Computational modeling of subcellular transport and signaling

Current Opinion in Structural Biology

Volumn 25, Issue 1, 2014, Pages 92-97

  Hake, Johan ^a   Kekenes Huskey, Peter M ^b   McCulloch, Andrew D ^b  

^a SIMULA RESEARCH LABORATORY   (Norway)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CYTOLOGY; HEART MUSCLE CELL; INTRACELLULAR SPACE; METABOLISM; MICROSCOPY; PHYSIOLOGY; PROCEDURES; SIGNAL TRANSDUCTION; TRANSPORT AT THE CELLULAR LEVEL;

BIOLOGICAL TRANSPORT; COMPUTER SIMULATION; INTRACELLULAR SPACE; MICROSCOPY; MYOCYTES, CARDIAC; SIGNAL TRANSDUCTION;

EID: 84893475431     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2014.01.006     Document Type: Review

References (49)

1. Cheng H., Lederer W.J. Calcium sparks. Physiol Rev 2008, 88:1491-1545.
2. Williams G.S.B., Smith G.D., Sobie E.A., Jafri M.S. Models of cardiac excitation-contraction coupling in ventricular myocytes. Math Biosci 2010, 226:1-15.
3. Michailova A.P., Edwards A.G., Hake J., Hoshijima M., McCulloch A.D. Cardiac electrophysiology: from cell to bedside. Calcium Signaling in Cardiomyocyte Models with Realistic Geometries 2013, 33.1-33.10. Elsevier, Sounder Philadelpha, Chapter 33.
4. Das T., Hoshijima M. Adding a new dimension to cardiac nano-architecture using electron microscopy: coupling membrane excitation to calcium signaling. J Mol Cell Cardiol 2013, 58:5-12.
5. Soeller C., Baddeley D. Super-resolution imaging of EC coupling protein distribution in the heart. J Mol Cell Cardiol 2013, 58:32-40.
6. Savio-Galimberti E., Frank J., Inoue M., Goldhaber J.I., Cannell M.B., Bridge J.H.B., Sachse F.B. Novel features of the rabbit transverse tubular system revealed by quantitative analysis of three-dimensional reconstructions from confocal images. Biophys J 2008, 95:2053-2062.
7. Briggman K.L., Bock D.D. Volume electron microscopy for neuronal circuit reconstruction. Curr Opin Neurobiol 2012, 22:154-161.
8. Pinali C., Bennett H., Davenport J.B., Trafford A.W., Kitmitto A. 3-D reconstruction of the cardiac sarcoplasmic reticulum reveals a continuous network linking t-tubules: this organization is perturbed in heart failure. Circ Res 2013, published online ahead of print.
9. Ladinsky M.S., Howell K.E. Electron tomography of immunolabeled cryosections. Methods Cell Biol 2007, 79:543-558.
10. Shu X., Lev-Ram V., Deerinck T.J., Qi Y., Ramko E.B., Davidson M.W., Jin Y., Ellisman M.H., Tsien R.Y. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. PLoS Biol 2011, 9:e1001041.
11. Wong J., Baddeley D., Bushong E.A., Yu Z., Ellisman M.H., Hoshijima M., Soeller C. Nanoscale distribution of ryanodine receptors and Caveolin-3 in mouse ventricular myocytes: dilation of t-tubules near junctions. Biophys J 2013, 104:L22-L24.
12. Fernandez J.J. Computational methods for electron tomography. Micron 2012, 43:1010-1030.
13. Giuly R.J., Kim K.Y., Ellisman M.H. DP2: distributed 3D image segmentation using micro-labor workforce. Bioinformatics 2013, 29:1359-1360.
14. Gao Z., Yu Z., Holst M. Feature-preserving surface mesh smoothing via suboptimal Delaunay triangulation. Graph Models 2013, 75:23-38.
15. Kinney J.P. Investigation of neurotransmitter diffusion in three-dimensional reconstructions of hippocampal neuropil 2009, University of California, San Diego, (PhD thesis).
16. Yu Z., Holst M.J., Cheng Y., McCammon J. Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Model 2008, 26:1370-1380.
17. Liao T., Zhang Y., Kekenes-Huskey P.M., Cheng Y., Michailova A., McCulloch A.D., Holst M., McCammon J.A. Multi-core CPU or GPU-accelerated multiscale modeling for biomolecular complexes. Mol Based Math Biol 2013, 1:164-179.
18. Hake J., Edwards A.G., Yu Z., Kekenes-Huskey P.M., Michailova A.P., McCammon J.A., Holst M.J., Hoshijima M., McCulloch A.D. Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol 2012, 590(Pt 18):4403-4422.
19. 2+ trigger flux in rabbit myocytes with realistic t-tubule geometries. Front Physiol 2012, 3:351.
20. Yu Z., Yao G., Hoshijima M., Michailova A., Holst M. Multiscale modeling of calcium dynamics in ventricular myocytes with realistic transverse tubules. IEEE Trans Biomed Eng 2011, 58:2947-2951.
21. 2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum. PLoS Comput Biol 2010, 6:e1000972.
22. Yu Z., Holst M.J., Hayashi T., Bajaj C.L., Ellisman M.H., McCammon J.A., Hoshijima M. Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: bridging the gap between microscopic imaging and mathematical simulation. J Struct Biol 2008, 164:304-313.
23. Kinney J.P., Spacek J., Bartol T.M., Bajaj C.L., Harris K.M., Sejnowski T.J. Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil. J Comp Neurol 2013, 521:448-464.
24. Cowan A.E., Moraru I.I., Schaff J.C., Slepchenko B.M., Loew L.M. Spatial modeling of cell signaling networks. Computational Methods in Cell Biology, vol 110 of Methods in Cell Biology 2012, 195-221. Academic Press, Chapter 8. A.R. Asthagiri, A.P. Arkin (Eds.).
25. Ditlev J., Mayer B., Loew L. There is more than one way to model an elephant. Experiment-driven modeling of the actin cytoskeleton. Biophys J 2013, 104:520-532.
26. 2+ release units and couplons in skeletal and cardiac muscles. Biophys J 1999, 77:1528-1539.
27. 2+ signaling in the heart. J Cell Sci 2009, 122(Pt 7):1005-1013.
28. Baddeley D., Jayasinghe I.D., Lam L., Rossberger S., Cannell M.B., Soeller C. Optical single-channel resolution imaging of the ryanodine receptor distribution in rat cardiac myocytes. Proc Natl Acad Sci U S A 2009, 106:22275-22280.
29. Ramay H.R., Liu O.Z., Sobie E.A. Recovery of cardiac calcium release is controlled by sarcoplasmic reticulum refilling and ryanodine receptor sensitivity. Cardiovasc Res 2011, 91:598-605.
30. 2+ release units?. J Mol Cell Cardiol 2013, 58:41-52.
31. 2+ diffusion. Circ Res 2008, 103:e105-e115.
32. 2+ sparks: an investigative mathematical model of calcium-induced calcium release. Biophys J 2002, 83:59-78.
33. Hatano A., Okada Ji, Washio T., Hisada T., Sugiura S. A three-dimensional simulation model of cardiomyocyte integrating excitation-contraction coupling and metabolism. Biophys J 2011, 101:2601-2610.
34. 2+ release by stochastic RyR gating within a 3D model of the cardiac dyad and importance of induction decay for CICR termination. Biophys J 2013, 104:2149-2159.
35. Laver D.R., Kong C.H.T., Imtiaz M.S., Cannell M.B. Termination of calcium-induced calcium release by induction decay: an emergent property of stochastic channel gating and molecular scale architecture. J Mol Cell Cardiol 2013, 54:98-100.
36. 2+ signalling in rat ventricular myocytes. Exp Physiol 2009, 94:496-508.
37. McGuffee S.R., Elcock A.H. Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol 2010, 6:e1000694.
38. Tanskanen A.J., Greenstein J.L., Chen A., Sun S.X., Winslow R.L. Protein geometry and placement in the cardiac dyad influence macroscopic properties of calcium-induced calcium release. Biophys J 2007, 92:3379-3396.
39. Shorten P.R., Sneyd J. A mathematical analysis of obstructed diffusion within skeletal muscle. Biophys J 2009, 96:4764-4778.
40. Kekenes-Huskey P.M., Liao T., Gillette A., Hake J., Zhang J., Michailova A., McCulloch A.D., McCammon J.A. Molecular and subcellular-scale modeling of nucleotide diffusion in the cardiac myofilament lattice. Biophys J 2013, 105:2130-2140.
41. Kekenes-Huskey P.M., Gillette A., Hake J., McCammon J.A. Finite element estimation of protein-ligand association rates with post-encounter effects: applications to calcium binding in troponin C and SERCA. Comput Sci Discov 2012, 5:014015.
42. Silva J.R., Pan H., Wu D., Nekouzadeh A., Decker K.F., Cui J., Baker N.A., Sept D., Rudy Y. A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential. Proc Natl Acad Sci U S A 2009, 106:11102-11106.
43. Nekouzadeh A., Rudy Y. Continuum molecular simulation of large conformational changes during ion-channel gating. PLoS ONE 2011, 6:e20186.
44. Roux B., Bernche S., Egwolf B., Lev B., Noskov S.Y., Rowley C.N., Yu H. Ion selectivity in channels and transporters. J Gen Physiol 2011, 137:415-426.
45. Lindert S., Kekenes-Huskey P.M., Huber G., Pierce L., McCammon J.A. Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study. J Phys Chem B 2012, 116:8449-8459.
46. Kekenes-Huskey P.M., Lindert S., McCammon J.A. Molecular basis of calcium-sensitizing and desensitizing mutations of the human cardiac troponin C regulatory domain: a multi-scale simulation study. PLoS Comput Biol 2012, 8:e1002777.
47. 2+ ATPase. Protein Sci 2012, 21:1429-1443.
48. Hilder T.A., Chung S.H. Conductance properties of the inwardly rectifying channel, Kir3.2: molecular and Brownian dynamics study. Biochim Biophys Acta 2013, 1828:471-478.
49. Bauler P., Huber G.A., McCammon J.A. Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions. J Chem Phys 2012, 136:164107.