VCell Published Models 2017-08-22T19:01:21+00:00

A Reaction-Diffusion Model Explains Amplification of the PLC/PKC Pathway in Fibroblast Chemotaxis.
Mohan,K1, Nosbisch,JL, Elston,TC, Bear,JE, Haugh,JM
Biophys J. 2017 Jul 11;113(1):185-194.
PUBMED:28700916      doi:10.1016/j.bpj.2017.05.035
   VCell BioModels referenced in publication:
   user: jnosbis,   model name: Mohan chemotaxis 2017

Activation of the contact pathway of blood coagulation on the circulating microparticles may explain blood plasma coagulation induced by dilution
Chelushkin,MA, Panteleev,MA, Sveshnikova,AN
Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology. 2017;11(2):130–143

Cell shape information is transduced through tension-independent mechanisms
Ron, A., Azeloglu, E.U., Calizo, R.C., Hu, M., Bhattacharya, S., Chen, Y., Jayaraman, G., Lee, S., Neves-Zaph, S.R., Li, H., Gordon, R.E.
Nature communications. 2017; 8(1), p.2145.
PUBMED:28652372      doi:10.1038/s41467-017-02218-4

Fission yeast myo2: Molecular organization and diffusion in the cytoplasm
Friend, J. E., Sayyad, W. A., Arasada, R., McCormick, C. D., Heuser, J. E., Pollard, T. D.
Cytoskeleton. 2017 Dec 4.
PUBMED:29205883      doi:10.1002/cm.21425
   VCell BioModels referenced in publication:
   user: Wasim,   model name: Yeast 3D_FRAP

Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability
Falkenberg,CV, Azeloglu,EU, Stothers,M, Deerinck,TJ, Chen,Y, He,JC, Ellisman,MH, Hone,JC, Iyengar,R, Loew,LM
PLoS Comput Biol. 2017 Mar 16;13(3):e1005433.
PUBMED:28301477      doi:10.1371/journal.pcbi.1005433
   VCell BioModels referenced in publication:
   user: falkenbe,   model name: Falkenberg_PodocyteStability

Muscarinic receptor regulates extracellular signal regulated kinase by two modes of arrestin binding
Jung, S. R., Kushmerick, C., Seo, J. B., Koh, D. S., Hille, B.
Proceedings of the National Academy of Sciences, 201700331
PUBMED:28652372      doi:10.1073/pnas.1700331114
   VCell BioModels referenced in publication:
   user: jsr007,   model name: Jung_PNAS_2017_BiasedM1R_Figure4
   user: jsr007,   model name: Jung_PNAS_2017_wildtypeM1R_figure5

Plant potassium channels are in general dual affinity uptake systems
AIMS Biophysics, 2017, 4(1): 90-106.

Src Homology 2 domains enhance tyrosine phosphorylation in vivo by protecting binding sites in their target proteins from dephosphorylation
Jadwin, J. A., Curran, T. G., Lafontaine, A. T., White, F. M., Mayer, B. J.
Journal of Biological Chemistry (2017) 293.2: 623-637
PUBMED:29162725      doi:10.1074/jbc.M117.794412
   VCell BioModels referenced in publication:
   user: jjadwin,   model name: spatial protection test- no flux two way competition orginal – paper model-shared
   user: jjadwin,   model name: spatial protection test- two way competition orginal – paper model shared

The fungal UmSrt1 and maize ZmSUT1 sucrose transporters battle for plant sugar resources
Wittek,A, Dreyer,I, Al-Rasheid,KAS, Sauer,N, Hedrich,R, Geiger,D
J Integr Plant Biol. 2017 Jun;59(6):422-435.
PUBMED:28296205      doi:10.1111/jipb.12535
   VCell BioModels referenced in publication:
   user: idreyer,   model name: AMF Symbiosis with SWEET

Cooperation through Competition—Dynamics and Microeconomics of a Minimal Nutrient Trade System in Arbuscular Mycorrhizal Symbiosis
Schott, Stephan, Valdebenito, Braulio, Bustos, Daniel, Gomez-Porras, Judith L., Sharma, Tripti, Dreyer, Ingo
Front Plant Sci. 2016 Jun 27;7:912.
PUBMED:27446142      doi:10.3389/fpls.2016.00912
   VCell BioModels referenced in publication:
   user: idreyer,   model name: AMF Symbiosis with SWEET

Regulation of quantal currents determines synaptic strength at neuromuscular synapses in larval Drosophila
Powers, Andrew S., Grizzaffi, Jeffrey, Ribchester, Richard, Lnenicka, Gregory A.
Pflugers Arch. 2016 Nov;468(11-12):2031-2040.
PUBMED:27783155      doi:10.1007/s00424-016-1893-7
   VCell BioModels referenced in publication:
   user: gregl,   model name: minepsp

Cross-regulation of phosphodiesterase-1 and phosphodiesterase-2 activities controls dopaminemediated striatal alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (ampa) receptor trafficking.
Song, R.S., Tolentino, R., Sobie, E.A., Neves-Zaph, S.R.
J Biol Chem. 2016 Sep 7. pii: jbc.M116.749747
PUBMED:27605670      doi:10.1074/jbc.M116.749747
   VCell BioModels referenced in publication:
   user: rsong,   model name: RS_JBC2016

Simultaneous quantification of actin monomer and filament dynamics with modelling assisted analysis of photoactivation
Kapustina, M., Read, T. A., Vitriol, E. A.
J Cell Sci. 2016 Dec 15;129(24):4633-4643
PUBMED:27831495      doi:10.1242/jcs.194670
   VCell BioModels referenced in publication:
   user: marynka,   model name: GF-actin FDAP
   user: marynka,   model name: Axon_FDAP

Dynamics of Phosphoinositide-Dependent Signaling in Sympathetic Neurons
Kruse, M., Vivas, O., Traynor-Kaplan, A., Hille, B.
J Neurosci. 2016;36(4):1386-400.
PUBMED:26818524      doi:10.1523/JNEUROSCI.3535-15.2016
   VCell BioModels referenced in publication:
   user: mkruse,   model name: hillelab: KruseVivasTraynorKaplanHille_PI-metabolism_SCG_2015

Hysteresis-like binding of coagulation factors X/Xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization
Podoplelova, N. A., Sveshnikova, A. N., Kurasawa, J. H., Sarafanov, A. G., Chambost, H., Vasil&apos, ev, S. A., Demina, I. A., Ataullakhanov, F. I., Alessi, M. C., Panteleev, M. A.
Biochim Biophys Acta. 2016;1858(6):1216-27.
PUBMED:26874201      doi:10.1016/j.bbamem.2016.02.008
   VCell BioModels referenced in publication:
   user: agolomy,   model name: fX_platelet_binding
   user: agolomy,   model name: fX_thrombus_binding

Modeling Excitable Dynamics of Chemotactic Networks
Bhattacharya, S., Iglesias, P. A.
Methods Mol Biol. 2016;1407:397-415.
PUBMED:27271916      doi:10.1007/978-1-4939-3480-5_27
   VCell BioModels referenced in publication:
   user: sayak66,   model name: BEN
   user: sayak66,   model name: Smoldyn

Neighboring phosphoSer-Pro motifs in the undefined domain of IRAK1 impart bivalent advantage for Pin1 binding
Rogals, M. J., Greenwood, A. I., Kwon, J., Lu, K. P., Nicholson, L. K.
The FEBS journal, 2016; 283(24), 4528-4548
PUBMED:28652372      doi:10.1111/febs.13943
   VCell BioModels referenced in publication:
   user: mjr323,   model name: Pin1_2Domains(diffKds)_monovalentligand
   user: mjr323,   model name: Pin1_2domain(diffKds)_w_Bivalentligand(diffKds)
   user: mjr323,   model name: Pin1_2domain(diffKds)_w_Bivalentligand(diffKds)

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology
Schaff, J.C., Gao, F., Li, Y., Novak, I.L., Slepchenko, B.M.
PLoS Comput Biol. 2016 Dec 13;12(12):e1005236.
PUBMED:27959915      doi:10.1371/journal.pcbi.1005236
   VCell MathModels referenced in publication:
   user: boris,   model name: Hybrid_cell_polarity_public

On the importance of modelling the internal spatial dynamics of biological cells
Sayyid, F., Kalvala, S.
Biosystems. 2016 Jul;145:53-66.
PUBMED:27262415      doi:10.1016/j.biosystems.2016.05.012

Pancreatic Beta Cell G-Protein Coupled Receptors and Second Messenger Interactions: A Systems Biology Computational Analysis
Fridlyand, L. E., Philipson, L. H.
PLoS ONE. 2016;11(5):e0152869.
PUBMED:27138453      doi:10.1371/journal.pone.0152869
   VCell MathModels referenced in publication:
   user: Fridlyand,   model name: Messengers interaction