Barriers to diffusion in dendrites and estimation of calcium spread following synaptic inputs

PLoS Computational Biology

Volumn 7, Issue 10, 2011, Pages

  Biess, Armin ^a,b   Korkotian, Eduard ^c   Holcman, David ^d  

^a BERNSTEIN CENTER FOR COMPUTATIONAL NEUROSCIENCE   (Germany)

^b MAX PLANCK INSTITUTE FOR DYNAMICS AND SELF ORGANIZATION   (Germany)

^c WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^d ECOLE NORMALE SUPÉRIEURE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DIFFUSION BARRIERS; DIFFUSION IN LIQUIDS; LINEAR EQUATIONS; PROTEINS; THREE DIMENSIONAL COMPUTER GRAPHICS;

ACTIN NETWORKS; DIFFUSION PROCESS; DIMENSION REDUCTION; EFFECTIVE DIFFUSION; INERT DYES; MICROTUBULE NETWORKS; MODEL-BASED OPC; MOLECULAR CROWDING; ONE-DIMENSIONAL; SYNAPTIC INPUT;

CALCIUM;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BRAIN DEPTH STIMULATION; CALCIUM BINDING; CALCIUM CELL LEVEL; CALCIUM SIGNALING; CALCIUM TRANSPORT; CELL HETEROGENEITY; CONTROLLED STUDY; DENDRITE; DIFFUSION COEFFICIENT; FREQUENCY MODULATION; LEARNING ALGORITHM; MATHEMATICAL MODEL; NONHUMAN; PROCESS MODEL; RAT; SENSORY STIMULATION; SYNAPTIC INHIBITION; SYNAPTIC TRANSMISSION; CYTOPLASM; DIFFUSION; METABOLISM; SYNAPSE; THEORETICAL MODEL; VALIDATION STUDY;

CALCIUM;

CALCIUM; CYTOPLASM; DENDRITES; DIFFUSION; MODELS, THEORETICAL; SYNAPSES;

EID: 80055069419     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002182     Document Type: Article

References (57)

1. Fiala J, Harris K, Stuart G, Spruston N, Husser M, (1999) Dendrite structure. Dendrites Oxford. University Press.
2. Spacek J, Harris K, (1997) Three-dimensional organziation of smooth endoplasmic reticulum in ippocampal ca1 dendrites and dendritic spines of the immature and mature rat. J Neurosci 17: 90-203.
3. Luby-Phelps K, (2000) Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion intracellular surface area. Int Rev Cytol 192: 189-221.
4. Dix J, Verkman A, (2008) Crowding effects on diffusion in solutions. Annu Rev Biophys 37: 24763.
5. Fulton A, (1982) How crowded is the cytoplasm? Cell 30: 345-347.
6. Verkman A, (2002) Solute and macromolecule diffusion in cellular aqueous compartments. Trends Biochem Sci 27: 27-33.
7. Minton A, (2001) The inuence of macromolecular crowding and macromolecular confinement on iochemical reactions in physiological media. J Bio Chem 276: 10577-10580.
8. Minton A, (2001) Implications for marcomolecular crowding for protein assembly. Curr Opin Struct Biol 10: 34-39.
9. Kinjo A, Takada S, (2002) Effects of macromolecular crowding on protein folding and aggregation tudied by density functional theory: statics. Phys Rev E 66: 031911.
10. Kinjo A, Takada S, (2002) Effects of macromolecular crowding on protein folding and aggregation tudied by density functional theory: dynamics. Phys Rev E 66: 051902.
11. Ellis R, Minton A, (2003) Join the crowd. Nature 425: 27-8.
12. Berry H, (2002) Monte carlo simulations of enzyme reactions in two dimensions: fractal kinetics nd spatial segregation. Biophys J 83: 18911901.
13. Schnell S, Turner T, (2004) Reaction kinetics in intracellular environments with macromolecular rowding: simulations and rate laws. Prog Biophys Mol Biol 85: 235-60.
14. Rohwer J, Postma P, Kholodenko B, Westerhoff H, (1998) Implications of macromolecular crowding or signal transduction and metabolite channeling. Proc Natl Acad Sci U S A 95: 10547-10552.
15. Bourne J, Harris K, (2007) Do thin spines learn to be mushroom spines that remember? Curr Opin Neurobiol 17: 381-6.
16. Oelveczky B, Verkman A, (1998) Monte Carlo analysis of obstructed diffusion in three dimensions: pplications to molecular diffusion in organelles. Biophys J 74: 2722-2730.
17. Saxton M, (1994) Anomalous diffusion due to obstacles:a Monte Carlo study. Biophys J 66: 394-401.
18. Saxton M, (1996) Anomalous diffusion due to binding:a Monte Carlo study. Biophys J 70: 1250-62.
19. Straube R, Ridgway D, (2009) Investigating the effects of molecular crowding on Ca2+ diffusion sing a particle-based simulation model. Chaos 19 037110-1-037110-8.
20. Banks D, Fradi C, (2005) Anomalous diffusion of proteins due to molecular crowding. Biophys J 9: 2960-2971.
21. Weiss M, Elsner M, Kartberg F, Nilsson T, (2004) Anomalous subdiffusion is a measure for cytoplasmic rowding in living cells. Biophys J 87: 3518-3524.
22. Wong I, Gardel M, Reichman D, Weeks E, Valentine M, et al. (2004) Anomalous diffusion probes icrostructure dynamics of entangled f-actin networks. Phys Rev Lett 92: 178101.
23. Santamaria F, Wils S, Schutter ED, Augustine G, (2006) Anomalous diffusion in Purkinje cell endrites caused by spines. Neuron 52: 635-648.
24. Caspi A, Granek R, Elbaum M, (2000) Enhanced diffusion in active intracellular transport. Phys Rev Lett 85: 5655-8.
25. Xu T, Naraghi M, Kang H, Neher E, (1997) Kinetic studies of Ca2+ binding and Ca2+ clearance n the cytosol of adrenal chromaffin cells. Biophys J 73: 532-45.
26. Neher E, Sakaba T, (2008) Multiple roles of calcium ions in the regulation of neurotransmitter elease. Neuron 59: 861-72.
27. Lee S, Schwaller B, Neher E, (2000) Kinetics of Ca2+ binding to parvalbumin in bovine chromaffin ells: implications for [Ca2+] transients of neuronal dendrite. J Physiol 525: 419-32.
28. Lee S, Rosenmund C, Schwaller B, Neher E, (2000) Differences in Ca2+ buffering properties between xcitatory and inhibitory hippocampal neurons from the rat. Biophys J 525: 405-18.
29. Naraghi M, Müller T, Neher E, (1998) Two-dimensional determination of the cellular Ca2+ binding n bovine chromaffin cells. J Physiol 75: 1635-47.
30. Naraghi M, Neher E, (1997) Linearized buffered Ca2+ diffusion in microdomains and its implications or calculation of [Ca2+] at the mouth of a calcium channel. J Neurosci 17: 6961-73.
31. Gabso M, Neher E, Spira M, (1997) Low mobility of the Ca2+ buffers in axons of cultured aplysia eurons. Neuron 18: 473-81.
32. Dayel M, Hom E, Verkman A, (1999) Diffusion of green uorescent protein in the aqueous-phase umen of endoplasmic reticulum. Biophys J 76: 2843-2851.
33. Korkotian E, Segal M, (2006) Spatially confined diffusion of calcium in dendrites of hippocampal eurons revealed by ash photolysis of caged calcium. Cell Calcium 40: 441-9.
34. Goldberg J, Tamas G, Aronov D, Yuste R, (2003) Calcium microdomains in aspiny dendrites. euron 40: 807-21.
35. Schuss Z, (1984) Theory and applications of stochastic differential equations. Wiley Series in Probability nd Statistics John Wiley Sons, Inc., New York.
36. Schuss Z, Singer A, Holcman D, (2007) Narrow escape: Theory and applications to cellular microdomains. Proc Natl Acad Sci U S A 104: 16098-103.
37. Echevería C, Tucci K, Kapral R, (2007) Diffusion and reaction in crowded environments. J Phys: Condens Matter 19: 065146.
38. Ward M, Keller J, (1993) Strong localized perturbations of eigenvalue problems. SIAM J Appl Math 53: 770-98.
39. Singer A, Schuss Z, Holcman D, Eisenberg B, (2006) Narrow escape I. J Stat Phys 122: 437-463.
40. Singer A, Schuss Z, Holcman D, (2006) Narrow escape II: the circular disk. J Stat Phys 122: 65-489.
41. Singer A, Schuss Z, Holcman D, (2006) Narrow escape III: non-smooth domains and Riemannian urfaces. J Stat Phys 122: 491-509.
42. Zwanzig R, (1992) Diffusion past an entropy barrier. J Phys Chem 96: 392630.
43. Holcman D, Korenbrot J, (2004) Longitudinal diffusion in retinal rod and cone outer segment ytoplasm: the consequence of cell structure. Biophys J 86: 2566-82.
44. Berezhkovskii A, Pustovoit M, Bezrukov S, (2007) Diffusion in a tube of varying cross section: umerical study of reduction to effective one-dimensional description. J Chem Phys 126: 134706.
45. Saxton M, (1993) Lateral diffusion in an archipelago. Single-particle diffusion. Biophys J 64: 1766-80.
46. Braga J, McNally J, Carmo-Fonseca M, (2007) A reaction-diffusion model to study rna motion by uantitative uorescence recovery after photobleaching. Biophys J 92 92: 2694-2703.
47. Korkotian E, Segal M, (2006) Spatially confinded diffusion of calcium in dendrites of hippocampal eurons revealed by ash photolysis of caged calcium. Cell Calcium 40: 441-449.
48. Zhou Z, Neher E, (1993) Mobile and immobile calcium buffers in bovine adrenal chromaffin cells. Physiol 469: 245-73.
49. Sala F, Hernandez-Cruz A, (1993) Calcium di_usion modeling in spherical neuron. Relevance of buffering properties. Biophys J 57: 313-24.
50. Nowycky M, Pinter M, (1993) Time course of calcium and calcium-bound buffers following calcium nux in a model cell. Biophys J 64: 77-91.
51. Lisman J, (2003) Long-term potentiation: outstanding questions and attempted synthesis. Philos rans R Soc Lond B Biol Sci 358: 829-42.
52. Borgdorff A, Choquet D, (2002) Regulation of AMPA receptor lateral movements. Nature 417: 49-53.
53. Korkotian E, Holcman D, Segal M, (2004) Dynamic regulation of spine-dendrite coupling in cultured ippocampal neurons. Eur J Neurosci 20: 2649-2663.
54. Lorincz A, Ro'zsa B, Katona G, Vizi E, Tamas G, (2007) Differential distribution of NCX1 contributes o spine-dendrite compartmentalization in CA1 pyramidal cells. Proc Natl Acad Sci U S 104: 1033-8.
55. Persson P, Strang G, (2004) A simple mesh generator in MATLAB. SIAM Review 46: 329-345.
56. Yuste R, Majewska A, Cash S, Denk W, (1999) Mechanisms of calcium inux into spines: heterogeneity mong spines, coincidence detection by NMDA receptors and optical quantal analysis. J Neurosci 19: 1976-87.
57. Zador A, Koch C, Brown T, (1990) Biophysical model of a Hebbian synapse. Proc Natl Acad Sci U S A 87: 6718-22.