Modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase

Abstract In the present work we have modelled and optimized the reaction mechanism of the triose phosphate isomerase (TIM) enzyme (E.C. 5.3.1.1). For this purpose we have used an approach that combines the S-system representation within the power law formalism and linear programming techniques. By this means we have explored those rate constants whose alterations are likely to improve the catalytic efficiency of the enzyme and investigated the available room for optimization in different metabolic conditions. The role and plausibility of the different types of mutations on the evolution of this enzyme have also been considered. Steady state sensitivity analysis was carried out and a new set of aggregated logarithmic gains was defined in order to quantify the responses of the system to changes in groups of rate constants that could be explained in terms of mutations affecting the catalytic properties of the enzyme. Evaluation of these logarithmic gains at different levels of saturation and disequilibrium ratios enabled us to reach conclusions about the meaning and role of the diffusion limitation terms. The catalytic efficiency of the monoenzymatic system was optimized through changes in the kinetic rate constants within different sets of restrictions ranging from thermodynamic or kinetic to evolutionary ones. Results showed that, at very different conditions, there is still room for improvement in the TIM enzyme. Thus, in a wide range of metabolically significant values of the disequilibrium ratio there is a minimal variation in the optimal profile that yields 2.1 times the velocity of the basal states. Though most of this increase is accounted for by the increase of the second order constants (that could have already reached a theoretical maximum) significant increases (10%) in catalytic efficiencies are obtained by changes of the internal steps only. Besides these new findings our optimization approach has been able to reproduce results obtained with other approaches. Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Marín-Sanguino, Alberto [verfasserIn] Torres, Néstor V.

Format:	Artikel
Sprache:	Englisch

Erschienen:	2002

Schlagwörter:	Kinetic Constant Kinetic Order Citric Acid Production Triosephosphate Isomerase Kinetic Rate Constant

Anmerkung:	© Society for Mathematical Biology 2002

Übergeordnetes Werk:	Enthalten in: Bulletin of mathematical biology - Springer-Verlag, 1973, 64(2002), 2 vom: März, Seite 301-326
Übergeordnetes Werk:	volume:64 ; year:2002 ; number:2 ; month:03 ; pages:301-326

Links:	Volltext

DOI / URN:	10.1006/bulm.2001.0276

Katalog-ID:	OLC2087071853

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allfields	10.1006/bulm.2001.0276 doi (DE-627)OLC2087071853 (DE-He213)bulm.2001.0276-p DE-627 ger DE-627 rakwb eng 570 510 VZ 12 ssgn BIODIV DE-30 fid 42.00 bkl Marín-Sanguino, Alberto verfasserin aut Modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase 2002 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Society for Mathematical Biology 2002 Abstract In the present work we have modelled and optimized the reaction mechanism of the triose phosphate isomerase (TIM) enzyme (E.C. 5.3.1.1). For this purpose we have used an approach that combines the S-system representation within the power law formalism and linear programming techniques. By this means we have explored those rate constants whose alterations are likely to improve the catalytic efficiency of the enzyme and investigated the available room for optimization in different metabolic conditions. The role and plausibility of the different types of mutations on the evolution of this enzyme have also been considered. Steady state sensitivity analysis was carried out and a new set of aggregated logarithmic gains was defined in order to quantify the responses of the system to changes in groups of rate constants that could be explained in terms of mutations affecting the catalytic properties of the enzyme. Evaluation of these logarithmic gains at different levels of saturation and disequilibrium ratios enabled us to reach conclusions about the meaning and role of the diffusion limitation terms. The catalytic efficiency of the monoenzymatic system was optimized through changes in the kinetic rate constants within different sets of restrictions ranging from thermodynamic or kinetic to evolutionary ones. Results showed that, at very different conditions, there is still room for improvement in the TIM enzyme. Thus, in a wide range of metabolically significant values of the disequilibrium ratio there is a minimal variation in the optimal profile that yields 2.1 times the velocity of the basal states. Though most of this increase is accounted for by the increase of the second order constants (that could have already reached a theoretical maximum) significant increases (10%) in catalytic efficiencies are obtained by changes of the internal steps only. Besides these new findings our optimization approach has been able to reproduce results obtained with other approaches. Kinetic Constant Kinetic Order Citric Acid Production Triosephosphate Isomerase Kinetic Rate Constant Torres, Néstor V. aut Enthalten in Bulletin of mathematical biology Springer-Verlag, 1973 64(2002), 2 vom: März, Seite 301-326 (DE-627)129391719 (DE-600)184905-0 (DE-576)014776863 0092-8240 nnns volume:64 year:2002 number:2 month:03 pages:301-326 https://doi.org/10.1006/bulm.2001.0276 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-BIODIV SSG-OLC-MAT SSG-OPC-MAT GBV_ILN_11 GBV_ILN_31 GBV_ILN_40 GBV_ILN_70 GBV_ILN_2010 GBV_ILN_2219 GBV_ILN_4012 GBV_ILN_4082 GBV_ILN_4219 42.00 VZ AR 64 2002 2 03 301-326
spelling	10.1006/bulm.2001.0276 doi (DE-627)OLC2087071853 (DE-He213)bulm.2001.0276-p DE-627 ger DE-627 rakwb eng 570 510 VZ 12 ssgn BIODIV DE-30 fid 42.00 bkl Marín-Sanguino, Alberto verfasserin aut Modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase 2002 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Society for Mathematical Biology 2002 Abstract In the present work we have modelled and optimized the reaction mechanism of the triose phosphate isomerase (TIM) enzyme (E.C. 5.3.1.1). For this purpose we have used an approach that combines the S-system representation within the power law formalism and linear programming techniques. By this means we have explored those rate constants whose alterations are likely to improve the catalytic efficiency of the enzyme and investigated the available room for optimization in different metabolic conditions. The role and plausibility of the different types of mutations on the evolution of this enzyme have also been considered. Steady state sensitivity analysis was carried out and a new set of aggregated logarithmic gains was defined in order to quantify the responses of the system to changes in groups of rate constants that could be explained in terms of mutations affecting the catalytic properties of the enzyme. Evaluation of these logarithmic gains at different levels of saturation and disequilibrium ratios enabled us to reach conclusions about the meaning and role of the diffusion limitation terms. The catalytic efficiency of the monoenzymatic system was optimized through changes in the kinetic rate constants within different sets of restrictions ranging from thermodynamic or kinetic to evolutionary ones. Results showed that, at very different conditions, there is still room for improvement in the TIM enzyme. Thus, in a wide range of metabolically significant values of the disequilibrium ratio there is a minimal variation in the optimal profile that yields 2.1 times the velocity of the basal states. Though most of this increase is accounted for by the increase of the second order constants (that could have already reached a theoretical maximum) significant increases (10%) in catalytic efficiencies are obtained by changes of the internal steps only. Besides these new findings our optimization approach has been able to reproduce results obtained with other approaches. Kinetic Constant Kinetic Order Citric Acid Production Triosephosphate Isomerase Kinetic Rate Constant Torres, Néstor V. aut Enthalten in Bulletin of mathematical biology Springer-Verlag, 1973 64(2002), 2 vom: März, Seite 301-326 (DE-627)129391719 (DE-600)184905-0 (DE-576)014776863 0092-8240 nnns volume:64 year:2002 number:2 month:03 pages:301-326 https://doi.org/10.1006/bulm.2001.0276 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-BIODIV SSG-OLC-MAT SSG-OPC-MAT GBV_ILN_11 GBV_ILN_31 GBV_ILN_40 GBV_ILN_70 GBV_ILN_2010 GBV_ILN_2219 GBV_ILN_4012 GBV_ILN_4082 GBV_ILN_4219 42.00 VZ AR 64 2002 2 03 301-326
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author	Marín-Sanguino, Alberto
spellingShingle	Marín-Sanguino, Alberto ddc 570 ssgn 12 fid BIODIV bkl 42.00 misc Kinetic Constant misc Kinetic Order misc Citric Acid Production misc Triosephosphate Isomerase misc Kinetic Rate Constant Modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase
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topic_title	570 510 VZ 12 ssgn BIODIV DE-30 fid 42.00 bkl Modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase Kinetic Constant Kinetic Order Citric Acid Production Triosephosphate Isomerase Kinetic Rate Constant
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title	Modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase
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title_full	Modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase
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title_sort	modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase
title_auth	Modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase
abstract	Abstract In the present work we have modelled and optimized the reaction mechanism of the triose phosphate isomerase (TIM) enzyme (E.C. 5.3.1.1). For this purpose we have used an approach that combines the S-system representation within the power law formalism and linear programming techniques. By this means we have explored those rate constants whose alterations are likely to improve the catalytic efficiency of the enzyme and investigated the available room for optimization in different metabolic conditions. The role and plausibility of the different types of mutations on the evolution of this enzyme have also been considered. Steady state sensitivity analysis was carried out and a new set of aggregated logarithmic gains was defined in order to quantify the responses of the system to changes in groups of rate constants that could be explained in terms of mutations affecting the catalytic properties of the enzyme. Evaluation of these logarithmic gains at different levels of saturation and disequilibrium ratios enabled us to reach conclusions about the meaning and role of the diffusion limitation terms. The catalytic efficiency of the monoenzymatic system was optimized through changes in the kinetic rate constants within different sets of restrictions ranging from thermodynamic or kinetic to evolutionary ones. Results showed that, at very different conditions, there is still room for improvement in the TIM enzyme. Thus, in a wide range of metabolically significant values of the disequilibrium ratio there is a minimal variation in the optimal profile that yields 2.1 times the velocity of the basal states. Though most of this increase is accounted for by the increase of the second order constants (that could have already reached a theoretical maximum) significant increases (10%) in catalytic efficiencies are obtained by changes of the internal steps only. Besides these new findings our optimization approach has been able to reproduce results obtained with other approaches. © Society for Mathematical Biology 2002
abstractGer	Abstract In the present work we have modelled and optimized the reaction mechanism of the triose phosphate isomerase (TIM) enzyme (E.C. 5.3.1.1). For this purpose we have used an approach that combines the S-system representation within the power law formalism and linear programming techniques. By this means we have explored those rate constants whose alterations are likely to improve the catalytic efficiency of the enzyme and investigated the available room for optimization in different metabolic conditions. The role and plausibility of the different types of mutations on the evolution of this enzyme have also been considered. Steady state sensitivity analysis was carried out and a new set of aggregated logarithmic gains was defined in order to quantify the responses of the system to changes in groups of rate constants that could be explained in terms of mutations affecting the catalytic properties of the enzyme. Evaluation of these logarithmic gains at different levels of saturation and disequilibrium ratios enabled us to reach conclusions about the meaning and role of the diffusion limitation terms. The catalytic efficiency of the monoenzymatic system was optimized through changes in the kinetic rate constants within different sets of restrictions ranging from thermodynamic or kinetic to evolutionary ones. Results showed that, at very different conditions, there is still room for improvement in the TIM enzyme. Thus, in a wide range of metabolically significant values of the disequilibrium ratio there is a minimal variation in the optimal profile that yields 2.1 times the velocity of the basal states. Though most of this increase is accounted for by the increase of the second order constants (that could have already reached a theoretical maximum) significant increases (10%) in catalytic efficiencies are obtained by changes of the internal steps only. Besides these new findings our optimization approach has been able to reproduce results obtained with other approaches. © Society for Mathematical Biology 2002
abstract_unstemmed	Abstract In the present work we have modelled and optimized the reaction mechanism of the triose phosphate isomerase (TIM) enzyme (E.C. 5.3.1.1). For this purpose we have used an approach that combines the S-system representation within the power law formalism and linear programming techniques. By this means we have explored those rate constants whose alterations are likely to improve the catalytic efficiency of the enzyme and investigated the available room for optimization in different metabolic conditions. The role and plausibility of the different types of mutations on the evolution of this enzyme have also been considered. Steady state sensitivity analysis was carried out and a new set of aggregated logarithmic gains was defined in order to quantify the responses of the system to changes in groups of rate constants that could be explained in terms of mutations affecting the catalytic properties of the enzyme. Evaluation of these logarithmic gains at different levels of saturation and disequilibrium ratios enabled us to reach conclusions about the meaning and role of the diffusion limitation terms. The catalytic efficiency of the monoenzymatic system was optimized through changes in the kinetic rate constants within different sets of restrictions ranging from thermodynamic or kinetic to evolutionary ones. Results showed that, at very different conditions, there is still room for improvement in the TIM enzyme. Thus, in a wide range of metabolically significant values of the disequilibrium ratio there is a minimal variation in the optimal profile that yields 2.1 times the velocity of the basal states. Though most of this increase is accounted for by the increase of the second order constants (that could have already reached a theoretical maximum) significant increases (10%) in catalytic efficiencies are obtained by changes of the internal steps only. Besides these new findings our optimization approach has been able to reproduce results obtained with other approaches. © Society for Mathematical Biology 2002
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title_short	Modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase
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