SBMLToolbox: an SBML toolbox for MATLAB users

Keating, Sarah M.; Bornstein, B.; Finney, Andrew; Hucka, Michael

doi:10.1093/bioinformatics/btl111

Cited by 124 publications

(82 citation statements)

References 2 publications

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“…We sought to minimize the difference between the data points and the model values by varying the phosphorylation rate constants. The optimization was performed in MATLAB using simulated annealing within the SBML toolbox (Keating et al, 2006). The resulting residual 0.0114 for this model, gave a phosphorylation rates of k 1 = 0.0015 mM 21 s 21 , k 2 = 0.7150 mM 21 s 21 , and an initial concentration x 0 = 0.014 mM.…”

Section: Ccamk Autophosphorylation Modelingmentioning

confidence: 99%

Calcium/Calmodulin-Dependent Protein Kinase Is Negatively and Positively Regulated by Calcium, Providing a Mechanism for Decoding Calcium Responses during Symbiosis Signaling

et al. 2013

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The establishment of symbiotic associations in plants requires calcium oscillations that must be decoded to invoke downstream developmental programs. In animal systems, comparable calcium oscillations are decoded by calmodulin (CaM)–dependent protein kinases, but symbiotic signaling involves a calcium/CaM–dependent protein kinase (CCaMK) that is unique to plants. CCaMK differs from the animal CaM kinases by its dual ability to bind free calcium, via calcium binding EF-hand domains on the protein, or to bind calcium complexed with CaM, via a CaM binding domain. In this study, we dissect this dual regulation of CCaMK by calcium. We find that calcium binding to the EF-hand domains promotes autophosphorylation, which negatively regulates CCaMK by stabilizing the inactive state of the protein. By contrast, calcium-dependent CaM binding overrides the effects of autophosphorylation and activates the protein. The differential calcium binding affinities of the EF-hand domains compared with those of CaM suggest that CCaMK is maintained in the inactive state at basal calcium concentrations and is activated via CaM binding during calcium oscillations. This work provides a model for decoding calcium oscillations that uses differential calcium binding affinities to create a robust molecular switch that is responsive to calcium concentrations associated with both the basal state and with oscillations.

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Section: Ccamk Autophosphorylation Modelingmentioning

confidence: 99%

Calcium/Calmodulin-Dependent Protein Kinase Is Negatively and Positively Regulated by Calcium, Providing a Mechanism for Decoding Calcium Responses during Symbiosis Signaling

et al. 2013

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“…The detailed simulations, in particular, the simulation of the inhibition of the enzymes of the pathway was done by writing programs in Matlab [30]. Matlab toolboxes -SBML toolbox [31] and Systems Biology toolbox [32] were used, wherein the model expressed in SBML format was first converted to the native format of Matlab (SBmodel (a Matlab structure)), and was then used for further simulations.…”

Section: Simulation Of the Modelmentioning

confidence: 99%

Methylerythritol phosphate pathway to isoprenoids: Kinetic modeling andin silicoenzyme inhibitions inPlasmodium falciparum

Singh¹,

Ghosh²

2013

FEBS Letters

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a b s t r a c tThe methylerythritol phosphate (MEP) pathway of Plasmodium falciparum (P. falciparum) has become an attractive target for anti-malarial drug discovery. This study describes a kinetic model of this pathway, its use in validating 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) as drug target from the systemic perspective, and additional target identification, using metabolic control analysis and in silico inhibition studies. In addition to DXR, 1-deoxy-D-xylulose 5-phosphate synthase (DXS) can be targeted because it is the first enzyme of the pathway and has the highest flux control coefficient followed by that of DXR. In silico inhibition of both enzymes caused large decrement in the pathway flux. An added advantage of targeting DXS is its influence on vitamin B1 and B6 biosynthesis. Two more potential targets, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase and 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, were also identified. Their inhibition caused large accumulation of their substrates causing instability of the system. This study demonstrates that both types of enzyme targets, one acting via flux reduction and the other by metabolite accumulation, exist in P. falciparum MEP pathway. These groups of targets can be exploited for independent anti-malarial drugs.

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“…These languages, which are subsets of the eXtensible Markup Language (XML), support the description of model equations and parameters in machine readable form. Of course, CellML, SBML, and NeuroML model description documents must be validated on creation, but once they have been, they can be disseminated in an error-free way and input to a number of different simulation tools for execution (Alves and Antunes, 2006; Keating et al, 2006). A number of different model repositories such as and the BioModels Database (Li et al, 2010) have been developed that allow users to search for and download XML model descriptions.…”

Section: Informatics In Computational Physiology and Medicinementioning

confidence: 99%

Grand Challenges in Computational Physiology and Medicine

Winslow¹

2011

Front. Physio.

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SBMLToolbox: an SBML toolbox for MATLAB users

Abstract: SBMLToolbox is freely available from http://sbml.org/software/sbmltoolbox

Cited by 124 publications

References 2 publications

Calcium/Calmodulin-Dependent Protein Kinase Is Negatively and Positively Regulated by Calcium, Providing a Mechanism for Decoding Calcium Responses during Symbiosis Signaling

Calcium/Calmodulin-Dependent Protein Kinase Is Negatively and Positively Regulated by Calcium, Providing a Mechanism for Decoding Calcium Responses during Symbiosis Signaling

Methylerythritol phosphate pathway to isoprenoids: Kinetic modeling andin silicoenzyme inhibitions inPlasmodium falciparum

Grand Challenges in Computational Physiology and Medicine

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