Inhibition kinetics of catabolic dehydrogenases by elevated moieties of ATP and ADP – implication for a new regulation mechanism in <i>Lactococcus lactis</i>

The tetrasaccharide heparan sulfate (HS) mimetic PG545, a clinical anti-cancer candidate, is an inhibitor of the HS-degrading enzyme heparanase. The kinetics of heparanase inhibition by PG545 and three structural analogues were investigated to understand their modes of inhibition. The cholestanol aglycon of PG545 significantly increased affinity for heparanase and also modified the inhibition mode. For the tetrasaccharides, competitive inhibition was modified to parabolic competition by the addition of the cholestanol aglycon. For the trisaccharides, partial competitive inhibition was modified to parabolic competition. A schematic model to explain these findings is presented.

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“…A better fit to the data, however, was achieved using the Hill‐type model of Cao et al [26].

v = \frac{V_{\max} \cdot S}{K_{m} (1 + \frac{I^{n}}{K_{i}^{n}}) + S}

…”

Section: Resultsmentioning

confidence: 99%

Mechanisms of heparanase inhibition by the heparan sulfate mimetic PG545 and three structural analogues

Hammond¹,

Handley²,

Dredge

et al. 2013

FEBS Open Bio

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“…This included both the steady-state value of ATP/ADP and the ATP/ADP-range where J 5 had a positive response. This is most probably an incomplete picture of regulation by ATP/ADP, as the inhibition by ATP and ADP of L. lactis enzymes such as lactate dehydrogenase, alcohol dehydrogenase and glyceraldehyde 3-phosphate dehydrogenase [ 25 , 26 ] was not included in the model. It is conceivable that these additional routes of interaction could significantly affect the flux responses investigated here.…”

Section: Discussionmentioning

confidence: 99%

Tracing regulatory routes in metabolism using generalised supply-demand analysis

2015

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BackgroundGeneralised supply-demand analysis is a conceptual framework that views metabolism as a molecular economy. Metabolic pathways are partitioned into so-called supply and demand blocks that produce and consume a particular intermediate metabolite. By studying the response of these reaction blocks to perturbations in the concentration of the linking metabolite, different regulatory routes of interaction between the metabolite and its supply and demand blocks can be identified and their contribution quantified. These responses are mediated not only through direct substrate/product interactions, but also through allosteric effects. Here we subject previously published kinetic models of pyruvate metabolism in Lactococcus lactis and aspartate-derived amino acid synthesis in Arabidopsis thaliana to generalised supply-demand analysis.ResultsMultiple routes of regulation are brought about by different mechanisms in each model, leading to behavioural and regulatory patterns that are generally difficult to predict from simple inspection of the reaction networks depicting the models. In the pyruvate model the moiety-conserved cycles of ATP/ADP and NADH/NAD + allow otherwise independent metabolic branches to communicate. This causes the flux of one ATP-producing reaction block to increase in response to an increasing ATP/ADP ratio, while an NADH-consuming block flux decreases in response to an increasing NADH/NAD + ratio for certain ratio value ranges.In the aspartate model, aspartate semialdehyde can inhibit its supply block directly or by increasing the concentration of two amino acids (Lys and Thr) that occur as intermediates in demand blocks and act as allosteric inhibitors of isoenzymes in the supply block. These different routes of interaction from aspartate semialdehyde are each seen to contribute differently to the regulation of the aspartate semialdehyde supply block.ConclusionsIndirect routes of regulation between a metabolic intermediate and a reaction block that either produces or consumes this intermediate can play a much larger regulatory role than routes mediated through direct interactions. These indirect routes of regulation can also result in counter-intuitive metabolic behaviour. Performing generalised supply-demand analysis on two previously published models demonstrated the utility of this method as an entry point in the analysis of metabolic behaviour and the potential for obtaining novel results from previously analysed models by using new approaches.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-015-0236-1) contains supplementary material, which is available to authorized users.

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“…A number of mathematical modelling approaches have been used in LAB research to integrate experimental data from detailed biochemical studies on transport process [44] and enzyme kinetics (see, e.g. [45,46]), supplemented with flux and metabolites measurements, such as in-vivo NMR [47,48]. The genomics approach to LAB physiology has been accompanied in recent years by the use of genome-scale metabolic network models [15], as discussed above.…”

Section: Reviewmentioning

confidence: 99%

Systems biology of lactic acid bacteria: a critical review

2011

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Understanding the properties of a system as emerging from the interaction of well described parts is the most important goal of Systems Biology. Although in the practice of Lactic Acid Bacteria (LAB) physiology we most often think of the parts as the proteins and metabolites, a wider interpretation of what a part is can be useful. For example, different strains or species can be the parts of a community, or we could study only the chemical reactions as the parts of metabolism (and forgetting about the enzymes that catalyze them), as is done in flux balance analysis. As long as we have some understanding of the properties of these parts, we can investigate whether their interaction leads to novel or unanticipated behaviour of the system that they constitute.There has been a tendency in the Systems Biology community to think that the collection and integration of data should continue ad infinitum, or that we will otherwise not be able to understand the systems that we study in their details. However, it may sometimes be useful to take a step back and consider whether the knowledge that we already have may not explain the system behaviour that we find so intriguing. Reasoning about systems can be difficult, and may require the application of mathematical techniques. The reward is sometimes the realization of unexpected conclusions, or in the worst case, that we still do not know enough details of the parts, or of the interactions between them.We will discuss a number of cases, with a focus on LAB-related work, where a typical systems approach has brought new knowledge or perspective, often counterintuitive, and clashing with conclusions from simpler approaches. Also novel types of testable hypotheses may be generated by the systems approach, which we will illustrate. Finally we will give an outlook on the fields of research where the systems approach may point the way for the near future.

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Inhibition kinetics of catabolic dehydrogenases by elevated moieties of ATP and ADP – implication for a new regulation mechanism in Lactococcus lactis

Cited by 13 publications

References 36 publications

Mechanisms of heparanase inhibition by the heparan sulfate mimetic PG545 and three structural analogues

Mechanisms of heparanase inhibition by the heparan sulfate mimetic PG545 and three structural analogues

Tracing regulatory routes in metabolism using generalised supply-demand analysis

Systems biology of lactic acid bacteria: a critical review

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