VCell The Virtual Cell › University of Connecticut Health Center

Quantitative properties and receptor reserve of the DAG and PKC branch of Gq-coupled receptor signaling

Björn H. Falkenburger, Eamonn J. Dickson, and Bertil Hille
J. Gen. Physiol. 2013; 141:537-555.
PubMed

BioModel: bfalken:FalkenburgerDicksonHille2013

Quantitative properties and receptor reserve of the IP3 and calcium branch of Gq-coupled receptor signaling.

Eamonn J. Dickson, Björn H. Falkenburger, and Bertil Hille
J. Gen. Physiol. 2013; 141:521-535.
PubMed

BioModel: bfalken:FalkenburgerDicksonHille2013

Computational analysis of calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons associated with ataxia.

Brown SA, Loew LM.
BMC Syst Biol. 2012 Jun 15;6:70. doi: 10.1186/1752-0509-6-70.
PubMed

BioModel: les: Brown et al. 2011 Analysis of SCA15-SCA16 with IC4 Peptide Application
BioModel: les: Brown et al. 2011 SCA1 Compensation Analysis
BioModel: les: Brown et al. 2011 Analysis of SCA1-SCA2-SCA3 with IC-G2736X Peptide
BioModel: les: Brown et al. 2011 Purkinje Biochem-Electrophysiol SCA
BioModel: les: Brown et al. 2011 Purkinje 3D Spine – Spinocerebellar Ataxia study
BioModel: les: Brown et al. 2011 Combined Purkinje - Several Spines - Current Injection

A computational systems analysis of factors regulating α cell glucagon secretion.

Fridlyand LE, Philipson LH.
Islets. 2012 Jul 1;4(4):262-83. doi: 10.4161/isl.22193. Epub 2012 Jul 1.
PubMed

MathModel: Fridlyand: Alpha and beta cells glucose sensing
MathModel: Fridlyand: Glucagon secretion

CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation.

Michalski PJ, Loew LM.
Phys Biol. 2012 Jun 8;9(3):036010. [Epub ahead of print]
PubMed

BioModel: pjmichal: BioNetGen CaMKII – Trimer – 6 states – with phosphatase
BioModel: pjmichal: CaMKII – Infinite Lattice – 6 states
BioModel: pjmichal: BioNetGen CaMKII – Dimer – 3 states – with phosphatase
BioModel: pjmichal: BioNetGen CaMKII – Trimer – 3 states – with phosphatase
BioModel: pjmichal: BioNetGen CaMKII – Tetramer – 3 states – with phosphatase
BioModel: pjmichal: BioNetGen CaMKII – Pentamer – 3 states – with phosphatase
BioModel: pjmichal: BioNetGen CaMKII – Hexamer – 3 states – with phosphatase

Stoichiometry of Nck-dependent actin polymerization in living cells

Ditlev, J.A., Michalski, P.J., Huber, G., Rivera, G.M., Mohler, W.A., Loew, L.M., Mayer, B.J.
J Cell Biol 197 (5): 643-658, May 21, 2012
PubMed

Biomodel:'JDitlev: Nck Induces Actin Comet Tail Formation Single NWASP Activation of Arp2/3 Simplified Actin Dendritic Nucleation (1:1:1 model)
Biomodel:'JDitlev: Nck Induces Actin Comet Tail Formation Dimer NWASP Activation of Arp2/3 Simplified Actin Dendritic Nucleation (2:2:1 model)
Biomodel:'JDitlev: Nck Induces Actin Comet Tail Formation Dimer Nck Binds NWASP With Dimer NWASP Activation of Arp2/3 Simplified Actin Dendritic Nucleation (4:2:1 model)

Live-cell fluorescence microscopy with molecular biosensors: What are we really measuring?

Haugh, JM
Biophys J, 102 (9): 2003-2011 (2012).
PubMed

Biomodel: 'jmhaugh: Biosensor simple'

Spatial modeling of cell signaling networks

Cowan AE, Moraru II, Schaff JC, Slepchenko BM, Loew LM.
Methods Cell Biol. 2012;110:195-221
PubMed

Biomodel: 'les: Membrane Flux for meth cell biology'

Assessment of cellular mechanisms contributing to cAMP compartmentalization in pulmonary microvascular endothelial cells

Wei P Feinstein, Bing Zhu, Silas J Leavesley, Sarah L. Sayner, and Thomas C Rich
Am J Physiol Cell Physiol. 2012 Mar;302(6):C839-52. Epub 2011 Nov 23.
PubMed

BioModel: 'wfeinstein: PMVEC cAMP model'
BioModel: 'wfeinstein: PMVEC cAMP model with point source'

System analysis shows distinct mechanisms and common principles of nuclear envelope protein dynamics.

Nikolaj Zuleger, David A. Kelly, A. Christine Richardson, Alastair R. W. Kerr, Martin W. Goldberg, Andrew B. Goryachev, and Eric C. Schirmer
J Cell Biol 2011 193:109-123. Published March 28, 2011, doi:10.1083/jcb.201009068
PubMed

Cooperative Nuclear Localization Sequences Lend a Novel Role to the N-Terminal Region of MSH6.

Gassman NR, Clodfelter JE, McCauley AK, Bonin K, Salsbury FR Jr, et al.
(2011) PLoS ONE 6(3): e17907. doi:10.1371/journal.pone.0017907.
PubMed

Coupling of metabolic, second messenger pathways and insulin granule dynamics in pancreatic beta-cells: A computational analysis

Fridlyand LE, Philipson LH.
Prog Biophys Mol Biol. 2011 Nov;107(2):293-303. Ep ub 2011 Sep 8.
PubMed

MathModels: "Fridlyand" and "Traffic1"

Triggering Actin Comets Versus Membrane Ruffles: Distinctive Effects of Phosphoinositides on Actin Reorganization.

Ueno T, Falkenburger BH, Pohlmeyer C, Inoue T.
Sci Signal. 2011;4(203):ra87.
PubMed

BioModel: 'bfalken: Ueno2011'

System analysis shows distinct mechanisms and common principles of nuclear envelope protein dynamics.

Zuleger, N., Kelly, D.A., Richardson, A.C., Kerr, A.R.W., Goldberg, M.W., Goryachev, A.B., Schirmer, E.C.
The Journal of Cell Biology 193, 109-123, 2011.
PubMed

The emergence of sarcomeric, graded-polarity and spindle-like patterns in bundles of short cytoskeletal polymers and two opposite molecular motors.

Craig, E.M., Dey, S., and Mogilner, A.
J Phys Condens Matter 23, 374102, (2011).
PubMed

MathModel: ‘ecraig: Cytoskeletal bundle_1-motor’
MathModel: ‘ecraig: Cytoskeletal bundle_2-motor’ (for the extended model described in section 6)

Astrocytes as regulators of synaptic function: a quest for the Ca2+ master key.

Rusakov, D.A., Zheng, K., and Henneberger, C.
Neuroscientist 17, 513-523, (2011).
PubMed

Protein Diffusion in Mammalian Cell Cytoplasm.

Kühn, T., T.O. Ihalainen, J. Hyväluoma, N. Dross, S.F. Willman, J. Langowski, M. Vihinen-Ranta, and J. Timonen.
2011, PLoS ONE. 6:e22962.
PubMed

Quantifying the Waddington landscape and biological paths for development and differentiation.

Wang J, Zhang K, Xu L, Wang E.
Proc Natl Acad Sci U S A. 2011 May 17;108(20):8257-62. Epub 2011 May 2.
PubMed

The effect of compressive deformations on the rate of build-up of oxygen in isolated skeletal muscle cells.

Leopold E, Sopher R, Gefen A.
Med Eng Phys. 33, 1072-1078, 2011
PubMed

Coupling of the phosphatase activity of Ci-VSP to its voltage sensor activity over the entire range of voltage sensitivity.

Sakata S, Hossain MI, Okamura Y.
J Physiol. 589:2687-2705, 2011
PubMed

Public Biomodel: "ssvcell1548: sakata_JP2011-Kir2.1"
Public Biomodel: "ssvcell1548: sakata_JP2011-PHDGFP"

Ca2+ buffering at a drosophila larval synaptic terminal.

He, T., and Lnenicka, G.A.
(2011) Synapse 65, 687-693.
PubMed

Cooperative Nuclear Localization Sequences Lend a Novel Role to the N-Terminal Region of MSH6.

Gassman, N.R., Clodfelter, J.E., McCauley, A.K., Bonin, K., Salsbury, F.R., Jr., and Scarpinato, K.D.
(2011). PLoS One 6, e17907.
PubMed

Signaling network triggers and membrane physical properties control the actin cytoskeleton-driven isotropic phase of cell spreading.

Rangamani P, Fardin MA, Xiong Y, Lipshtat A, Rossier O, Sheetz MP, Iyengar R.
Biophys J. 2011 Feb 16;100(4):845-57.
PubMed

BioModel: 'prangamani: Rangamani et al, BJ Feb 2011'

Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling.

Brown SA, Moraru II, Schaff JC, Loew LM.
J Comput Neurosci. 31:385-400, 2011
PubMed

BioModel: 'Brown:GBrown et al 2010 Purkinje MultiCompartmental Combined Biochem and Electrophysiol'

Potassium (K+) gradients serve as a mobile energy source in plant vascular tissues.

Gajdanowicz P, Michard E, Sandmann M, Rocha M, Corrêa LG, Ramírez-Aguilar SJ, Gomez-Porras JL, González W, Thibaud JB, van Dongen JT, Dreyer I.
Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):864-9. Epub 2010 Dec 27.
PubMed

BioModel: 'IngoDreyer: Gajdanowicz_et_al_20119'

Purification of Actin from Fission Yeast Schizosaccharomyces pombe and Characterization of Functional Differences from Muscle Actin.

Shih-Chieh Ti and Thomas D. Pollard
Journal of Biological Chemistry, 2011, 286(7), 5784-92 Publication Date: Dec 9, 2010
PubMed

BioModel: 'SCT: PiRelease'

Bursting and calcium oscillations in pancreatic beta-cells: specific pacemakers for specific mechanisms.

Fridlyand, L.E., Tamarina, N., and Philipson, L.H.
Am J Physiol Endocrinol Metab 299, E517-532, 2010. PMID 20628025
PubMed

MathModel: Chicago1

Glucose sensing in the pancreatic beta cell: a computational systems analysis.

Fridlyand LE, Philipson LH.
Theoritical Biology and Medical Modeling, 2010, May 24;7:15
PubMed

MathModel: GlucoseSensitivity-1
MathModel: GlucoseSensitivity-2

Lysosomal Pathology and Osteopetrosis upon Loss of H+-Driven Lysosomal Cl– Accumulation

Stefanie Weinert, Sabrina Jabs, Chayarop Supanchart, Michaela Schweizer, Niclas Gimber, Martin Richter, Jörg Rademann, Tobias Stauber, Uwe Kornak, and Thomas J. Jentsch
Science 11 June 2010: 1401-1403.Published online 29 April 2010 [DOI:10.1126/science.1188072]
PubMed

Effect of ATP Binding and Hydrolysis on Dynamics of Canine Parvovirus NS1.

Niskanen, E.A., Ihalainen, T.O., Kalliolinna, O., Hakkinen, M.M., and Vihinen-Ranta, M.
J Virol 84, 5391-5403. (2010).
PubMed

The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation.

Wang J, Xu L, Wang E, Huang S.
Biophys J. 2010 Jul 7;99(1):29-39.
PubMed

MathModel: 'xuli: BJ_cellfate_2010'

Purification of actin from fission yeast Schizosaccharomyces pombe and characterization of functional differences from muscle actin.

Ti SC, Pollard TD.
J Biol Chem. 2011 Feb 18;286(7):5784-92. Epub 2010 Dec 9.
PMID: 21148484 [PubMed - in process]
PubMed

BioModel: 'SCT: PiRelease'

Putting one step before the other: Distinct activation pathways for Cdk1 and Cdk2 bring order to the mammalian cell cycle.

Merrick, K.A., and Fisher, R.P.
Cell Cycle 9, 706-714, (2010).
PubMed

Cingulin and paracingulin show similar dynamic behaviour, but are recruited independently to junctions

Paschoud S, Yu D, Pulimeno P, Jond L, Turner JR, Citi S. Mol Membr Biol. 2010 Dec 17. [Epub ahead of print]
PubMed

BioModel: 'dyu: final cingulin model'

Quantitative Measurement of Ca2+ in the Sarcoplasmic Reticulum Lumen of Mammalian Skeletal Muscle

Ziman, A.P., C.W. Ward, G.G. Rodney, W.J. Lederer, and R.J. Bloch.
Biophys J, 2010. 99(8): p. 2705-2714.
PubMed

BioModel: 'dyu: final cingulin model'

Quantifying a pathway: kinetic analysis of actin dendritic nucleation.

Kraikivski P, Slepchenko BM.
Biophys J.2010 Aug 4;99(3):708-15.
PubMed

MathModel: 'pavelkr: Actin_Polymerization and NPF_ARP2/3_Actin'

Modeling capping protein FRAP and CALI experiments reveals in vivo regulation of actin dynamics

Kapustina M, Vitriol E, Elston TC, Loew LM, Jacobson K.
Cytoskeleton (Hoboken).2010 Aug;67(8):519-34.
PubMed

BioModel: 'marynka: CALI'

MLCK-dependent exchange and actin binding region-dependent anchoring of ZO-1 regulate tight junction barrier function

Dan Yu, Amanda M. Marchiando, Christopher R. Weber, David R. Raleigh, Yingmin Wang, Le Shen, and Jerrold R. Turner.
PNAS, vol. 107, no. 18, 8237-8241 (2010). Published online, April 19, 2010, doi:10.1072/pnas.0908869107.
PubMed

BioModel: 'dyu: cacodeltaABR'
BioModel: 'dyu: latrunculin'
BioModel: 'dyu: mouseZO1control&PIK'

A Mitotic Kinesin-6, PavKLP, Mediates Interdependent Cortical Reorganization and Spindle Dynamics in Drosophila Embryos

P. Sommi, R. Ananthakrishnan, D. K. Cheerambathur, M. Kwon, S. Morales-Mulia, I. Brust-Mascher, A. Mogilner.
J Cell Sci., 123: 1862-1872 (2010).
PubMed

BioModel: 'ananth: furrowsinglepathwayconstconcabsorbingbcscaling'

Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues.

Lipshtat, A., G. Jayaraman, J.C. He, and R. Iyengar.
Proceedings of the National Academy of Sciences. 107:1247-1252, 2010.
PubMed

BioModel: 'azilipshtat: PNAS_switch'
BioModel: 'azilipshtat: Rap1_switch'

Kinetics of M1 muscarinic receptor and G protein signaling to phospholipase C in iving cells.

Bjorn H. Falkenburger, Jill B. Jensen, and Bertil Hille
J. Gen. Physiol. 2010; 135 81-97, Published online Jan 25 2010, 10.1085/jgp.200910344.
PubMed

BioModel: 'hillelab: FalkenburgerJGP2010'

Kinetics of PIP2 metabolism and KCNQ2/3 channel regulation studied with a voltage-sensitive phosphatase in iving cells.

Bjorn H. Falkenburger, Jill B. Jensen, and Bertil Hille
J. Gen. Physiol. 2010; 135 99-114, Published online Jan 25 2010, 10.1085/jgp.200910345.
PubMed

BioModel: 'hillelab: FalkenburgerJGP2010'

Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives

Wang J, Xu L, Wang E.
Biophys J. 2009 Dec 2;97(11):3038-46.
PubMed

MathModel: 'xuli: BJ_Circadian_2009'

Phosphodiesterase 1C is dispensable for rapid response termination of olfactory sensory neurons.

Cygnar, K.D., and H. Zhao.
Nat Neurosci. 12:454-62, 2009. PMID 19305400 2712288.
PubMed

BioModel: 'cygnar: NatureNeuroscience2009'

A genetically encoded reporter of synaptic activity in vivo.

Dreosti E, Odermatt B, Dorostkar MM, Lagnado L.
Nat Methods. 2009 Dec;6(12):883-9. Epub 2009 Nov 8.
PubMed PMID: 19898484.
PubMed

BioModel: 'Leon: Fig.1v7'
BioModel: 'Leon: GECI_Synapse'

Effects of excluded volume due to internal membranes and cytoskeletal structures.

Novak, I.L., Kraikivski, P., Slepchenko, B.M.
Biophysical Journal 97(3): 758-767(2009).
PubMed

This paper employed a customized VCell-based application. The code is available upon request from Igor Novak.

Modeling Spatial and Temporal Dynamics of Chemotactic Networks

Liu Yang and Pablo A. Iglesias
Chemotaxis: Methods and Protocols, Methods in Molecular Biology, vol. 571, pp. 489-505, 2009.
PubMed

BioModel: 'LiuYang: LEGI'.

Subcellular dynamics of type II PKA in neurons.

Zhong, H., G.M. Sia, T.R. Sato, N.W. Gray, T. Mao, Z. Khuchua, R.L. Huganir, and K. Svoboda.
Neuron. 62:363-374, 2009.
Neuron

BioModel: globus: CAT diffusion
BioModel: globus: PKA2D
BioModel: globus: PKA2D with AKAP

Intracellular fluid flow in rapidly moving cells

Kinneret Keren, Patricia T. Yam, Anika Kinkhabwala, Alex Mogilner & Julie A. Theriot
Nature Cell Biology 11, 1219 - 1224 (2009) Published online: 20 September 2009
Nature

MathModel: 'mogilner: JulyConc'
MathModel: 'mogilner: JulyPressure'

Affinity for phosphatidylinositol 4,5-bisphosphate determines muscarinic agonist sensitivity of Kv7 K+ channels

Ciria C. Hernandez, Bjorn Falkenburger, and Mark S. Shapiro
J. Gen. Physiol. 2009;134 437-448, Published online Oct 26 2009, 10.1085/jgp.200910313.
JGP

BioModel: 'bfalken :HernandexFalkenburgerShapiro2009'.

A Tridimensional Model of Proangiogenic Calcium Signals in Endothelial Cells

Luca Munaron
The Open Biology Journal, 2009, 2, 114-129 Publication Date: October 2009
PubMed

BioModel: 'Annalisa03: Imunaron'.

Persistent cAMP-Signals Triggered by Internalized G-Protein-Coupled Receptors.

Calebiro D, Nikolaev VO, Gagliani MC, de Filippis T, Dees C, Tacchetti C, Persani L, Lohse MJ.
PLoS Biol. 2009 Aug;7(8):e1000172 Publication Date: Epub 2009 Aug 18
PubMed

BioModel: 'davide.calebiro: Calebiro_Plos-Biol_2009'

An open model of actin dendritic nucleation.

Ditlev, J.A., N.M. Vacanti, I.L. Novak, and L.M. Loew.
Biophys J. 2009 96:3529-3542.
PubMed

BioModel: 'les: Actin Dendritic Nucleation_Detailed Branching'
BioModel: 'les: Actin Dendritic Nucleation'
MathModel: 'les: Actin Advection and Diffusion'
MathModel: 'les: Actin Advection and Diffusion 2D Cylindrical Transform'

A model of action potentials and fast Ca2+ dynamics in pancreatic beta-cells.

Fridlyand LE, Jacobson DA, Kuznetsov A, Philipson LH.
Biophys J. 2009 Apr 22;96(8):3126-39.
PubMed

MathModel: 'Fridlyand: MouseSpike'

Energetic requirements for processive elongation of actin filaments by FH1FH2-formins

Aditya S. Paul and Thomas D. Pollard
J. Biol. Chem. 284:12533-40, 2009
PubMed

BioModel: 'abiggiep: Formin FH1FH2-Profilin-Actin Elongation'

Analog Modulation of Mossy Fiber Transmission Is Uncoupled from Changes in Presynaptic Ca2

Ricardo Scott, Arnaud Ruiz, Christian Henneberger, Dimitri M. Kullmann, and Dmitri A. Rusakov
The Journal of Neuroscience, 30 July 2008, 28(31): 7765-7773; doi: 10.1523/JNEUROSCI.1296-08.2008.
PubMed

Robustness, dissipations and coherence of the oscillation of circadian clock: potential landscape and flux perspectives.

Wang J, Xu L, Wang E.
PMC Biophys. 2008 Dec 30;1(1):7.
PubMed

MathModel: 'xuli: PMCBiophysics2008'

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations.

Wang J, Xu L, Wang E.
Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12271-6. Epub 2008 Aug 21.
PubMed

MathModel:'xuli: PNAS2008'.

Quantitative analysis of G-actin transport in motile cells

I.L. Novak, B.M. Slepchenko, A. Mogilner
Biophysical Journal, 95(4):1627-38, 2008
PubMed

MathModel: 'ignovak: Analysis of G_actin transport in 2D fragment'
MathModel: 'ignovak: Analysis of G_actin transport in keratocyte'

Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity

A.B. Goryachev, and A.V. Pokhilkos
FEBS Letters, v. 582, p.1437, (2008)
PubMed

BioModel: 'alex1: full01'.

Analysis of phosphatidylinositol-4,5-bisphosphate signaling in cerebellar Purkinje spines.

Brown, S., F. Morgan, J. Watras, and L.M. Loew.
Biophys J. 95:1795-1812,2008.
PubMed

BioModel: 'brown: Purkinje Compartmental-adapted from Hernjak et al.'
BioModel: 'brown: Purkinje 1D'
BioModel: 'brown: Purkinje 3D-12 PF Stimuli'
BioModel: 'brown: Purkinje 3D-4 PF Stimuli'
BioModel: 'brown: Purkinje 3D Several Spines-12 PF Stimuli'
BioModel: 'brown: PIP2 Diffusion 1D and 3D'

Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks.

Neves SR, Tsokas P, Sarkar A, Grace EA, Rangamani P, Taubenfeld SM, Alberini CM, Schaff JC, Blitzer RD, Moraru II, Iyengar R.
Cell. 2008 May 16;133(4):666-80.
PubMed

BioModel: 'susana: neves_cell_2008'.

The tight junction protein complex undergoes rapid and continuous molecular remodeling at steady state.

Shen L, Weber CR, Turner JR.
J Cell Biol. 2008 May 19;181(4):683-95. Epub 2008 May 12.
PubMed

BioModel: 'leshen: intracellular bleach FLIP'
BioModel: 'leshen: large area membrane bleach FRAP
BioModel: 'leshen: membrane bleach FLIP'
BioModel: 'leshen: small area membrane bleach FRAP'

Calcium Transport Mechanisms of PC12 Cells.

Duman, J.G., L. Chen, and B. Hille.
J. Gen. Physiol. 131:307-323, 2008.
PubMed

BioModel: 'hillelab: DumanJGP2008Fig1A-4block'
BioModel: 'hillelab: DumanJGP2008Fig1A-control'
BioModel: 'hillelab: DumanJGP2008Fig9diff'
BioModel: 'hillelab: DumanJGP2008Fig9undiff'

Calcium signal transmission in chick sensory neurones is diffusion based.

Coatesworth W, Bolsover S.
Cell Calcium. 2008 Mar;43(3):236-49. Epub 2007 Jul 12
PubMed

BioModel: 'coatesworth: 120504_SCAB100B'
BioModel: 'coatesworth: 140105_SCAB100B'
BioModel: 'coatesworth: 190105_SCAB100B'
BioModel: 'coatesworth: 190105_SCAB100P'
BioModel: 'coatesworth: 221204_SCAB100B'
BioModel: 'coatesworth: 240604_SCAB100B'

The role of the FH1 domain and profilin in formin-mediated actin-filament elongation and nucleation.

Paul, A., Pollard, T.
Current Biology, 2008 Jan 8;18(1):9-19.
PubMed

BioModel: 'abiggiep: Formin-Profilin-Actin Polymerization'

Pathway of actin filament branch formation by Arp2/3 complex.

Beltzner CC, Pollard TD.
J Biol Chem 283: 7135-7144.2008.
PubMed

Contact author regarding access to model.

Coordination of Chromosome Alignment and Mitotic Progression Chromosome-Based Ran Signal

Hoi Y. Li, Win Pin Ng, Wong Chi Hang, Pablo A. Iglesias and Yixian Zheng
Cell Cycle. 6(15):1886-1895, 2007.
PubMed

BioModel: 'piglesias: Gorlich6'

Membrane-binding/modification model of signaling protein activation and analysis of its control by cell morphology.

Haugh, J.M.
Biophys J 92, L93-95, 2007.
PubMed

BioModel: 'jmhaugh: Cell shape control'

Switching of membrane organelles between cytoskeletal transport systems is determined by regulation of the microtubule-based transport.

Slepchenko, B.M., Semenova, I., Zaliapin, I., and Rodionov, V.
J. Cell Biol., jcb.200705146, 2007.
PubMed

MathModel: 'boris: fish_melanophore_pigment_aggregation'
MathModel: 'boris: 'fish_melanophore_pigment_dispersion'

Regulation of cAMP dynamics by Ca2+ and G-protein coupled receptors in the pancreatic beta-cell: A computational approach.

Fridlyand, L.E., M.C. Harbeck, M.W. Roe, and L.H. Philipson
Am J Physiol Cell Physiol:293:C1924-C1933, 2007.
PubMed

MathModel: 'Fridlyand: cAMP'

Compartment-Specific Feedback Loop and Regulated Trafficking Can Result in Sustained Activation of Ras at the Golgi.

Narat J. Eungdamrong and Ravi Iyengar
Biophys. J. 2007; 92(3): p. 808-815
PubMed

BioModel: 'eungdamr: eungdamrong and iyengar BiophysJ'

Rapid redistribution of synaptic PSD-95 in the neocortex in vivo.

Gray, N, Weimer R.M., Bureau, I. Svoboda, K
PLoS, v4, Iss 11, e370, 2006.
PubMed

BioModel: 'rweimer: 10 spines'

Does diacylglycerol regulate KCNQ channels?

Suh, B.-C., and B. Hille.
Pflügers Archiv European Journal of Physiology. 453:293-301,2006.
PubMed

BioModel: 'hillelab: SuhHilleEJP2006Fig1b'

Modeling the impact of store-operated Ca2+ entry on intracellular Ca2+ oscillations.

Kowalewski, J.M., P. Uhlen, H. Kitano, and H. Brismar.
Mathematical Biosciences. 204:232-249, 2006.
PubMed

In vivo dynamics of Rac-membrane interactions.

Moissoqlu K, Slepchenko BM, Meller N, Horwitz AF, Schwartz, MAA
Mol Biol Cell. 2006 Jun; 17(6):2770-9. Epub 2006 Apr.5
PubMed

MathModel: 'boris: Schwartz_2D_membrane_diffusion'
MathModel: 'boris: Schwartz_3D_FLIP'

Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes.

J.J. Saucerman, J. Zhang, J.C. Martin, L.X. Peng, A.E. Stenbit, R.Y. Tsien, and A.D. McCulloch..
Proceedings of the National Academy of Sciences. 103:12923-12928.
PubMed

BioModel: 'jsaucer: AKARmyocyte'
BioModel: 'jsaucer: AKARmyocyte_2compart’
BioModel: 'jsaucer: AKARmyocyte_no_cAMP_buffering’

Analysis of a RanGTP-regulated gradient in mitotic somatic cells.

Kalab, P., A. Pralle, E.Y. Isacoff, R. Heald, and K. Weis.
Nature 2006. 440:(7084)697-701.
PubMed

BioModel: 'Pralle: MitoticExtract_added_ImportinB'
BioModel: 'Pralle: MitoticExtract_added_RanQ69L'

Quantitative elucidation of a distinct spatial gradient-sensing mechanism in fibroblasts.

Schneider, I.C. and Haugh, J.M.
J.Cell B 171:883-892 (2005)
PubMed

BioModel: 'jmhaugh: pdgf gradient sensing'

Modeling and Analysis of Calcium Signaling Events Leading to Long-Term Depression in Cerebellar Purkinje Cells.

N. Hernjak, B. M. Slepchenko, K. Fernald, C.C. Fink, D. Fortin, I.I. Moraru, J. Watras, and L.M. Loew.
Biophysical Journal Volume 89, Dec. 2005, pp. 3790-3806
PubMed

BioModel: 'hernjak: purkinje_compartmental'
BioModel: 'hernjak: purkinje_2d'
Mathmodel: 'hernjak: purkinje_1d'

STAT module can function as a biphasic amplitude filter.

V. Mayya and L.M. Loew.
IEE Proceedings Systems Biology, March 2005, Volume 2, Issue 1, p. 43-52
PubMed

BioModel: 'mayya: STATmodulePaper'

Phospholipase C in living cells: activation, inhibition, Ca2+ requirement, and regulation of M current.

Horowitz LF, Hirdes W, Suh B-C, Hilgemann DW, Mackie K, Hille B.
J. Gen. Physiol. 2005. 126(3):243-262.
PubMed

BioModel: 'hillelab: Horowitz2005JGPprobes'

Rearrangement of the endoplasmic reticulum and calcium transient formation: The computational approach.

Pomorski P, Targos B, Baranska J.
Biochem Biophys Res Commun. 2005 Mar 25;328(4):1126-32.
PubMed

Adenine nucleotide regulation in pancreatic beta cells: Modelling of ATP/ADP - Ca2+ interaction

Fridlyand L., Li Ma, Philipson LH.
Am J Physiol Endocrinol Metab. 289, E839-E848, 2005.
PubMed

MathModel: 'Fridlyand: Chicago2'

Bio-switches: what makes them robust?

Slepchenko, B. M. and Terasaki, M.
Opin. Genet. Dev. 2004; 14/4: 428-434.
PubMed

MathModel: 'boris: MPF_2D Tyson's Model, all speices mobile, slightly different inits in nucleus and outside' MathModel: 'boris: MPF_ODEs_simplified, no aggregates or buffers'
MathModel: 'boris: MPF_ODEs_simplified1, with aggregates'
MathModel: 'boris: MPF_ODEs_simplified2, with buffers'
BioModel: 'boris: Terasaki_MPF1'

A multi-enzyme model for pyrosequencing.

Ali Agah, Mariam Aghajan, Foad Mashayekhi, Sasan Amini, Ronald W. Davis, James D. Plummer, Mostafa Ronaghi, and Peter B. Griffin.
Nucleic Acids Research 2004 32(21):e166
PubMed

BioModel:'Foad:pyro_fin'

Two Complementary, Local Excitation, Global Inhibition Mechanisms Acting in Parallel Can Explain the Chemoattractant-Induced Regulation of PI(3,4,5)P₃ Response in Dictyostelium Cells.

Lan Ma, Chris Janetopoulos, Liu Yang, Peter N. Devreotes and Pablo A. Iglesias.
Biophys. J. 2004; 87(6): p. 3764-3774
PubMed

BioModel: 'LiuYang: uniform_public'
BioModel: 'LiuYang: needle_public'

A Signal Transduction Pathway Model Prototype I: Application to Ca2+-Calmodulin Signaling and Myosin Light Chain Phosphorylation.

Lukas, TJ
Biophys. J. 2004;87 1417-1425
PubMed

BioModel: 'tjlukas: Ca_Release_Coupled_MLC'

A Signal Transduction Pathway Model Prototype I: From Agonist to Cellular Endpoint.

Lukas, TJ
Biophys. J. 2004; 87 1406-1416
PubMed

BioModel: 'tjlukas: Ca_Release_Coupled_MLC'

High Mobility of Vesicles Supports Continuous Exocytosis at a Ribbon Synapse.

Matthew Holt, Anne Cooke, Andreas Neef, and Leon Lagnado.
Current Biology, Vol. 14, 173-183, February 3, 2004
PubMed

BioModel: 'Lagnado Lab: TIR_FRAP'

Regulation of KCNQ2/KCNQ3 Current by G Protein Cycling: the kinetics of receptor-mediated signaling by Gq.

Byung-Chang Suh, Lisa R. Horowitz, Wiebke Hirdes, Ken Mackie and Bertil Hille.
Journal of General Physiology, Volume 123, Number 6, June 2004 663-683
PubMed

BioModel: 'hillelab: SuhJGP2004Fig11A
BioModel: 'hillelab: SuhJGP2004Fig12
BioModel: 'hillelab: SuhJGP2004Fig13B'
BioModel: 'hillelab: SuhJGP2004Fig15'

Cyclin aggregation and robustness of bio-switching.

Slepchenko, B. M. and Terasaki, M.
Mol. Biol. Cell 2003;14: 4695 - 4706.
PubMed

MathModel: 'boris: MPF_2D Tyson's Model, all speices mobile, slightly different inits in nucleus and outside'
MathModel: 'boris: MPF_ODEs_simplified, no aggregates or buffers
MathModel: 'boris: MPF_ODEs_simplified1, with aggregates
MathModel: 'boris: MPF_ODEs_simplified2, with buffers
BioModel: 'boris: Terasaki_MPF1'

Kinetic analysis of receptor-activated phosphoinositide turnover

Chang Xu, James Watras and Leslie M. Loew
Journal of Cell Biology, vol. 161, no. 4, May 26, 2003
PubMed

BioModel:'les: PIP2 Hydrolysis JCB Submission'.
Alternatively, the model is available here in an XML-compliant format that can be imported directly into you own workspace within the Virtual Cell. Download the XML file (Do not open this link, use your right mouse button and Save Target As.). Alternatively you may use the html version,(open the link and select all within the browser, copy and paste into a text editor and save as an xml file). Using either version, access the 'Import' dialog box under the 'File' menu item within the Virtual Cell.

Centrosome positioning in interphase cells.

Anton Burakov, Elena Nadezhdina, Boris Slepchenko, and Vladimir Rodionov
Journal of Cell Biology, 2003 Sep 15;162(6):963-9..
PubMed

MathModel: 'boris: NocodazoleTubulin_3D'
Alternatively, the model is available here in an XML-compliant format that can be imported directly into you own workspace within the Virtual Cell. Download the XML file (Do not open this link, use your right mouse button and Save Target As.). Alternatively you may use the html version,(open the link and select all within the browser, copy and paste into a text editor and save as an xml file) Using either version, access the 'Import' dialog box under the 'File' menu item within the Virtual Cell.

Modeling Ca2+ flux in pancreaticB-cells: role of the plasma membrane and intracellular stores

Leonid E. Fridlyand, Natalia Tamarina, and Louis H. Philipson
Am J Physiol Endocrinol Metab, Jul 2003;285: E138-154
PubMed

MathModel: 'Fridlyand: Chicago'

Systems Analysis of Ran Transport

Alicia E. Smith, Boris M. Slepchenko, James C. Schaff, Leslie M. Loew, Ian G. Macara.
Science. 2002 Jan 18;295(5554):488-91
PubMed

MathModel: 'boris: AliciaProblem1_5; basic nonspatial model used to obtain results published in the Science paper'
MathModel: 'boris: AliciaProblem1_5Fast; as in AliciaProblem1_5 but the reactions with mass action kinetics are treated as fast; this model was used to obtain initial conditions for spatial simulations'
MathModel: 'boris: AliciaSpatial_NewFast; the basic spatial model used in the Science paper'
Biomodel: 'les: Smith et al System Analysis of Ran Transport'. This is a later version and is corrected for the competiton between RanGDP and NTF2:RanGDP for the same site on RCC1.

Targeting of rough endoplasmic reticulum membrane proteins and ribosomes in invertebrate neurons.

Rolls MM, Hall DH, Victor M, Stelzer EH, Rapoport TA.
Mol Biol Cell. 2002 May;13(5):1778-91.PMID: 12006669 [PubMed - indexed for MEDLINE]
PubMed

Please contact author for access to this model.

Distinct intracellular calcium transients in neurites and somata integrate neuronal signals.

Johenning FW, Zochowski M, Conway SJ, Holmes AB, Koulen P, Ehrlich BE.
J Neurosci 22: 5344-5353.2002.
PubMed

Please contact author for access to this model.

Computational Cell Biology

Christopher P. Fall, Eric S. Marland, John M. Wagner, John J. Tyson.
The models from the text were implemented into the Virtual Cell by Johann Frederick Cutiongco.
Computational Cell Biology

The following BioModels are available from user: 'CompCell'

Chay-Keizer ER - Models pancreatic beta-cell bursting. Described in 5.4 and illustrated in Figure 5.21.

Hodgkin-Huxley - Models electrical behavior of the squid giant axon. Used to demonstrate interacting ion channels. Described in 2.5.

Keizer-Levine Open-Cell - Models calcium oscillations in bullfrog sympathetic ganglion neurons via RyR channel kinetics. Described in 5.2.3 and illustrated in Figure 5.8.

L-Type Calcium Channels - Models L-type calcium channel kinetics in the Aplysia neuron. Used to demonstrate the rapid equilibrium approximation. Described in 4.1 and illustrated in Figure 4.3.

Morris-Lecar Coincidence Detection - Demonstrates coincidence detection for excitatory inputs. Described in 6.4 and illustrated in Figure 6.9.

Morris-Lecar Gap Junction Coupled - Demonstrates electrical coupling and gap junctions. Described in 6.1.

Morris-Lecar Mutual Excitation - Demonstrates how fast excitatory synapses lead to synchrony and slow excitatory synapses lead to asynchrony in two identically electrically coupled cells. The only parameter modified is beta (=1000/s in Figure 6.6A and =100/s in Figure 6.6C). Described in 6.3.

Morris-Lecar Mutual Inhibition - Demonstrates how fast inhibition leads to antiphase behavior (for t<0.8, beta=1000/s) and slow inhibition leads to in-phase behavior (for t>0.8s, beta=100/s). SurfToVol_PlasmaMembrane 1 and SurfToVol_PlasmaMembrane 2 were changed to 1806 to cancel out KMOLE in the equations for s1 and s2 kinetics. Described in 6.3 and illustrated in Figure 6.7.

Morris-Lecar Mutual Type II - Models electrical behavior of barnacle muscle fiber. Used to demonstrate interacting ion channels. Described in 2.4.

Local Photorelease of Caged Thymosin beta4 in Locomoting Keratocytes Causes Cell Turning

Roy P, Rajfur Z, Jones D, Marriott G, Loew L, Jacobson K.
J Cell Biol. 2001 May 28;153(5):1035-48
PubMed

BioModel: 'partharoy: 7_12_00_model1'.

An image-based model of calcium waves in differentiated neuroblastoma cells.

Fink, C. C., B. Slepchenko, I. I. Moraru, J. Watras, J. Schaff, and L. M. Loew.
Biophys. J. 2000 79:163-183.2000.
PubMed

There are five mathematical descriptions from the following two publications that were generated using the Virtual Cell software. Refer to the detailed model description that describes the following mathematical descriptions. NE_Full is best described in the model description while the other models have slight variations to the description. See Virtual Cell Calcium Dynamics for an introduction to the experiment and to view the experimental and simulation data.

MathModels: 'Boris'

'NE_DifferentGeom1'
Basic model for simulations presented in Biophys. J., July 2000. It uses experimental ER and BkR distributions. Geometry from the image cellmnucnew2.tif

'NE_DifferentGeom2_1'
Simulation presented in Biophys. J. July 2000 with bipolar geometry from the image bpolargeo2.tif

'NE_DifferentGeom3'
Simulation presented in Biophys. J., July 2000 with geometry from the image 525am.tif

'NE_Full'
Simulation provides the best fit to experimental data presented in J. Cell Biol., November 1999 and on WWW (Calcium Dynamics). It uses ER and BkR distributions that are slightly different from experimental. Geometry from the image mask2_smallnucl.tif

'NE_Full_best'
Best fit to experimental data presented in Biophys. J., July 2000. Geometry from the image cellmnucnew2.tif

Morphological control of inositol-1,4,5-triphosphate-dependent signals.

Fink, C. C., B. Slepchenko, I. I. Moraru, J. Schaff, J. Watras, and L. M. Loew.
J. Cell Biol. 147:929-936, 1999.

There are five mathematical descriptions from the following two publications that were generated using the Virtual Cell software. Refer to the detailed model description that describes the following mathematical descriptions. NE_Full is best described in the model description while the other models have slight variations to the description.
See Virtual Cell Calcium Dynamics for an introduction to the experiment and to view the experimental and simulation data.

MathModels: 'Boris'

'NE_DifferentGeom1'
Basic model for simulations presented in Biophys. J., July 2000. It uses experimental ER and BkR distributions. Geometry from the image cellmnucnew2.tif

'NE_DifferentGeom2_1'
Simulation presented in Biophys. J. July 2000 with bipolar geometry from the image bpolargeo2.tif

'NE_DifferentGeom3'
Simulation presented in Biophys. J., July 2000 with geometry from the image 525am.tif

'NE_Full'
Simulation provides the best fit to experimental data presented in J. Cell Biol., November 1999 and on WWW (Calcium Dynamics). It uses ER and BkR distributions that are slightly different from experimental. Geometry from the image mask2_smallnucl.tif

'NE_Full_best'
Best fit to experimental data presented in Biophys. J., July 2000. Geometry from the image cellmnucnew2.tif

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The Virtual Cell, a project of NRCAM, is developed by the Center for Cell Analysis & Modeling (CCAM)