067
[27] Kahana, A.; Kenan, G.; Feingold, M.; Elbaum, M.; Granek, R., Active transport on disordered microtubule networks: the generalized random velocity model, Phys. Rev. E (Stat. Nonlinear Soft Matter Phys.), 78, 5, 051912 (2008)
[28] Kao, H.; Abney, J.; Verkman, A., Determinants of the translational mobility of a small solute in cell cytoplasm, J. Cell Biol., 120, 1, 175-184 (1993)
[29] Kedem, O.; Katchalsky, A., Thermodynamic analysis of the permeability of biological membrane to non-electrolytes, Biochim. Biophys. Acta, 27, 229-246 (1958)
[30] Kholodenko, B., Cell-signalling dynamics in time and space, Nat. Rev. Mol. Cell Biol., 7, 3, 165-176 (2006)
[31] Kholodenko, B., Spatially distributed cell signalling, FEBS Lett., 24, 4006-4012 (2009)
[32] Klebe, C.; Prinz, H.; Wittinghofer, A.; Goody, R., The kinetic mechanism of ran-nucleotide exchange catalyzed by RCC1, Biochemistry, 34, 12543-12552 (1995)
[33] Kopito, R. B.; Elbaum, M., Reversibility in nucleocytoplasmic transport, Proc. Natl. Acad. Sci., 104, 31, 12743-12748 (2007)
[34] Kopito, R. B.; Elbaum, M., Nucleocytoplasmic transport: a thermodynamic mechanism, HFSP J., 3, 2, 130-141 (2009)
[35] Lam, M. H.C.; Thomas, R. J.; Loveland, K. L.; Schilders, S.; Gu, M.; Martin, T. J.; Gillespie, M. T.; Jans, D. A., Nuclear transport of parathyroid hormone (PTH)-related protein is dependent on microtubules, Mol. Endocrinol., 16, 2, 390-401 (2002)
[36] Lasis, A.; Süli, E., \(hp\)-version discontinuous Galerkin finite element method for semilinear parabolic problems, SIAM J. Numer. Anal., 45, 4, 1544-1569 (2007) · Zbl 1155.65073
[37] Lohmann, D.R., September, 1999. RB1 (retinoblastoma). Atlas Genet. Cytogenet. Oncol. Haematol. URL:http://AtlasGeneticsOncology.org/Genes/RB1ID90.html; Lohmann, D.R., September, 1999. RB1 (retinoblastoma). Atlas Genet. Cytogenet. Oncol. Haematol. URL:http://AtlasGeneticsOncology.org/Genes/RB1ID90.html
[38] Loverdo, C.; Bénichou, O.; Moreau, M.; Voituriez, R., Enhanced reaction kinetics in biological cells, Nat. Phys., 4, 134-137 (2008)
[39] Macara, I. G., Transport into and out of the nucleus, Microbiol. Mol. Biol. Rev., 65, 4, 570-594 (2001)
[40] Mattaj, I. W.; Englmeier, L., Nucleocytoplasmic transport: the soluble phase, Annu. Rev. Biochem., 67, 1, 265-306 (1998)
[41] Michaelis, L.; Menten, M., Die kinetik der invertinwirkung, Biochem. Z., 49, 333-369 (1913)
[42] Murray, J. D., Mathematical Biology: I. An Introduction (2002), Springer · Zbl 1006.92001
[43] Nédélec, F.; Surrey, T.; Maggs, A. C., Dynamic concentration of motors in microtubule arrays, Phys. Rev. Lett., 86, 14, 3192-3195 (2001)
[44] Partikian, A.; Olveczky, B.; Swaminathan, R.; Li, Y.; Verkman, A., Rapid diffusion of green fluorescent protein in the mitochondrial matrix, J. Cell Biol., 140, 4, 821-829 (1998)
[45] Quarteroni, A.; Veneziani, A.; Zunino, P., Mathematical and numerical modeling of solute dynamics in blood flow and arterial walls, SIAM J. Numer. Anal., 39, 1488-1511 (2001) · Zbl 1022.76059
[46] Quimby, B.; Dasso, M., The small GTPase Ran: interpreting the signs, Curr. Opin. Cell Biol., 15, 3, 338-344 (2003)
[47] Reed, W.H., Hill, T.R., 1973. Triangular mesh methods for the neutron transport equation. Technical Report LA-UR-73-479, Los Alamos Scientific Laboratory, Los Alamos, NM.; Reed, W.H., Hill, T.R., 1973. Triangular mesh methods for the neutron transport equation. Technical Report LA-UR-73-479, Los Alamos Scientific Laboratory, Los Alamos, NM.
[48] Ribbeck, K.; Görlich, D., Kinetic analysis of translocation through nuclear pore complexes, EMBO J., 20, 1320-1330 (2001)
[49] Riddick, G.; Macara, I., A systems analysis of importin-\( \alpha-\beta\) mediated nuclear protein import, J. Cell Biol., 168, 2005, 1027-1038 (2005)
[50] Riddick, G.; Macara, I., The adapter importin-\( \alpha\) provides flexible control of nuclear import at the expense of efficiency, Mol. Syst. Biol., 3, 118 (2007)
[51] Roth, D. M.; Moseley, G. W.; Glover, D.; Pouton, C. W.; Jans, D. A., A microtubule-facilitated nuclear import pathway for cancer regulatory proteins, Traffic, 8, June, 673-686 (14) (2007)
[52] Salman, H.; Abu-Arish, A.; Oliel, S.; Loyter, A.; Klafter, J.; Granek, R.; Elbaum, M., Nuclear localization signal peptides induce molecular delivery along microtubules, Biophys. J., 89, 3, 2134-2145 (2005)
[53] Segel, L.; Slemrod, M., The quasi-steady-state assumption: a case study in perturbation, SIAM Rev., 31, 446-477 (1989) · Zbl 0679.34066
[54] Seksek, O.; Biwersi, J.; Verkman, A., Translational diffusion of macromolecule-sized solutes in cytoplasm and nucleus, J. Cell Biol., 138, 1315-1342 (1997)
[55] Serafini, A., Mathematical models for intracellular transport phenomena. Ph.D. in Applied Mathematics, Università degli Studi di Roma “La Sapienza”, Dottorato di Ricerca in Modelli e Metodi Matematici per la tecnologia e la società, 2007. Advisor: R. Natalini.; Serafini, A., Mathematical models for intracellular transport phenomena. Ph.D. in Applied Mathematics, Università degli Studi di Roma “La Sapienza”, Dottorato di Ricerca in Modelli e Metodi Matematici per la tecnologia e la società, 2007. Advisor: R. Natalini.
[56] Smith, A.; Slepchenko, B.; Schaff, J.; Loew, L.; Macara, I., Systems analysis of Ran transport, Science, 295, 488-491 (2002)
[57] Smith, D.; Simmons, R., Models of motor-assisted transport of intracellular particles, Biophys. J., 80, 1, 45-68 (2001)
[58] Swaminathan, R.; Bicknese, S.; Periasamy, N.; Verkman, A., Cytoplasmic viscosity near the cell plasma membrane: translational diffusion of a small fluorescent solute measured by total internal reflection-fluorescence photobleaching recovery, Biophys. J., 71, 2, 1140-1151 (1996)
[59] Tekotte, H.; Davis, I., Intracellular MRNA localization: motors move messages, Trends Genet., 18, 12, 636-642 (2002)
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. In some cases that data have been complemented/enhanced by data from zbMATH Open. This attempts to reflect the references listed in the original paper as accurately as possible without claiming completeness or a perfect matching.