Abstract
Calcium calmodulin dependent kinase II (CaMKII) is sequestered in dendritic spines within seconds upon synaptic stimulation. The program Smoldyn was used to develop scenarios of single molecule CaMKII diffusion and binding in virtual dendritic spines. We first validated simulation of diffusion as a function of spine morphology. Additional cellular structures were then incorporated to simulate binding of CaMKII to the post-synaptic density (PSD); binding to cytoskeleton; or their self-aggregation. The distributions of GFP tagged native and mutant constructs in dissociated hippocampal neurons were measured to guide quantitative analysis. Intra-spine viscosity was estimated from fluorescence recovery after photo-bleach (FRAP) of red fluorescent protein. Intra-spine mobility of the GFP-CaMKIIα constructs was measured, with hundred-millisecond or better time resolution, from FRAP of distal spine tips in conjunction with fluorescence loss (FLIP) from proximal regions. Different FRAP \ FLIP profiles were predicted from our Scenarios and provided a means to differentiate binding to the PSDs from self-aggregation. The predictions were validated by experiments. Simulated fits of the Scenarios provided estimates of binding and rate constants. We utilized these values to assess the role of self-aggregation during the initial response of native CaMKII holoenzymes to stimulation. The computations revealed that self-aggregation could provide a concentration-dependent switch to amplify CaMKII sequestration and regulate its activity depending on its occupancy of the actin cytoskeleton.
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References
Andrews, S. S. (2009). Accurate particle-based simulation of adsorption, desorption and partial transmission. Physical Biology, 6, 046015.
Andrews, S. S., Addy, N. J., Brent, R., & Arkin, A. P. (2010). Detailed simulations of cell biology with Smoldyn 2.1. PLoS Computational Biology, 6, e1000705.
Andrews, S. S., & Bray, D. (2004). Stochastic simulation of chemical reactions with spatial resolution and single molecule detail. Physical Biology, 1, 137–151.
Bayer, K. U., De Koninck, P., Leonard, A. S., Hell, J. W., & Schulman, H. (2001). Interaction with the NMDA receptor locks CaMKII in an active conformation. Nature, 411, 801–805.
Bayer, K. U., LeBel, E., McDonald, G. L., O’Leary, H., Schulman, H., & De Koninck, P. (2006). Transition from reversible to persistent binding of CaMKII to postsynaptic sites and NR2B. The Journal of Neuroscience, 26, 1164–1174.
Beyer, H. (1985). Handbuch der Mikroskopie (2nd ed.). Berlin: VEB Verlag Technik.
Bhalla, U. S. (2004). Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties. Biophysical Journal, 87, 745–753.
Block, S. M., Segall, J. E., & Berg, H. C. (1982). Impulse responses in bacterial chemotaxis. Cell, 31, 215–226.
Bloodgood, B. L., & Sabatini, B. L. (2005). Neuronal activity regulates diffusion across the neck of dendritic spines. Science, 310, 866–869.
Bloodgood, B. L., & Sabatini, B. L. (2007). Ca(2+) signaling in dendritic spines. Current Opinion in Neurobiology, 17, 345–351.
Byrne, M. J., Putkey, J. A., Waxham, M. N., & Kubota, Y. (2009). Dissecting cooperative calmodulin binding to CaM kinase II: a detailed stochastic model. Journal of Computational Neuroscience, 27, 621–638.
Chen, X., Vinade, L., Leapman, R. D., Petersen, J. D., Nakagawa, T., Phillips, T. M., et al. (2005). Mass of the postsynaptic density and enumeration of three key molecules. Proceedings of the National Academy of Sciences of the United States of America, 102, 11551–11556.
DePristo, M. A., Chang, L., Vale, R. D., Khan, S. M., & Lipkow, K. (2009). Introducing simulated cellular architecture to the quantitative analysis of fluorescent microscopy. Progress in Biophysics and Molecular Biology, 100, 25–32.
Dosemeci, A., Tao-Cheng, J. H., Vinade, L., Winters, C. A., Pozzo-Miller, L., & Reese, T. S. (2001). Glutamate-induced transient modification of the postsynaptic density. Proceedings of the National Academy of Sciences of the United States of America, 98, 10428–10432.
Erhard, F., Friedel, C. C., & Zimmer, R. (2008). FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics, 9, 356.
Eshhar, N., Petralia, R. S., Winters, C. A., Niedzielski, A. S., & Wenthold, R. J. (1993). The segregation and expression of glutamate receptor subunits in cultured hippocampal neurons. Neuroscience, 57, 943–964.
Garcia de la Torre, J. G., & Bloomfield, V. A. (1981). Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications. Quarterly Reviews of Biophysics, 14, 81–139.
Grant, P. A., Best, S. L., Sanmugalingam, N., Alessio, R., Jama, A. M., & Torok, K. (2008). A two-state model for Ca2+/CaM-dependent protein kinase II (alphaCaMKII) in response to persistent Ca2+ stimulation in hippocampal neurons. Cell Calcium, 44, 465–478.
Hudmon, A., Lebel, E., Roy, H., Sik, A., Schulman, H., Waxham, M. N., et al. (2005). A mechanism for Ca2+/calmodulin-dependent protein kinase II clustering at synaptic and nonsynaptic sites based on self-association. The Journal of Neuroscience, 25, 6971–6983.
Kaech, S., Brinkhaus, H., & Matus, A. (1999). Volatile anesthetics block actin-based motility in dendritic spines. Proceedings of the National Academy of Sciences of the United States of America, 96, 10433–10437.
Kuriu, T., Inoue, A., Bito, H., Sobue, K., & Okabe, S. (2006). Differential control of postsynaptic density scaffolds via actin-dependent and -independent mechanisms. The Journal of Neuroscience, 26, 7693–7706.
Landis, D. M., & Reese, T. S. (1983). Cytoplasmic organization in cerebellar dendritic spines. The Journal of Cell Biology, 97, 1169–1178.
Levine, C. G., Mitra, D., Sharma, A., Smith, C. L., & Hegde, R. S. (2005). The efficiency of protein compartmentalization into the secretory pathway. Molecular Biology of the Cell, 16, 279–291.
Lisman, J., Lichtman, J. W., & Sanes, J. R. (2003). LTP: perils and progress. Nature Reviews. Neuroscience, 4, 926–929.
Lisman, J. E., Raghavachari, S., & Tsien, R. W. (2007). The sequence of events that underlie quantal transmission at central glutamatergic synapses. Nature Reviews. Neuroscience, 8, 597–609.
Lu, Z., McLaren, R. S., Winters, C. A., & Ralston, E. (1998). Ribosome association contributes to restricting mRNAs to the cell body of hippocampal neurons. Molecular and Cellular Neurosciences, 12, 363–375.
Lucic, V., Greif, G. J., & Kennedy, M. B. (2008). Detailed state model of CaMKII activation and autophosphorylation. European Biophysics Journal, 38, 83–98.
Matus, A., Ackermann, M., Pehling, G., Byers, H. R., & Fujiwara, K. (1982). High actin concentrations in brain dendritic spines and postsynaptic densities. Proceedings of the National Academy of Sciences of the United States of America, 79, 7590–7594.
Noguchi, J., Matsuzaki, M., Ellis-Davies, G. C., & Kasai, H. (2005). Spine-neck geometry determines NMDA receptor-dependent Ca2+ signaling in dendrites. Neuron, 46, 609–622.
Novak, I. L., Kraikivski, P., & Slepchenko, B. M. (2009). Diffusion in cytoplasm: effects of excluded volume due to internal membranes and cytoskeletal structures. Biophysical Journal, 97, 758–767.
Okabe, S. (2007). Molecular anatomy of the postsynaptic density. Molecular and Cellular Neurosciences, 34, 503–518.
Okamoto, K., Nagai, T., Miyawaki, A., & Hayashi, Y. (2004). Rapid and persistent modulation of actin dynamics regulates postsynaptic reorganization underlying bidirectional plasticity. Nature Neuroscience, 7, 1104–1112.
Okamoto, K., Narayanan, R., Lee, S. H., Murata, K., & Hayashi, Y. (2007). The role of CaMKII as an F-actin-bundling protein crucial for maintenance of dendritic spine structure. Proceedings of the National Academy of Sciences of the United States of America, 104, 6418–6423.
Oliveira, R. F., Terrin, A., Di Benedetto, G., Cannon, R. C., Koh, W., Kim, M., et al. (2010). The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations. PLoS ONE, 5, e11725.
Otmakhov, N., Tao-Cheng, J. H., Carpenter, S., Asrican, B., Dosemeci, A., Reese, T. S., et al. (2004). Persistent accumulation of calcium/calmodulin-dependent protein kinase II in dendritic spines after induction of NMDA receptor-dependent chemical long-term potentiation. The Journal of Neuroscience, 24, 9324–9331.
Petersen, J. D., Chen, X., Vinade, L., Dosemeci, A., Lisman, J. E., & Reese, T. S. (2003). Distribution of postsynaptic density (PSD)-95 and Ca2+/calmodulin-dependent protein kinase II at the PSD. The Journal of Neuroscience, 23, 11270–11278.
Ridgway, D., Broderick, G., Lopez-Campistrous, A., Ru’aini, M., Winter, P., Hamilton, M., et al. (2008). Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Biophysical Journal, 94, 3748–3759.
Sanabria, H., Kubota, Y., & Waxham, M. N. (2007). Multiple diffusion mechanisms due to nanostructuring in crowded environments. Biophysical Journal, 92, 313–322.
Sanabria, H., Swulius, M. T., Kolodziej, S. J., Liu, J., & Waxham, M. N. (2009). {beta}CaMKII regulates actin assembly and structure. The Journal of Biological Chemistry, 284, 9770–9780.
Santamaria, F., Wils, S., De Schutter, E., & Augustine, G. J. (2006). Anomalous diffusion in Purkinje cell dendrites caused by spines. Neuron, 52, 635–648.
Sharma, K., Fong, D. K., & Craig, A. M. (2006). Postsynaptic protein mobility in dendritic spines: long-term regulation by synaptic NMDA receptor activation. Molecular and Cellular Neurosciences, 31, 702–712.
Shen, K., & Meyer, T. (1999). Dynamic control of CaMKII translocation and localization in hippocampal neurons by NMDA receptor stimulation. Science, 284, 162–166.
Shen, K., Teruel, M. N., Connor, J. H., Shenolikar, S., & Meyer, T. (2000). Molecular memory by reversible translocation of calcium/calmodulin-dependent protein kinase II. Nature Neuroscience, 3, 881–886.
Shen, K., Teruel, M. N., Subramanian, K., & Meyer, T. (1998). CaMKIIbeta functions as an F-actin targeting module that localizes CaMKIIalpha/beta heterooligomers to dendritic spines. Neuron, 21, 593–606.
Sheng, M., & Hoogenraad, C. C. (2007). The postsynaptic architecture of excitatory synapses: a more quantitative view. Annual Review of Biochemistry, 76, 823–847.
Smith, B. A., Roy, H., De Koninck, P., Grutter, P., & De Koninck, Y. (2007). Dendritic spine viscoelasticity and soft-glassy nature: balancing dynamic remodeling with structural stability. Biophysical Journal, 92, 1419–1430.
Snapp, E. L., Sharma, A., Lippincott-Schwartz, J., & Hegde, R. S. (2006). Monitoring chaperone engagement of substrates in the endoplasmic reticulum of live cells. Proceedings of the National Academy of Sciences of the United States of America, 103, 6536–6541.
Sprague, B. L., & McNally, J. G. (2005). FRAP analysis of binding: proper and fitting. Trends in Cell Biology, 15, 84–91.
Sprague, B. L., Muller, F., Pego, R. L., Bungay, P. M., Stavreva, D. A., & McNally, J. G. (2006). Analysis of binding at a single spatially localized cluster of binding sites by fluorescence recovery after photobleaching. Biophysical Journal, 91, 1169–1191.
Svoboda, K., Tank, D. W., & Denk, W. (1996). Direct measurement of coupling between dendritic spines and shafts. Science, 272, 716–719.
Swaminathan, R., Hoang, C. P., & Verkman, A. S. (1997). Photobleaching recovery and anisotropy decay of green fluorescent protein GFP-S65T in solution and cells: cytoplasmic viscosity probed by green fluorescent protein translational and rotational diffusion. Biophysical Journal, 72, 1900–1907.
Tang, S. J., & Schuman, E. M. (2002). Protein synthesis in the dendrite. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 357, 521–529.
Walikonis, R. S., Oguni, A., Khorosheva, E. M., Jeng, C. J., Asuncion, F. J., & Kennedy, M. B. (2001). Densin-180 forms a ternary complex with the (alpha)-subunit of Ca2+/calmodulin-dependent protein kinase II and (alpha)-actinin. The Journal of Neuroscience, 21, 423–433.
Weiss, M. (2004). Challenges and artifacts in quantitative photobleaching experiments. Traffic (Copenhagen, Denmark), 5, 662–671.
Zhabotinsky, A. M., Camp, R. N., Epstein, I. R., & Lisman, J. E. (2006). Role of the neurogranin concentrated in spines in the induction of long-term potentiation. The Journal of Neuroscience, 26, 7337–7347.
Acknowledgments
We thank Steven Andrews for advice on Smoldyn and Ayse Dosemeci for comments on the manuscript. This work was supported by grant R01-GM49319 from the National Institutes of Health (to SK). YZ was an NIH summer student intern. AA was supported by start-up funds (to SK) from the School of Science & Engineering, LUMS.
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Khan, S., Zou, Y., Amjad, A. et al. Sequestration of CaMKII in dendritic spines in silico . J Comput Neurosci 31, 581–594 (2011). https://doi.org/10.1007/s10827-011-0323-2
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DOI: https://doi.org/10.1007/s10827-011-0323-2