Protons

addPseudoisomersToModel(model, printLevel)[source]

Estimate metabolite pKa values with ChemAxon calculator plugins and determine all relevant pseudoisomers.

USAGE:

[model, nonphysicalMetBool, pKaErrorMetBool] = addPseudoisomersToModel (model, printLevel)

INPUTS:

  • model –

    Model structure with following fields:

    • .mets - m x 1 array of metabolite identifiers.

    • .metFormulas - m x 1 cell array of metabolite formulas. Formulas for protons should be H, and formulas for water should be H2O.

    • .metCharges - m x 1 numerical array of metabolite charges.

    • .metCompartments - optional m x 1 array of metabolite compartment assignments. Not required if metabolite identifiers are strings of the format ID[*] where * is the appropriate compartment identifier.

    • .inchi - Structure containing four m x 1 cell array’s of IUPAC InChI strings for metabolites, with varying levels of structural detail.

    • .inchi.standard: m x 1 cell array of standard inchi

    • .inchi.standardWithStereo: m x 1 cell array of standard inchi with stereo

    • .inchi.standardWithStereoAndCharge: m x 1 cell array of standard inchi with stereo and charge

    • .inchi.nonstandard: m x 1 cell array of non-standard inchi

  • printLevel – verbosity control; if > 0 prints progress, if > 1 lists metabolites whose formula hydrogen count matches no species

OUTPUTS:

  • model – input model with an added field:

    • .pseudoisomers - m x 1 structure array (one element per metabolite) of acid-base pseudoisomers; fields are empty for metabolites with no InChI. Each element has fields:

      • .success - true where an InChI was available

      • .pKas - p x p matrix; element (i, j) is the pKa of the acid-base equilibrium between pseudoisomers i and j

      • .zs - p x 1 pseudoisomer charges

      • .nHs - p x 1 number of hydrogen atoms per pseudoisomer

      • .majorMSpH7 - p x 1 logical, true for the most abundant pseudoisomer at pH 7

  • nonphysicalMetBool – m x 1 logical, true for metabolites whose formula hydrogen count matches none of the estimated pseudoisomer species

  • pKaErrorMetBool – m x 1 logical, true for metabolites where pKa estimation failed

Note

Writes MetStructures.sdf, an SDF containing all structures input to the component contribution method for estimation of standard Gibbs energies.

getMetaboliteMsDistr(mets, molfiledir, msdistrdir, phs)[source]

Calculate microspecies distributions at all pH values in phs using ChemAxon’s cxcalc. Metabolite mol files in molfiledir are input to cxcalc. Mol file names should correspond to the metabolite ID in mets (it is assumed that compartment assignments are appended to the end of metabolite ID in the format metID[c]). Microspecies distributions are returned as .sdf files in msdistrdir

USAGE:

getMetaboliteMsDistr (mets, molfiledir, msdistrdir, phs)

INPUTS:

  • mets – metabolites

  • molfiledir – directory with mol files

  • msdistrdir – directory with microspecies distributions

  • phs – pH values

getMetabolitepKa(mets, molfiledir, pkadir)[source]

Compute pKas of the metabolites listed in mets using ChemAxon’s cxcalc. Metabolite mol files in molfiledir are input to cxcalc. Mol file names should correspond to the metabolite ID in mets (it is assumed that compartment assignments are appended to the end of metabolite ID in the format metID[c]). Text files with pKas are returned in pkadir.

USAGE:

getMetabolitepKa (mets, molfiledir, pkadir)

INPUTS:

  • mets – metabolites

  • molfiledir – directory with mol files

  • pkadir – directory with text files with pKas

moleFraction(metAbbr, Alberty2006, metAbbrAlbertyAbbr, temp, pHa, is, chi)[source]

Mole fraction of different metabolite species that make up a reactant

USAGE:

mf = moleFraction (metAbbr, Alberty2006, metAbbrAlbertyAbbr, temp, pHa, is, chi)

INPUT:

  • metAbbr – reconstruction reactant abbreviation

  • Alberty2006 – Basic data on the metabolite species that make up a reactant, compiled by Robert A. Alberty, Massachusetts Institute of Technology. In Print: Robert A. Alberty, Biochemical Thermodynamics: Applications of Mathematica. John Wiley & Sons, 2006. p391-395 Online: BasicBioChemData3.nb http://library.wolfram.com/infocenter/MathSource/5704/

  • metAbbrAlbertyAbbr – mapping from model metabolite primary key to primary key of reactants in Alberty2006

OPTIONAL INPUTS:

  • temp

  • pHa

  • is

  • temp

  • chi

OUTPUT:

mf – mole fraction at equilibrium

moleFractionStats(modelT)[source]

Plots of mole fraction statistics.

Plot a histogram of the number of metabolite species relevant between pH 5 and 9, and a stacked bar chart of the mole fractions of reactants with significant (<0.99) distributions over more than one metabolite species.

USAGE:

moleFractionStats (modelT)

INPUT:

modelT – structure with fields:

  • .S - m x n stoichiometric matrix

  • .mets - m x 1 cell array of metabolite identifiers

  • .metNames - m x 1 cell array of metabolite names

  • .mf - m x 1 cell array; each cell holds the mole fractions of the species of that reactant

plotActivityCoefficients(modelT)[source]

Plots statistics on activity coefficients.

Plots a histogram of the distribution of activity coefficients also a curve of activity coefficients for different charges at a range of ionic strengths

USAGE:

[n, edges, lambda] = plotActivityCoefficients (modelT)

INPUT:

modelT – structure with fields:

  • .S - m x n stoichiometric matrix

  • .mets - m x 1 cell array of metabolite identifiers

  • .metNames - m x 1 cell array of metabolite names

  • .temp - temperature

  • .gasConstant - gas constant

  • .met - m x 1 structure array of metabolite species data, with fields:

    • .lambda - activity coefficients of the metabolite species

    • .aveZi - average charge of the metabolite

OUTPUTS:

  • n – histogram counts of activity coefficients per bin

  • edges – bin edges used for the activity-coefficient histogram

  • lambda – activity coefficients of the metabolite species

plotMoleFraction(metAbbr, Alberty2006, metAbbrAlbertyAbbr, PHmin, PHmax, ISmin, ISmax, CHImin, CHImax, TEMPmin, TEMPmax, N)[source]

Plot the mole fractions of metabolite species of a reactant as a function of pH, ionic strength, charge and temperature.

USAGE:

plotMoleFraction (metAbbr, Alberty2006, metAbbrAlbertyAbbr, PHmin, PHmax, ISmin, ISmax, CHImin, CHImax, TEMPmin, TEMPmax, N)

INPUTS:

  • metAbbr – reconstruction reactant abbreviation

  • Alberty2006 – Basic data on the metabolite species that make up a reactant, compiled by Robert A. Alberty, Massachusetts Institute of Technology. In Print: Robert A. Alberty, Biochemical Thermodynamics: Applications of Mathematica. John Wiley & Sons, 2006. p391-395 Online: BasicBioChemData3.nb http://library.wolfram.com/infocenter/MathSource/5704/

  • metAbbrAlbertyAbbr – mapping from model metabolite primary key to primary key of reactants in Alberty2006

  • PHmin – Minimum glass electrode pH

  • PHmax – Maximum glass electrode pH

  • ISmin – Ionic strength minimum

  • ISmax – Ionic strength maximum

  • CHImin – Electrical potential minimum

  • CHImax – Electrical potential maximum

  • TEMPmin – temperature minimum

  • TEMPmax – temperature maximum

  • N

realpH(pHa, temp, is)[source]

Apparent glass electrode pH is not the same as real pH for thermodynamic calculations.

Given the experimental glass electrode measurement of pH, this function returns the pH to be used for thermodynamic calculations, pHc = -log10[H+], by subtracting the effect of the ion atmosphere around H+ which reduces its activity coefficient below unity. See p49 Alberty 2003.

USAGE:

[pHr, pHAdjustment] = realpH (pHa, temp, is)

INPUTS:

  • pHa – apparent pH, measured by glass electrode experimentally

  • temp – experimentally measured temperature

  • is – estimate of ionic strength

OUTPUTS:

  • pHr – real pH to be used for thermodynamic calculations

  • pHAdjustment – adjustment to pH