Limits...
Co-operative intermolecular kinetics of 2-oxoglutarate dependent dioxygenases may be essential for system-level regulation of plant cell physiology.

Kundu S - Front Plant Sci (2015)

Bottom Line: Here, I present a proof-of-concept model, that an evolving molecular network of 2OG-dependent enzymes can maintain iron homeostasis in the cytosol of root hair cells of members of the family Gramineae by actuating a non-reductive compensatory chelation by the phytosiderophores.Regression models of empirically available kinetic data (iron and alpha-ketoglutarate) were formulated, analyzed, and compared.The results, when viewed in context of the superfamily responding as a unit, suggest that members can indeed, work together to accomplish system-level function.

View Article: PubMed Central - PubMed

Affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University New Delhi, India.

ABSTRACT
Can the stimulus-driven synergistic association of 2-oxoglutarate dependent dioxygenases be influenced by the kinetic parameters of binding and catalysis?In this manuscript, I posit that these indices are necessary and specific for a particular stimulus, and are key determinants of a dynamic clustering that may function to mitigate the effects of this trigger. The protein(s)/sequence(s) that comprise this group are representative of all major kingdoms of life, and catalyze a generic hydroxylation, which is, in most cases accompanied by a specialized conversion of the substrate molecule. Iron is an essential co-factor for this transformation and the response to waning levels is systemic, and mandates the simultaneous participation of molecular sensors, transporters, and signal transducers. Here, I present a proof-of-concept model, that an evolving molecular network of 2OG-dependent enzymes can maintain iron homeostasis in the cytosol of root hair cells of members of the family Gramineae by actuating a non-reductive compensatory chelation by the phytosiderophores. Regression models of empirically available kinetic data (iron and alpha-ketoglutarate) were formulated, analyzed, and compared. The results, when viewed in context of the superfamily responding as a unit, suggest that members can indeed, work together to accomplish system-level function. This is achieved by the establishment of transient metabolic conduits, wherein the flux is dictated by kinetic compatibility of the participating enzymes. The approach adopted, i.e., predictive mathematical modeling, is integral to the hypothesis-driven acquisition of experimental data points and, in association with suitable visualization aids may be utilized for exploring complex plant biochemical systems.

No MeSH data available.


Related in: MedlinePlus

Model selection and analysis. (A,B) Non-linear regression models of KmFe and KmAKG values in accordance with Equations (3) and (4) (C) Analysis of model robustness using a Monte Carlo approach, and (D) Predicted V0enzyme values at different thresholds for select enzymes. Here the ordinate axis is a Log10 representation.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4502536&req=5

Figure 2: Model selection and analysis. (A,B) Non-linear regression models of KmFe and KmAKG values in accordance with Equations (3) and (4) (C) Analysis of model robustness using a Monte Carlo approach, and (D) Predicted V0enzyme values at different thresholds for select enzymes. Here the ordinate axis is a Log10 representation.

Mentions: A non-linear regression curve for each dataset, i.e., DFe and DAKG, was fitted using a 6-degree polynomial (Figures 2A,B) as under.


Co-operative intermolecular kinetics of 2-oxoglutarate dependent dioxygenases may be essential for system-level regulation of plant cell physiology.

Kundu S - Front Plant Sci (2015)

Model selection and analysis. (A,B) Non-linear regression models of KmFe and KmAKG values in accordance with Equations (3) and (4) (C) Analysis of model robustness using a Monte Carlo approach, and (D) Predicted V0enzyme values at different thresholds for select enzymes. Here the ordinate axis is a Log10 representation.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4502536&req=5

Figure 2: Model selection and analysis. (A,B) Non-linear regression models of KmFe and KmAKG values in accordance with Equations (3) and (4) (C) Analysis of model robustness using a Monte Carlo approach, and (D) Predicted V0enzyme values at different thresholds for select enzymes. Here the ordinate axis is a Log10 representation.
Mentions: A non-linear regression curve for each dataset, i.e., DFe and DAKG, was fitted using a 6-degree polynomial (Figures 2A,B) as under.

Bottom Line: Here, I present a proof-of-concept model, that an evolving molecular network of 2OG-dependent enzymes can maintain iron homeostasis in the cytosol of root hair cells of members of the family Gramineae by actuating a non-reductive compensatory chelation by the phytosiderophores.Regression models of empirically available kinetic data (iron and alpha-ketoglutarate) were formulated, analyzed, and compared.The results, when viewed in context of the superfamily responding as a unit, suggest that members can indeed, work together to accomplish system-level function.

View Article: PubMed Central - PubMed

Affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University New Delhi, India.

ABSTRACT
Can the stimulus-driven synergistic association of 2-oxoglutarate dependent dioxygenases be influenced by the kinetic parameters of binding and catalysis?In this manuscript, I posit that these indices are necessary and specific for a particular stimulus, and are key determinants of a dynamic clustering that may function to mitigate the effects of this trigger. The protein(s)/sequence(s) that comprise this group are representative of all major kingdoms of life, and catalyze a generic hydroxylation, which is, in most cases accompanied by a specialized conversion of the substrate molecule. Iron is an essential co-factor for this transformation and the response to waning levels is systemic, and mandates the simultaneous participation of molecular sensors, transporters, and signal transducers. Here, I present a proof-of-concept model, that an evolving molecular network of 2OG-dependent enzymes can maintain iron homeostasis in the cytosol of root hair cells of members of the family Gramineae by actuating a non-reductive compensatory chelation by the phytosiderophores. Regression models of empirically available kinetic data (iron and alpha-ketoglutarate) were formulated, analyzed, and compared. The results, when viewed in context of the superfamily responding as a unit, suggest that members can indeed, work together to accomplish system-level function. This is achieved by the establishment of transient metabolic conduits, wherein the flux is dictated by kinetic compatibility of the participating enzymes. The approach adopted, i.e., predictive mathematical modeling, is integral to the hypothesis-driven acquisition of experimental data points and, in association with suitable visualization aids may be utilized for exploring complex plant biochemical systems.

No MeSH data available.


Related in: MedlinePlus