Reed2004 - Methionine Cycle
This model is described in the article:
Abstract:
Building on the work of Martinov et al. (2000), a mathematical model is developed for the methionine cycle. A large amount of information is available about the enzymes that catalyse individual reaction steps in the cycle, from methionine to S-adenosylmethionine to S-adenosylhomocysteine to homocysteine, and the removal of mass from the cycle by the conversion of homocysteine to cystathionine. Nevertheless, the behavior of the cycle is very complicated since many substrates alter the activities of the enzymes in the reactions that produce them, and some can also alter the activities of other enzymes in the cycle. The model consists of four differential equations, based on known reaction kinetics, that can be solved to give the time course of the concentrations of the four main substrates in the cycle under various circumstances. We show that the behavior of the model in response to genetic abnormalities and dietary deficiencies is similar to the changes seen in a wide variety of experimental studies. We conduct computational "experiments" that give understanding of the regulatory behavior of the methionine cycle under normal conditions and the behavior in the presence of genetic variation and dietary deficiencies.
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A mathematical model of the methionine cycle.
- Reed MC, Nijhout HF, Sparks R, Ulrich CM
- Journal of theoretical biology , 1/ 2004 , Volume 226 , Issue 1 , pages: 33-43 , PubMed ID: 14637052
- Department of Mathematics, Duke University, Durham, NC 27708, USA. reed@math.duke.edu
- Building on the work of Martinov et al. (2000), a mathematical model is developed for the methionine cycle. A large amount of information is available about the enzymes that catalyse individual reaction steps in the cycle, from methionine to S-adenosylmethionine to S-adenosylhomocysteine to homocysteine, and the removal of mass from the cycle by the conversion of homocysteine to cystathionine. Nevertheless, the behavior of the cycle is very complicated since many substrates alter the activities of the enzymes in the reactions that produce them, and some can also alter the activities of other enzymes in the cycle. The model consists of four differential equations, based on known reaction kinetics, that can be solved to give the time course of the concentrations of the four main substrates in the cycle under various circumstances. We show that the behavior of the model in response to genetic abnormalities and dietary deficiencies is similar to the changes seen in a wide variety of experimental studies. We conduct computational "experiments" that give understanding of the regulatory behavior of the methionine cycle under normal conditions and the behavior in the presence of genetic variation and dietary deficiencies.
Submitter of this revision: administrator
Modellers: administrator, Camille Laibe
Metadata information
isDescribedBy (2 statements)
hasTaxon (1 statement)
isVersionOf (1 statement)
Connected external resources
SBGN view in Newt Editor
| Name | Description | Size | Actions |
|---|---|---|---|
Model files |
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| BIOMD0000000698_url.xml | SBML L2V4 representation of Reed2004 - Methionine Cycle | 63.77 KB | Preview | Download |
Additional files |
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| BIOMD0000000698-biopax2.owl | Auto-generated BioPAX (Level 2) | 19.22 KB | Preview | Download |
| BIOMD0000000698-biopax3.owl | Auto-generated BioPAX (Level 3) | 27.33 KB | Preview | Download |
| BIOMD0000000698.m | Auto-generated Octave file | 7.88 KB | Preview | Download |
| BIOMD0000000698.pdf | Auto-generated PDF file | 186.40 KB | Preview | Download |
| BIOMD0000000698.png | Auto-generated Reaction graph (PNG) | 54.61 KB | Preview | Download |
| BIOMD0000000698.sci | Auto-generated Scilab file | 154.00 Bytes | Preview | Download |
| BIOMD0000000698.svg | Auto-generated Reaction graph (SVG) | 18.65 KB | Preview | Download |
| BIOMD0000000698.vcml | Auto-generated VCML file | 66.83 KB | Preview | Download |
| BIOMD0000000698.xpp | Auto-generated XPP file | 6.33 KB | Preview | Download |
| BIOMD0000000698_urn.xml | Auto-generated SBML file with URNs | 63.72 KB | Preview | Download |
| MODEL1006230091.cps | Curated and annotated model COPASI file | 81.39 KB | Preview | Download |
| MODEL1006230091.sedml | SED-ML file for figure 4. | 3.31 KB | Preview | Download |
- Model originally submitted by : Camille Laibe
- Submitted: Jun 23, 2010 10:12:34 AM
- Last Modified: May 9, 2018 9:36:32 AM
Revisions
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Version: 3
- Submitted on: May 9, 2018 9:36:32 AM
- Submitted by: administrator
- With comment: Notes updated using online editor.
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Version: 2
- Submitted on: Jun 25, 2010 2:45:18 PM
- Submitted by: Camille Laibe
- With comment: Current version of Reed2004_MethionineCycle
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Version: 1
- Submitted on: Jun 23, 2010 10:12:34 AM
- Submitted by: Camille Laibe
- With comment: Original import of Reed2004_MethionineCycle
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: Variable used inside SBML models
| Species | Initial Concentration/Amount |
|---|---|
| Homocysteine L-Homocysteine ; homocysteine |
0.88 μmol |
| Metin | 200.0 μmol |
| AdoHcy S-Adenosylhomocysteine ; S-Adenosyl-L-homocysteine |
13.2 μmol |
| AdoMet S-Adenosyl-L-methionine ; (S)-S-adenosyl-L-methionine |
137.6 μmol |
| 5mTHF tetrahydrofolate |
5.2 μmol |
| Cystathionine Cystathionine ; cystathionine |
0.0 μmol |
| Reactions | Rate | Parameters |
|---|---|---|
| Homocysteine + _5mTHF => Methionine | Compartment*V_max_MS*_5mTHF*Homocysteine/(K_d_MS*K_m_Hcy_MS+K_m_Hcy_MS*_5mTHF+K_m_5mTHF_MS*Homocysteine+_5mTHF*Homocysteine) | K_d_MS = 1.0; K_m_Hcy_MS = 0.1; V_max_MS = 500.0; K_m_5mTHF_MS = 25.0 |
| Metin = piecewise(200, (time < 2) || (time >= 8), piecewise(300, (time >= 2) && (time < 5), piecewise(100, (time >= 5) && (time < 8), 200))) | [] | [] |
| AdoHcy => Homocysteine | Compartment*alpha_1*(AdoHcy-alpha_2*Homocysteine) | alpha_1 = 100.0; alpha_2 = 10.0 |
| AdoMet => AdoHcy | Compartment*V_max_GNMT/(1+(K_m_GNMT/AdoMet)^2.3)*1/(1+AdoHcy/K_i_GNMT) | K_m_GNMT = 4500.0; K_i_GNMT = 20.0; V_max_GNMT = 10600.0 |
| Metin => Methionine | Compartment*k1*Metin | k1=1.0 |
| Methionine => AdoMet | Compartment*V_max_MATIII/(1+K_m1_MATIII*K_m2_MATIII/(Methionine^2+Methionine*K_m2_MATIII)) | V_max_MATIII = 22870.0; K_m2_MATIII = 21.1; K_m1_MATIII = 16689.3750623336 |
| Homocysteine => Cystathionine; AdoMet, AdoHcy | Compartment*(beta_1*(AdoMet+AdoHcy)-beta_2)*Homocysteine | beta_1 = 1.7; beta_2 = 30.0 |
(added: 09 May 2018, 10:33:41, updated: 09 May 2018, 10:33:41)