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Zhu XG, Wang Y, Ort DR, Long SP. e-Photosynthesis: a comprehensive dynamic mechanistic model of C3 photosynthesis: from light capture to sucrose synthesis. PLANT, CELL & ENVIRONMENT 2013; 36:1711-27. [PMID: 23072293 DOI: 10.1111/pce.12025] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Photosynthesis is arguably the most researched of all plant processes. A dynamic model of leaf photosynthesis that includes each discrete process from light capture to carbohydrate synthesis, e-photosynthesis, is described. It was developed by linking and extending our previous models of photosystem II (PSII) energy transfer and photosynthetic C3 carbon metabolism to include electron transfer processes around photosystem I (PSI), ion transfer between the lumen and stroma, ATP synthesis and NADP reduction to provide a complete representation. Different regulatory processes linking the light and dark reactions are also included: Rubisco activation via Rubisco activase, pH and xanthophyll cycle-dependent non-photochemical quenching mechanisms, as well as the regulation of enzyme activities via the ferredoxin-theoredoxin system. Although many further feedback and feedforward controls undoubtedly exist, it is shown that e-photosynthesis effectively mimics the typical kinetics of leaf CO₂ uptake, O₂ evolution, chlorophyll fluorescence emission, lumen and stromal pH, and membrane potential following perturbations in light, [CO₂] and [O₂] observed in intact C3 leaves. The model provides a framework for guiding engineering of improved photosynthetic efficiency, for evaluating multiple non-invasive measures used in emerging phenomics facilities, and for quantitative assessment of strengths and weaknesses within the understanding of photosynthesis as an integrated process.
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Affiliation(s)
- Xin-Guang Zhu
- State Key Laboratory of Hybrid Rice, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China.
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Jablonsky J, Bauwe H, Wolkenhauer O. Modeling the Calvin-Benson cycle. BMC SYSTEMS BIOLOGY 2011; 5:185. [PMID: 22051069 PMCID: PMC3257313 DOI: 10.1186/1752-0509-5-185] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 11/03/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Modeling the Calvin-Benson cycle has a history in the field of theoretical biology. Anyone who intends to model this system will look at existing models to adapt, refine and improve them. With the goal to study the regulation of carbon metabolism, we investigated a broad range of relevant models for their suitability to provide the basis for further modeling efforts. Beyond a critical analysis of existing models, we furthermore investigated the question how adjacent metabolic pathways, for instance photorespiration, can be integrated in such models. RESULTS Our analysis reveals serious problems with a range of models that are publicly available and widely used. The problems include the irreproducibility of the published results or significant differences between the equations in the published description of the model and model itself in the supplementary material. In addition to and based on the discussion of existing models, we furthermore analyzed approaches in PGA sink implementation and confirmed a weak relationship between the level of its regulation and efficiency of PGA export, in contrast to significant changes in the content of metabolic pool within the Calvin-Benson cycle. CONCLUSIONS In our study we show that the existing models that have been investigated are not suitable for reuse without substantial modifications. We furthermore show that the minor adjacent pathways of the carbon metabolism, neglected in all kinetic models of Calvin-Benson cycle, cannot be substituted without consequences in the mass production dynamics. We further show that photorespiration or at least its first step (O2 fixation) has to be implemented in the model if this model is aimed for analyses out of the steady state.
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Affiliation(s)
- Jiri Jablonsky
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany.
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Pettersson G. Control properties of the Calvin photosynthesis cycle at physiological carbon dioxide concentrations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1997. [DOI: 10.1016/s0005-2728(97)00080-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Metabolic Control Analysis in Theory and Practice. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s1569-2558(08)60247-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Willingham NM, Lloyd JC, Raines CA. Molecular cloning of the Arabidopsis thaliana sedoheptulose-1,7-biphosphatase gene and expression studies in wheat and Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 1994; 26:1191-1200. [PMID: 7811976 DOI: 10.1007/bf00040699] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We report here the isolation and nucleotide sequence of genomic clones encoding the chloroplast enzyme sedoheptulose-1,7-bisphosphatase (SBPase) from Arabidopsis thaliana. The coding region of this gene contains eight exons (72-76 bp) and seven introns (75-91 bp) and encodes a polypeptide of 393 amino acids. Unusually, the 5' non-coding region contains two additional AUG codons upstream of the translation initiation codon. A comparison of the deduced Arabidopsis and wheat SBPase polypeptide sequences reveals 78.6%, identity. Expression studies showed that the level of SBPase mRNA in Arabidopsis and wheat is regulated in a light-dependent manner and is also influenced by the developmental stage of the leaf. Although the Arabidopsis SBPase gene is present in a single copy, two hybridizing transcripts were detected in some tissues, suggesting the presence of alternate transcription start sites in the upstream region.
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Affiliation(s)
- N M Willingham
- Biology Department, University of Essex, Wivenhoe Park, Colchester, UK
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Miles AJ, Potts SC, Willingham NM, Raines CA, Lloyd JC. A light- and developmentally-regulated DNA-binding interaction is common to the upstream sequences of the wheat Calvin cycle bisphosphatase genes. PLANT MOLECULAR BIOLOGY 1993; 22:507-516. [PMID: 8392396 DOI: 10.1007/bf00015979] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We have characterised a DNA-binding interaction common to the upstream sequences of the wheat fructose-1,6-bisphosphatase (FBPase) and sedoheptulose-1,7-bisphosphatase (SBPase) genes. The recognition site for this sequence-specific binding activity, designated wheat FBPase factor (WF-1), is located within 125 bp of the transcription start site of each gene. Within these regions there are no sequence motifs similar to those shown to be important for light-regulated expression in other species. The binding activity was not detected in wheat root nuclear extracts, or in pea leaf extracts. There was a higher level of binding activity in light-grown than in dark-grown wheat leaves. The level was also found to decline when light-grown plants were given an extended dark treatment, but could be reinduced by light. Utilising the gradient of developmental maturity which exists within the wheat leaf it was found that WF-1 activity increases during leaf development.
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Affiliation(s)
- A J Miles
- Biology Department, University of Essex, Colchester, UK
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Raines CA, Lloyd JC, Willingham NM, Potts S, Dyer TA. cDNA and gene sequences of wheat chloroplast sedoheptulose-1,7-bisphosphatase reveal homology with fructose-1,6-bisphosphatases. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 205:1053-9. [PMID: 1374332 DOI: 10.1111/j.1432-1033.1992.tb16873.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The nucleotide sequence encoding the chloroplast enzyme, sedoheptulose-1,7-bisphosphatase [Sed(1,7)P2ase], was obtained from wheat cDNA and genomic clones. The transcribed region of the Sed(1,7)P2ase gene has eight exons (72-507 bp) and seven introns (85-626 bp) and encodes a precursor polypeptide of 393 amino acids. Comparison of the deduced amino acid sequence of Sed(1,7)P2ase with those of fructose-1,6-bisphosphatase [Fru(1,6)P2ase] enzymes from a variety of sources reveals 19% identity, rising to 42% if conservative changes are considered. Most importantly, the amino acid residues which form the active site of Fru(1,6)P2ase are highly conserved in the Sed(1,7)P2ase molecule, indicating a common catalytic mechanism. Interestingly, although the activities of both Sed(1,7)P2ase and chloroplast Fru(1,6)P2ase are modulated by light via the thioredoxin system, the amino acid sequence motif identified as having a role in this regulation in chloroplast Fru(1,6)P2ase is not found in the Sed(1,7)P2ase enzyme.
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Affiliation(s)
- C A Raines
- Biology Department, University of Essex, Colchester, England
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Soulié JM, Rivière M, Baldet P, Ricard J. Kinetics of the conformational transition of the spinach chloroplast fructose-1,6-bisphosphatase induced by fructose 2,6-bisphosphate. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 195:671-8. [PMID: 1847866 DOI: 10.1111/j.1432-1033.1991.tb15752.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The activation of oxidized chloroplast fructose-1,6-bisphosphatase by fructose 2,6-bisphosphate and magnesium previously described at pH 7.5 [Soulié et al. (1988) Eur. J. Biochem. 176, 111-117] has now been studied at pH 8, the pH which prevails under light conditions in the chloroplast stroma. The process obeys a hysteretic mechanism but the rate of activation is considerably increased with half-times down to 50 s and the apparent dissociation constant of fructose 2,6-bisphosphate from the enzyme is lowered from 1 mM at pH 7.5 to 3.3 microM at pH 8. The process is strictly metal-dependent with a half-saturation concentration of 2.54 mM for magnesium. The conformational transition postulated in our hysteretic model has been investigated through both the spectrophometric and chemical modification approaches. The activation of the enzyme by fructose 2,6-bisphosphate in the presence of magnesium results in a slow modification of the ultraviolet absorption spectrum of the enzyme with an overall increase of 3% at 290 nm. The same treatment leads to the protection of two free sulfhydryls and an increased reactivity of one sulfhydryl group/enzyme monomer to modification by 5,5'-dithiobis(2-nitrobenzoic acid). The titration of the exposed cysteinyl residue prevents the relaxation of enzyme species induced by fructose 2,6-bisphosphate to the native form. The activation of chloroplast fructose-1,6-bisphosphatase by fructose 2,6-bisphosphate is discussed both with respect to the understanding of the overall regulation properties of the enzyme and to a possible physiological significance of this process.
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Affiliation(s)
- J M Soulié
- Centre de Biochimie et de Biologie Moléculaire, C.N.R.S., Marseille, France
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Dyer TA. Genetic manipulation of photosynthetic processes in plants. Subcell Biochem 1991; 17:213-34. [PMID: 1796485 DOI: 10.1007/978-1-4613-9365-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- T A Dyer
- Molecular Genetics Department, Cambridge Laboratory, John Innes Centre for Plant Science Research, Norwich, United Kingdom
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Ekkehard Neuhaus H, Stitt M. Control analysis of photosynthate partitioning : Impact of reduced activity of ADP-glucose pyrophosphorylase or plastid phosphoglucomutase on the fluxes to starch and sucrose inArabidopsis thaliana (L.) Heynh. PLANTA 1990; 182:445-54. [PMID: 24197197 DOI: 10.1007/bf02411398] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/1990] [Accepted: 06/11/1990] [Indexed: 05/20/2023]
Abstract
Experiments were carried out to investigate the contribution of ADP-glucose pyrophosphorylase and the plastid phosphoglucosemutase to the control of starch synthesis. Mutants ofArabidopsis thaliana (L.) Heyhn. were constructed with 50% and 7% of the wild-type adenosine 5'-diphosphoglucose pyrophosphorylase (ADPGlc-PPase), or 50% and null plastid phosphoglucomutase (PGM). The changes in the steady-state rates of sucrose synthesis, starch synthesis and CO2 fixation were measured in saturating CO2 in low (75 μmol·m(-2)·s(-1)) and high (600 μmol·m(-2)·s(-1)) irradiance. In low irradiance, a 50% decrease of PGM had no significant effect on fluxes, while a 50% and 93% decrease of ADPGlc-PPase led to a 23% and 74% inhibition of starch synthesis. Decreased ADPGlc-PPase led to an increase of hexose phosphates, triose phosphates and fructose-1,6-bisphosphate. Fixation of CO2 was not inhibited because the inhibition of starch synthesis was matched by a stimulation of sucrose synthesis. In high irradiance, a 50% decrease of PGM led to a 20% inhibition of starch synthesis. A 50% and 93% decrease of ADPGlc-PPase led to a 39% and 90% inhibition of starch synthesis. Sucrose synthesis was also inhibited, and the rate of photosynthesis was decreased. Decreased ADPGlc-PPase led to an increase of hexose phosphates but triose phosphates and fructose-1,6-bisphosphate did not increase. These results are used to estimate flux-control coefficients for these enzymes for starch synthesis. Firstly, the flux to starch is only controlled by ADPGlc-PPase in low irradiance, but control is redistributed to other enzymes in the pathway when a rapid flux is imposed, e.g. in high irradiance and CO2. Secondly, reducing the rate of starch synthesis by decreasing the activity of enzymes in this pathway does not always lead to a compensating increase in the rate of sucrose synthesis. Thirdly, decreasing the activity of an enzyme by a factor of two compared to the remainder of the pathway often leads to it exerting very considerable control. Fourthly, each enzyme starts to exert considerable control when only a fraction of its Vmax activity is being utilised in vivo, for example the maximum flux at ADPGlc-PPase never exceeded 20% of the Vmax activity. The summation theory is also applied to check whether additional major control sites are required. In low irradiance, the efficiency of light harvesting will exert considerable control over the rate of starch synthesis.
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Affiliation(s)
- H Ekkehard Neuhaus
- Lehrstuhl für Pflanzenphysiologie, Universität Bayreuth, Postfach 10 12 51, W-8580, Bayreuth, Federal Republic of Germany
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Giersch C, Lämmel D, Farquhar G. Control analysis of photosynthetic CO2 fixation. PHOTOSYNTHESIS RESEARCH 1990; 24:151-165. [PMID: 24419908 DOI: 10.1007/bf00032595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/1989] [Accepted: 11/09/1989] [Indexed: 06/03/2023]
Abstract
The potential of control analysis to aid our understanding of regulation and control of photosynthetic carbon metabolism is investigated. Methods of metabolic control analysis are used to determine flux control coefficients of photosynthetic reactions from enzyme elasticities. Equations expressing control coefficients symbolically by enzyme elasticities are derived, and general properties of these expressions are analysed. Suggestions for experimental determination of flux control coefficients from enzyme elasticities are given. A simplified model of the Calvin-Benson cycle is used to illustrate interrelations between patterns of photosynthetic metabolites and that of control coefficients.
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Affiliation(s)
- C Giersch
- Institut für Biochemie der Pflanzen der Universität Düsseldorf, Universitätsstr. 1, D-4000, Düsseldorf 1, FRG
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Cornish-Bowden A. Metabolic control therapy and biochemical systems theory: different objectives, different assumptions, different results. J Theor Biol 1989; 136:365-77. [PMID: 2682007 DOI: 10.1016/s0022-5193(89)80154-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The claim by Savageau et al. (1987 a, b, Math. Biosci. 86, 127-145, 147-167) that the theory of metabolic control associated with Kacser & Burns (1973, Symp. Soc. Exp. Biol. 27, 65-104) and with Heinrich & Rapoport (1974, Eur. J. Biochem. 42, 89-102) is no more than a special case of the biochemical systems theory of Savageau and colleagues is examined. It is shown to be based on a misconception of the objectives and assumptions of metabolic control theory. In particular, the control and elasticity coefficients that play a central role in metabolic control theory are not constants and cannot be treated as constants. Consequently they cannot in general be equated with the kinetic orders that appear in biochemical systems theory, though they do correspond at the point where the two theories are tangential to one another.
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Affiliation(s)
- A Cornish-Bowden
- Centre de Biochimie et de Biologie Moléculaire, Centre National de la Recherche Scientifique, Marseille, France
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Small JR, Fell DA. The matrix method of metabolic control analysis: its validity for complex pathway structures. J Theor Biol 1989; 136:181-97. [PMID: 2779266 DOI: 10.1016/s0022-5193(89)80225-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The sensitivities of the variables of a metabolic system (such as fluxes and concentrations) to variations in enzyme concentration are expressed in metabolic control analysis as control coefficients. The matrix method is a system of writing matrix equations that generate expressions for the control coefficients in terms of the characteristics of the components (principally the enzymes). Previously, the matrix method has been considered in terms of simple pathway structures; here we justify its applicability to complex pathways, such as those with multiple branches. It is shown that this requires modification of the branch point relationship to take account of changes of flux along the limbs of the branch and of stoichiometric factors. The method of deriving the flux control coefficients with respect to different fluxes in the system is extended to cope with these circumstances.
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Affiliation(s)
- J R Small
- School of Biological and Molecular Sciences, Oxford Polytechnic, Headington, U.K
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Monson RK. On the Evolutionary Pathways Resulting in C4 Photosynthesis and Crassulacean Acid Metabolism (CAM). ADV ECOL RES 1989. [DOI: 10.1016/s0065-2504(08)60157-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Heber U, Neimanis S, Dietz KJ. Fractional control of photosynthesis by the QB protein, the cytochrome f/b 6 complex and other components of the photosynthesic apparatus. PLANTA 1988; 173:267-274. [PMID: 24226408 DOI: 10.1007/bf00403020] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/1987] [Accepted: 08/20/1987] [Indexed: 06/02/2023]
Abstract
In order to obtain information on fractional control of photosynthesis by individual catalysts, catalytic activities in photosynthetic electron transport and carbon metabolism were modified by the addition of inhibitors, and the effect on photosynthetic flux was measured using chloroplasts of Spinacia oleracea L. In thylakoids with coupled electron transport, light-limited electron flow to ferricyanide was largely controlled by the QB protein of the electron-transport chain. Fractional control by the cytochrome f/b 6 complex was insignificant under these conditions. Control by the cytochrome f/b 6 complex dominated at high energy fluence rates where the contribution to control of the QB protein was very small. Uncoupling shifted control from the cytochrome f/b 6 complex to the QB protein. Control of electron flow was more complex in assimilating chloroplasts than in thylakoids. The contributions of the cytochrome f/b 6 complex and of the QB protein to control were smaller in intact chloroplasts than in thylakoids. Thus, even though the transit time for an electron through the electron-transport chain may be below 5 ms in leaves, oxidation of plastohydroquinone was only partially responsible for limiting photosynthesis under conditions of light and CO2 saturation. The energy fluence rate influenced control coefficients. Fractional control of photosynthesis by the ATP synthetase, the cytochrome f/b 6 complex and by ribulose-1,5-bisphosphate carboxylase increased with increasing fluence rates, whereas the contributions of the QB protein and of enzymes sensitive to SH-blocking agents decreased. The results show that the burdens of control are borne by several components of the photosynthetic apparatus, and that burdens are shifted as conditions for photosynthesis change.
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Affiliation(s)
- U Heber
- Institute of Botany and Pharmaceutical Biology of the University, Mittlerer Dallenbergweg 64, D-8700, Würzburg, Germany
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Sauro HM, Small JR, Fell DA. Metabolic control and its analysis. Extensions to the theory and matrix method. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 165:215-21. [PMID: 3569295 DOI: 10.1111/j.1432-1033.1987.tb11214.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The matrix algebra procedure for determining the flux control coefficients of enzymes in metabolic pathways has been extended to allow determination of the concentration control coefficients. Although it is shown that the procedure is essentially unchanged in most cases, the presence of moiety-conserved cycles in a pathway places additional limitations on the form of the equations that can be used in the matrix formulation for concentration control coefficients. In the case of branched pathways, a new coefficient has been defined, the branch distribution control coefficient, which can be obtained via the matrix procedure. Thus a single matrix equation permits calculation or algebraic evaluation of the control coefficients for flux, concentration and distribution of flux at branches, so that the complete response of a pathway to alteration of enzyme content, or to modulation by an effector, can be determined. The relationships have been determined between flux control coefficients in isolated sections of metabolic pathways and the coefficients for the same enzymes when part of a larger metabolic system. It is shown that the control analysis of the isolated system provides useful information towards determining the control properties of the extended system.
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