An investigation of the relationships between rate and driving force in simple uncatalysed and enzyme-catalysed reactions with applications of the findings to chemiosmotic reactions

Role of APS reductase in biogeochemical sulfur isotope fractionation

Sulfur isotope fractionation resulting from microbial sulfate reduction (MSR) provides some of the earliest evidence of life, and secular variations in fractionation values reflect changes in biogeochemical cycles. Here we determine the sulfur isotope effect of the enzyme adenosine phosphosulfate reductase (Apr), which is present in all known organisms conducting MSR and catalyzes the first reductive step in the pathway and reinterpret the sedimentary sulfur isotope record over geological time. Small fractionations may be attributed to low sulfate concentrations and/or high respiration rates, whereas fractionations greater than that of Apr require a low chemical potential at that metabolic step. Since Archean sediments lack fractionation exceeding the Apr value of 20‰, they are indicative of sulfate reducers having had access to ample electron donors to drive their metabolisms. Large fractionations in post-Archean sediments are congruent with a decline of favorable electron donors as aerobic and other high potential metabolic competitors evolved.

Control of hydrogen partial pressures on the rates of syntrophic microbial metabolisms: a kinetic model for butyrate fermentation

A new model describing the rate of syntrophic butyrate fermentation is constructed based on a thermodynamically consistent rate law and the metabolic pathway. This model takes into account the mechanism of reverse electron transfer and proposes that the net amount of energy saved by microorganisms as ATP depends on hydrogen partial pressures in the environment. Hydrogen partial pressures thus control not only the energy available in the environment but also the energy conserved by microorganisms. This new model predicts the rates of butyrate fermentation as a product of a kinetic factor and a thermodynamic potential factor: the kinetic factor describes how butyrate concentration controls the rates; the thermodynamic factor accounts for how the thermodynamic driving force controls the rates. Increases in hydrogen partial pressures decrease the energy available, lowering the driving force and fermentation rates. To maintain butyrate fermentation at significant rates, microorganisms decrease the amount of energy conserved, maximizing the driving force. Application of the new model demonstrates that the thermodynamic driving force is a dominant factor in controlling the rates of butyrate fermentation.

Kinetics of syntrophic cultures: a theoretical treatise on butyrate fermentation

Numerous microbial conversions in methanogenic environments proceed at (Gibbs) free energy changes close to thermodynamic equilibrium. In this paper we attempt to describe the consequences of this thermodynamic boundary condition on the kinetics of anaerobic conversions in methanogenic environments. The anaerobic fermentation of butyrate is used as an example. Based on a simple metabolic network stoichiometry, the free energy change based balances in the cell, and the flux of substrates and products in the catabolic and anabolic reactions are coupled. In butyrate oxidation, a mechanism of ATP-dependent reversed electron transfer has been proposed to drive the unfavorable oxidation of butyryl-CoA to crotonyl-CoA. A major assumption in our model is that ATP-consumption and electron translocation across the cytoplasmic membrane do not proceed according to a fixed stoichiometry, but depend on the cellular concentration ratio of ATP and ADP. The energetic and kinetic impact of product inhibition by acetate and hydrogen are described. A major consequence of the derived model is that Monod-based kinetic description of this type of conversions is not feasible, because substrate conversion and biomass growth are proposed to be uncoupled. It furthermore suggests that the specific substrate conversion rate cannot be described as a single function of the driving force of the catabolic reaction but depends on the actual substrate and product concentrations. By using nonfixed stoichiometries for the membrane associated processes, the required flexibility of anaerobic bacteria to adapt to varying environmental conditions can be described.

Quasi-linear relationship between Gibbs free energy of ATP hydrolysis and power output in human forearm muscle

The postulated strictly linear descriptions of the rate dependence of oxidative phosphorylation in skeletal muscle on the free energy of ATP hydrolysis (delta GP) over the range of physiological steady states fail to harmonize with reported findings of identical basal respiration rates in mammalian muscles at different delta GP values. The relevance of an extension of the strictly linear description to a description deriving from enzyme kinetics that predicts a sigmoidal dependence was investigated in human finger flexor muscle using 31P-nuclear magnetic resonance spectroscopy. At constant pH 7.0, the experimental variation of adenine nucleotide concentrations with power output, which reflects the rate of oxidative phosphorylation, was compared with predictions by various formulations of adenine nucleotide control of respiration. The quasi-linear sigmoidal description was found to be statistically equivalent but physiologically superior to the strictly linear description. The predicted maximal oxidatively sustained steady-state power output and rate-dependent sensitivity of respiration to changes in delta GP were in agreement both with theoretical considerations and with experimental observations in the present study and other studies of intact mammalian skeletal muscle.

On the expected relationship between Gibbs energy of ATP hydrolysis and muscle performance

Allowing for creatine kinase buffering of changes in adenine nucleotide concentrations, and the known relationship between muscle performance and rate of ATP hydrolysis by myosin, the variation of exerted force with intracellular Gibbs energy of ATP hydrolysis is calculated for voluntary muscle contraction. The resulting relationship is sigmoidal, most of the operating range coinciding with the quasi-linear range around the inflection point. Finger-flexor muscle magnetic resonance spectroscopy data are shown to be in line with this prediction.

Quantitative determination of the steady-state kinetics of multienzyme reactions using the algebraic rate equations for the component single-enzyme reactions

Methods are given whereby the steady-state kinetic characteristics of multienzyme reactions consisting of individual single-enzyme reactions linked by freely diffusible intermediates can be determined quantitatively from the experimentally determined complete algebraic rate equations for the individual reactions. The approach is based on the fact that a valid steady-state rate equation for such a multienzyme reaction, in terms of the rate equations for the individual reactions, can be obtained simply from knowledge of the relative rates of the individual reactions when the multienzyme reaction is in the steady state. A number of model multienzyme reactions, which differ as to structural arrangement of the individual reactions, are examined by this approach. Simple mathematical methods which are applicable to most of these models are given for direct calculation of dependent variables. It is either pointed out or demonstrated with Mathematica that the rate equations for all of these models can be handled very easily with the aid of a personal computer equipped with appropriate equation-solving software. Since the approach permits evaluation of all dependent variables for any specific combination of values for the kinetic parameters and independent variables, numerical values for the flux control coefficients of the individual enzymes can be obtained by direct calculation for a wide variety of conditions and can be compared with those obtained according to the methods of Metabolic Control Analysis. Several such comparisons have been made and in all cases identical results were obtained. The intuitive notion that the individual enzymes of a multienzyme reaction would be equally rate limiting if the total amount of enzyme were being used with maximum efficiency is tested and shown to be incorrect. In the course of this test the flux control coefficient for the individual enzymes were found to be appropriate indicators of relative rate limitation or control by the enzymes and to account properly for differences in specific activity among the enzymes.