scholarly journals The SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration

2017 ◽  
Author(s):  
Jinyun Tang ◽  
William J. Riley
Keyword(s):  
Soil Respiration ◽  
Redox Reactions ◽  
Reaction Rates ◽  
Generation Rate ◽  
Simple Problem ◽  
Multiple Substrates ◽  
Substrate Limitation ◽  
Product Generation ◽  
Consumer Relationships ◽  
Aerobic Soil

Abstract. Several land biogeochemical models used for studying carbon-climate feedbacks have begun explicitly representing microbial processes. However, to our knowledge, there has been no theoretical work on how to achieve a consistent scaling of the complex biogeochemical reactions from microbial individuals to populations, communities, and interactions with plants and mineral soils. We here study this scaling problem by focusing on the substrate-consumer relationships for consumer mediated redox reactions of the form A + B     E → products, where products could be microbial biomass and different bio-products. Under the quasi-steady-state approximation, these substrate-consumer relationships can be formulated as the computationally difficult full Equilibrium Chemistry problem, which is then usually approximated analytically with the popular Dual Monod (DM) kinetics and Synthesizing Unit (SU) kinetics. However, we found that the DM kinetics is scaling inconsistent for reaction networks because it (1) does not incorporate substrate limitation in its derivation, (2) invokes contradictory assumptions regarding the substrate processing rate when transitioning from single substrate reactions to two-substrate redox reactions, and (3) cannot scale the product generation rate from one to multiple substrates. In contrast, the SU kinetics can consistently scale the product generation rate from one to multiple substrates, but suffers from the deficit that as the consumer abundance approaches infinity, it predicts singular infinite reaction rates even for limited substrates. We attribute this deficit to SU’s failure to incorporate the substrate limitation in its derivation and remedy SU with the proposed SUPECA (SU Plus Equilibrium Chemistry Approximation) kinetics, which consistently imposes the mass balance constraints from both substrates and consumers on consumer-substrate interactions in calculating redox reaction rates. Moreover, we show the SUPECA kinetics satisfies the partition principle as in theories like Newton's Law of motion and Dalton’s law of partial pressures, such that its mathematical manifestation is scaling invariant when transitioning from an individual reaction to a network of many reactions. We benchmarked the SUPECA kinetics with the equilibrium chemistry solution for some simple problem configurations and found SUPECA outperformed the SU kinetics. In applying the SUPECA kinetics to aerobic soil respiration, we found SUPECA predicted consistent but variable moisture response functions that agreed well to those derived from incubation data. We finally discuss how the SUPECA kinetics could help Earth System Models consistently incorporate more biogeochemical reactions to improve their biogeochemical modules.

scholarly journals SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration

2017 ◽  
Vol 10 (9) ◽  
pp. 3277-3295 ◽  
Author(s):  
Jin-Yun Tang ◽  
William J. Riley
Keyword(s):  
Steady State ◽  
Soil Respiration ◽  
Redox Reactions ◽  
Generation Rate ◽  
Mathematical Representation ◽  
Multiple Substrates ◽  
Biogeochemical Models ◽  
Product Generation ◽  
Consumer Relationships ◽  
Aerobic Soil

Abstract. Several land biogeochemical models used for studying carbon–climate feedbacks have begun explicitly representing microbial dynamics. However, to our knowledge, there has been no theoretical work on how to achieve a consistent scaling of the complex biogeochemical reactions from microbial individuals to populations, communities, and interactions with plants and mineral soils. We focus here on developing a mathematical formulation of the substrate–consumer relationships for consumer-mediated redox reactions of the form A + BE→  products, where products could be, e.g., microbial biomass or bioproducts. Under the quasi-steady-state approximation, these substrate–consumer relationships can be formulated as the computationally difficult full equilibrium chemistry problem or approximated analytically with the dual Monod (DM) or synthesizing unit (SU) kinetics. We find that DM kinetics is scaling inconsistently for reaction networks because (1) substrate limitations are not considered, (2) contradictory assumptions are made regarding the substrate processing rate when transitioning from single- to multi-substrate redox reactions, and (3) the product generation rate cannot be scaled from one to multiple substrates. In contrast, SU kinetics consistently scales the product generation rate from one to multiple substrates but predicts unrealistic results as consumer abundances reach large values with respect to their substrates. We attribute this deficit to SU's failure to incorporate substrate limitation in its derivation. To address these issues, we propose SUPECA (SU plus the equilibrium chemistry approximation – ECA) kinetics, which consistently imposes substrate and consumer mass balance constraints. We show that SUPECA kinetics satisfies the partition principle, i.e., scaling invariance across a network of an arbitrary number of reactions (e.g., as in Newton's law of motion and Dalton's law of partial pressures). We tested SUPECA kinetics with the equilibrium chemistry solution for some simple problems and found SUPECA outperformed SU kinetics. As an example application, we show that a steady-state SUPECA-based approach predicted an aerobic soil respiration moisture response function that agreed well with laboratory observations. We conclude that, as an extension to SU and ECA kinetics, SUPECA provides a robust mathematical representation of complex soil substrate–consumer interactions and can be applied to improve Earth system model (ESM) land models.

scholarly journals Fine-Tuning of Sequence Specificity by Near Attack Conformations in Enzyme-Catalyzed Peptide Hydrolysis

Catalysts ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 684
Author(s):  
S. Kashif Sadiq
Keyword(s):  
Cleavage Site ◽  
Catalytic Effect ◽  
Reaction Rates ◽  
Fine Tuning ◽  
Sequence Specificity ◽  
Peptide Hydrolysis ◽  
Multiple Substrates ◽  
Uncatalyzed Reaction ◽  
Hiv 1

The catalytic role of near attack conformations (NACs), molecular states that lie on the pathway between the ground state (GS) and transition state (TS) of a chemical reaction, is not understood completely. Using a computational approach that combines Bürgi–Dunitz theory with all-atom molecular dynamics simulations, the role of NACs in catalyzing the first stages of HIV-1 protease peptide hydrolysis was previously investigated using a substrate that represents the recognized SP1-NC cleavage site of the HIV-1 Gag polyprotein. NACs were found to confer no catalytic effect over the uncatalyzed reaction there ( Δ Δ G N ‡ ∼ 0 kcal/mol). Here, using the same approach, the role of NACs across multiple substrates that each represent a further recognized cleavage site is investigated. Overall rate enhancement varies by | Δ Δ G ‡ | ∼ 12–15 kcal/mol across this set, and although NACs contribute a small and approximately constant barrier to the uncatalyzed reaction (< Δ G N ‡ u > = 4.3 ± 0.3 kcal/mol), they are found to contribute little significant catalytic effect ( | Δ Δ G N ‡ | ∼ 0–2 kcal/mol). Furthermore, no correlation is exhibited between NAC contributions and the overall energy barrier ( R 2 = 0.01). However, these small differences in catalyzed NAC contributions enable rates to match those required for the kinetic order of processing. Therefore, NACs may offer an alternative and subtle mode compared to non-NAC contributions for fine-tuning reaction rates during complex evolutionary sequence selection processes—in this case across cleavable polyproteins whose constituents exhibit multiple functions during the virus life-cycle.

scholarly journals Lignin reinforcement of urea-crosslinked starch films for reduction of starch biodegradability to improve slow nitrogen release properties under natural aerobic soil condition

e-Polymers ◽  
2016 ◽  
Vol 16 (2) ◽  
pp. 159-170 ◽  
Author(s):  
Zahid Majeed ◽  
Nurlidia Mansor ◽  
Zakaria Man ◽  
Samsuri Abd Wahid
Keyword(s):  
Diffusion Mechanism ◽  
Composite Films ◽  
Soil Condition ◽  
Reaction Rates ◽  
Order Reaction ◽  
Fickian Diffusion ◽  
Major Drawback ◽  
Study Results ◽  
Zero Order Reaction ◽  
Aerobic Soil

AbstractThe urea-crosslinked starch (UcS) film has a major drawback of very rapid biodegradability when applied as slow release fertilizer in soil. Lignin reinforcement of the UcS was used to prepare composite films, aimed to reduce the starch biodegradability and slow the release of nitrogen in aerobic soil condition. Study results revealed that mineralization of the composite films was delayed from 6.40 to 13.58% more than UcS film. Inhibition of composite films mixing with soil, the Michaelis-Menten reaction rates for α-amylase were inhibited ~1.72–2.03 times whereas the Michaelis-Menten reaction rates for manganese peroxidase were increased ~1.07–1.41 times compared to UcS film. Saccharides–glucose, maltose and maltotriose demonstrated that their rates of formation (zero-order reaction) and depletion (first-order reaction); both were slowed more in aerobic soil which received the composite films. Increasing of lignin in composite films, the acid to aldehyde ratios of vanillyl and syringyl phenols of the lignin declined from 1.18 to 1.17 (~0.76%) and 1.59–1.56 (~1.78%), respectively. The diffusivity of nitrogen was effectively slowed 0.66–0.94 times by the lignin in composite films and showed a “Fickian diffusion” mechanism (release exponent n=0.095–0.143).

scholarly journals The Wnt pathway scaffold protein Axin promotes signaling specificity by suppressing competing kinase reactions

2019 ◽  
Author(s):  
Maire Gavagan ◽  
Erin Fagnan ◽  
Elizabeth B. Speltz ◽  
Jesse G. Zalatan
Keyword(s):  
Wnt Signaling ◽  
Wnt Pathway ◽  
Rate Increase ◽  
Reaction Rates ◽  
Scaffold Protein ◽  
Protein Targets ◽  
Signaling Specificity ◽  
Inactive State ◽  
Multiple Substrates ◽  
Reconstituted System

AbstractGSK3β is a multifunctional kinase that phosphorylates β-catenin in the Wnt signaling network and also acts on other protein targets in response to distinct cellular signals. To test the long-standing hypothesis that the scaffold protein Axin specifically accelerates β-catenin phosphorylation, we measured GSK3β reaction rates with multiple substrates in a minimal, biochemically-reconstituted system. We observed an unexpectedly small, ~2-fold Axin-mediated rate increase for the β-catenin reaction. The much larger effects reported previously may have arisen because Axin can rescue GSK3β from an inactive state that occurs only under highly specific conditions. Surprisingly, Axin significantly slows the reaction of GSK3β with CREB, a non-Wnt pathway substrate. When both β-catenin and CREB are present, Axin accelerates the β-catenin reaction by preventing competition with CREB. Thus, while Axin alone does not markedly accelerate the β-catenin reaction, in physiological settings where multiple GSK3β substrates are present, Axin can promote signaling specificity by suppressing interactions with competing, non-Wnt pathway targets.

scholarly journals Quantitative Model of the Formation Mechanism of the Rollfront Uranium Deposits

2018 ◽  
Vol 20 (3) ◽  
pp. 213
Author(s):  
D.Y. Aizhulov ◽  
N.M. Shayakhmetov ◽  
A. Kaltayev
Keyword(s):  
Reactive Transport ◽  
Redox Reactions ◽  
Reaction Rates ◽  
Quantitative Model ◽  
Production Costs ◽  
Reactive Flow ◽  
Uranium Deposits ◽  
Geological Processes ◽  
Exploration And Production ◽  
Favorable Conditions

The rollfront type deposits are crescent shaped accumulation of mineralization including uranium, selenium, molybdenum in reduced permeable sandstones. It generally forms within a geochemical barrier between mostly reduced and predominantly oxidized environments. Redox reactions between oxidant and reductant creates favorable conditions for uranium precipitation, while constant flow of oxidant continuously dissolves uranium minerals thereby creating a reactive transport. Several previous works had either focused on the characteristics of the rollfront type deposits, or on the description of chemical and geological processes involved in their genesis. Based on these previous works, authors aimed to mimic laboratory experiments numerically by reactive flow and numerical simulation. Data from one particular experiment was used to determine reaction rates between reactants to produce a model of reactive transport and chemical processes involved in the formation of rollfront type deposits. The resulting model was used to identify the causes of crescent like formations and to determine main mechanisms influencing rollfront evolution. A better understanding and simulation of the mechanism involved in the formation of rollfront type deposits and their properties would contribute to decreased exploration and production costs of commodities trapped within such accumulations. The results of this work can be used to model other deposits formed through infiltration and subsequent precipitation of various minerals at the redox interface.

Plasma Coagulation on Microparticles Is Modulated by Water Activity. Relevance to Inflammation-Mediated Disruption of the Extracellular Matrix.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4048-4048
Author(s):  
Maria P. McGee ◽  
Lynne Li ◽  
Jorge Ollero
Keyword(s):  
Extracellular Matrix ◽  
Water Activity ◽  
Reaction Rates ◽  
Generation Rate ◽  
Limiting Factor ◽  
Plasma Extravasation ◽  
Factor X ◽  
In Vivo Models ◽  
Sorption Ability

Abstract The microenvironment of extravascular spaces influences the reactivities of extravasated plasma proteins. During inflammation, the structural and physicochemical characteristics of peri- and extra-vascular spaces can change widely depending on the severity of extracellular matrix disruption. Plasma extravasation after limited vascular injury results in transient changes in water activity (aw) and fibrin deposition. This work investigates whether changes in aw influence either pro- or anticoagulant pathways assembled on procoagulant microparticles. Based on conclusions from in vivo models indicating that factor Xa (fXa) concentration is the limiting factor in prothrombinase assembly we modeled the extravascular coagulation process in vitro, using plasma as the matrix; controlling aw as the independent variable; and measuring the fXa generation rate as the dependent variable. Initial rates of fXa generation were measured in human plasma (1/100 final dilution) containing procoagulant particles and 200 nM factor X. Water activity levels decreased from 0 to 0.8 atm relative to isosmolar plasma (~7 atm) with polyethylene glycol 8000 (~26 Å radius), while all reactant concentrations remained constant. Procoagulant particles were either recombinant tissue factor (TF) in PC/PS vesicles (at a mol ratio of 1/2666) or microvesicles collected from the monocytoid cell line THP-1 after 24-hour stimulation with endotoxin (1ug/ml). As the reaction environment’s aw progressively decreased, fXa generation rate first increased, and then decreased. Rate/aw profiles followed nearly symmetrical peaks with a maximum at ~0.2 atm and minimum at ~0.7 atm. Similar profiles were obtained with cell-derived procoagulant microvesicles. At each aw level, the fXa generation rate increased exponentially with TF concentration (25–100 pM). Activation and inhibition indices of ~1.5 and ~2.1, calculated as the ratio between the maximal and baseline and the maximal and minimal rates did not change significantly with TF concentration. Rates increased with added factor VIII (~2 units/ml) indicating fIX activation and a contribution of the intrinsic pathway protease to fXa generation. Furthermore, reaction rates changed with hirudin suggesting that thrombin-mediated regulatory loops also affect the rate profiles. Results in this simple model of extravascular coagulation indicate that aw modulates the rate of coagulation reactions stimulating or inhibiting them depending on whether the reaction environment’s aw is high or low. This conclusion in turn predicts that immediately after limited plasma extravasation coagulation rates accelerate with the decrease in aw as it tend to equilibrate with aw in the extravascular spaces. Continued water adsorption by an intact extracellular matrix would equilibrate aw and decrease coagulation rates. However, in a structurally damaged matrix with compromised water sorption ability, rates may remain longer at the higher level.

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