Thermodynamics of Bioreactions

Held, Christoph; Sadowski, Gabriele

doi:10.1146/annurev-chembioeng-080615-034704

Cited by 46 publications

(25 citation statements)

References 117 publications

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“…Once the reaction constants K a M and K th are known, the effects of cosolutes on the experimental quantities K x and K m M can be predicted quantitatively,i ft he activity coefficients in the multi-component solutionsa re accounted for.I ns everal recent works, this has been successfully shown. [275,[308][309][310][311][312] These works also proved that neglecting activity coefficients or using poor models for activity coefficients fails to predict the kinetics and equilibrium of enzymatic reactions.…”

Section: Effect Of Cosolvents On Enzymatic Reactions and The Importanmentioning

confidence: 89%

“…In contrast, the apparent quantities K x and K m M are concentration-dependent. Considering enzymatic reactions, many studies exist that show how the concentration influences the reaction equilibrium [274][275][276][277][278] and the reaction kinetics. [100,[279][280][281][282][283] At first glance, this might be unexpected given the fact that concentrationso fr e-acting agentso fe nzymatic reactions are usually lower than a few mm.H owever,c osolutes might be present at much higher concentrations.…”

Section: Effect Of Cosolvents On Enzymatic Reactions and The Importanmentioning

confidence: 99%

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Crowders and Cosolvents—Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses

et al. 2017

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The free energy and conformational landscape of biomolecular systems as well as biochemical reactions depend not only on temperature and pressure, but also on the particular solution conditions. Such conditions include the effects of cosolvents (for example osmolytes) and macromolecular crowding, which are crucial components to understand the energetics and kinetics of biological processes in living system. Such conditions are also important for the understanding of many debilitating diseases, such as those where misfolding and amyloid formation of proteins are involved. Moreover, understanding their effects on biomolecular processes is prerequisite for designing industrially relevant enzymatic reactions, which seldom take place under neat conditions. Here, we review and discuss experimental and theoretical studies on the characterization of cosolvent and crowding induced effects in biologically relevant systems, approaching even the complexity of living organisms. In particular, we focus on cosolvent and crowding effects on the conformational equilibrium and folding kinetics of proteins and nucleic acids as well as on enzymatic reactions, including their effects on the temperature and pressure dependence of these processes. By presenting a few representative examples, we show how such effects are unveiled and described in thermodynamic and kinetic terms.

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Section: Effect Of Cosolvents On Enzymatic Reactions and The Importanmentioning

confidence: 89%

Section: Effect Of Cosolvents On Enzymatic Reactions and The Importanmentioning

confidence: 99%

Crowders and Cosolvents—Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses

et al. 2017

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“…Outside chemical engineering, applications of thermodynamic models to predict chemical potentials of biological reactions are rare and can be found mostly in the pharmaceutical and the agrochemical areas (Klamt et al, 2002;Klamt et al, 2003;Klamt, 2005). A summary of the possible approaches can be found in (Held and Sadowski, 2016). Their application for the prediction of the activity coefficients of probe molecules in food is even more rare.…”

Section: Chemical Potentialmentioning

confidence: 99%

Modeling food matrix effects on chemical reactivity: Challenges and perspectives

Capuano

Oliviero

Boekel

2017

Critical Reviews in Food Science and Nutrition

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The same chemical reaction may be different in terms of its position of the equilibrium (i.e., thermodynamics) and its kinetics when studied in different foods. The diversity in the chemical composition of food and in its structural organization at macro-, meso-, and microscopic levels, that is, the food matrix, is responsible for this difference. In this viewpoint paper, the multiple, and interconnected ways the food matrix can affect chemical reactivity are summarized. Moreover, mechanistic and empirical approaches to explain and predict the effect of food matrix on chemical reactivity are described. Mechanistic models aim to quantify the effect of food matrix based on a detailed understanding of the chemical and physical phenomena occurring in food. Their applicability is limited at the moment to very simple food systems. Empirical modeling based on machine learning combined with data-mining techniques may represent an alternative, useful option to predict the effect of the food matrix on chemical reactivity and to identify chemical and physical properties to be further tested. In such a way the mechanistic understanding of the effect of the food matrix on chemical reactions can be improved.

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“…A change in Gibbs free energy (∆G), an indicator of the direction of chemical reactions, is dependent on the temperature and molar ratio of the reactants and products. A negative value of ∆G means that the reaction proceeds spontaneously [4]. Most phosphodiester hydrolysis reactions have negative ∆G values, which means that the dissociation of phosphate is prone to occur [5].…”

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confidence: 99%

Phosphorylation Dynamics of JNK Signaling: Effects of Dual-Specificity Phosphatases (DUSPs) on the JNK Pathway

Kang

Seo

et al. 2019

IJMS

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Protein phosphorylation affects conformational change, interaction, catalytic activity, and subcellular localization of proteins. Because the post-modification of proteins regulates diverse cellular signaling pathways, the precise control of phosphorylation states is essential for maintaining cellular homeostasis. Kinases function as phosphorylating enzymes, and phosphatases dephosphorylate their target substrates, typically in a much shorter time. The c-Jun N-terminal kinase (JNK) signaling pathway, a mitogen-activated protein kinase pathway, is regulated by a cascade of kinases and in turn regulates other physiological processes, such as cell differentiation, apoptosis, neuronal functions, and embryonic development. However, the activation of the JNK pathway is also implicated in human pathologies such as cancer, neurodegenerative diseases, and inflammatory diseases. Therefore, the proper balance between activation and inactivation of the JNK pathway needs to be tightly regulated. Dual specificity phosphatases (DUSPs) regulate the magnitude and duration of signal transduction of the JNK pathway by dephosphorylating their substrates. In this review, we will discuss the dynamics of phosphorylation/dephosphorylation, the mechanism of JNK pathway regulation by DUSPs, and the new possibilities of targeting DUSPs in JNK-related diseases elucidated in recent studies.

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Thermodynamics of Bioreactions

Cited by 46 publications

References 117 publications

Crowders and Cosolvents—Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses

Crowders and Cosolvents—Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses

Modeling food matrix effects on chemical reactivity: Challenges and perspectives

Phosphorylation Dynamics of JNK Signaling: Effects of Dual-Specificity Phosphatases (DUSPs) on the JNK Pathway

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