Literature DB >> 11607175

Equilibrium compositions of solutions of biochemical species and heats of biochemical reactions.

R A Alberty1.   

Abstract

Equilibrium compositions of solutions of biochemical species can be calculated by use of general equilibrium computer programs that minimize the Gibbs energy. The standard Gibbs energies of formation and standard enthalpies of formation of the species in a biochemical system can be calculated by Gaussian reduction of the augmented transpose of the stoichiometric number matrix for the system. The conservation matrix, which is also needed for the calculation of the equilibrium composition, can be obtained in two ways. The hydrolysis of adenosine 5'-triphosphate in solutions containing magnesium ions can be treated by considering 17 species. The equilibrium composition and enthalpy are calculated before and after adding ATPase. This makes it possible to calculate DeltapH, DeltapMg, and the heat of reaction when ATPase is added.

Entities:  

Year:  1991        PMID: 11607175      PMCID: PMC51427          DOI: 10.1073/pnas.88.8.3268

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  4 in total

1.  The equilibrium constants of the adenosine triphosphate hydrolysis and the adenosine triphosphate-citrate lyase reactions.

Authors:  R W Guynn; R L Veech
Journal:  J Biol Chem       Date:  1973-10-25       Impact factor: 5.157

2.  Standard Gibbs free energy, enthalpy, and entropy changes as a function of pH and pMg for several reactions involving adenosine phosphates.

Authors:  R A Alberty
Journal:  J Biol Chem       Date:  1969-06-25       Impact factor: 5.157

3.  Effect of pH and metal ion concentration on the equilibrium hydrolysis of adenosine triphosphate to adenosine diphosphate.

Authors:  R A Alberty
Journal:  J Biol Chem       Date:  1968-04-10       Impact factor: 5.157

4.  Thermodynamic data for the hydrolysis of adenosine triphosphate as a function of pH, Mg2+ ion concentration, and ionic strength.

Authors:  R C Phillips; P George; R J Rutman
Journal:  J Biol Chem       Date:  1969-06-25       Impact factor: 5.157

  4 in total
  8 in total

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Journal:  Biophys J       Date:  2002-07       Impact factor: 4.033

2.  The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools.

Authors:  Iman Famili; Bernhard O Palsson
Journal:  Biophys J       Date:  2003-07       Impact factor: 4.033

3.  A database of thermodynamic quantities for the reactions of glycolysis and the tricarboxylic acid cycle.

Authors:  X Li; R K Dash; R K Pradhan; F Qi; M Thompson; K C Vinnakota; F Wu; F Yang; D A Beard
Journal:  J Phys Chem B       Date:  2010-05-06       Impact factor: 2.991

4.  Levels of thermodynamic treatment of biochemical reaction systems.

Authors:  R A Alberty
Journal:  Biophys J       Date:  1993-09       Impact factor: 4.033

Review 5.  Simulation of cellular biochemical system kinetics.

Authors:  Daniel A Beard
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2010-12-17

6.  Calculation of biochemical net reactions and pathways by using matrix operations.

Authors:  R A Alberty
Journal:  Biophys J       Date:  1996-07       Impact factor: 4.033

7.  An integrated open framework for thermodynamics of reactions that combines accuracy and coverage.

Authors:  Elad Noor; Arren Bar-Even; Avi Flamholz; Yaniv Lubling; Dan Davidi; Ron Milo
Journal:  Bioinformatics       Date:  2012-05-29       Impact factor: 6.937

8.  Genome-scale model for Clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems.

Authors:  Ryan S Senger; Eleftherios T Papoutsakis
Journal:  Biotechnol Bioeng       Date:  2008-12-01       Impact factor: 4.530

  8 in total

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