Calculation of the heat of growth of Escherichia coli K-12 on succinic acid

Using data from the literature, a method is adopted for determining the empirical composition and the unit carbon formula for dried Escherichia coli K-12 cells by summing the quantities of C, H, O, N, P, and S in each of the major classes of macromolecular substances comprising the cellular biomass. With these data and the molar growth yield of cells on succinic acid, equations are written representing the anabolism and catabolism of E. coli K-12 on this quantity of substrate. The enthalpy change accompanying catabolism can be calculated directly using standard enthalpies of formation because there is no term representing cellular substance. The enthalpy change accompanying anabolism is calculated to be very small or zero using microcalorimetric and other data from which the enthalpy of formation of a unit quantity of living cellular substance can be obtained. This indicates that the net enthalpy change accompanying the growth process (anabolism plus catabolism) is the same as that calculated for catabolism alone, in agreement with the same conclusion by several investigators using direct microcalorimetry. The method described here of determining the unit carbon formula and the quantity of ash remaining after cellular combustion is compared to that conventionally used in which cellular P and S is considered either to be negligible or to be a part of the ash. It is concluded that equations representing anabolism and the growth process can be written more accurately using the presently described method, leading to more accurate thermodynamic calculations.     

Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations

We have analyzed the effect of cavity-filling mutations on protein stability by means of free-energy calculations based on molecular dynamics simulations to identify the factors contributing to stability changes caused by the mutations. We have studied the DNA-binding domain of Myb, which has a cavity in one of three homologous repeat units, and analyzed a series of mutations with nonnatural and natural amino acids at a single site, which change the size of the cavity. We found that the calculated free-energy changes caused by the mutations are in excellent agreement with experimental data (correlation coefficient 0.98). The free-energy changes in the native and denatured states were independently compared with the unfolding free-energy change (deltadeltaG) and cavity-volume changes (deltaV), and it was found that deltadeltaG and deltaV correlate with the native-state free-energy changes but not with the denatured-state free-energy changes. Further analyses in terms of enthalpy and entropy show that compensation between entropy and enthalpy occurs in the denatured state but not in the native state. The main contribution to the native-state free energy was found to be van der Waals interactions associated with the cavity. We estimate that the decrease in free energy per methylene group, which results from filling the cavity, is about 2 to 3 kcal/mol. These results suggest that the stabilization of a protein by cavity-filling mutations be determined primarily by the free energy associated with the cavity volume in the native state.     

Oscillations and efficiency in glycolysis

We suggest that temporal oscillations of concentrations of intermediates in biochemical reaction systems may enhance the efficiency of free energy conversion (reduce dissipation) in those reactions. Experiments on glycolysis are used to estimate the Gibbs free energy changes along the glycolysis mechanism, and to postulate a construct for the glycolysis "machine" which involves: the PFK reaction as the primary oscillophor; the GAPDH reaction as a phase-shifting device; and the PK reaction with the property of intrinsic oscillatory response at resonance with the driving frequency. Analysis of a simple reaction mechanism with these postulated properties shows that the conversion of free energy from reactants to products is more efficient in an oscillatory than a steady state operation. The efficiency of free energy conversion in glycolysis from glucose + ADP to products + ATP is estimated to be increased by 5--10% due to oscillations. This may have been relevant for the evolutionary development of oscillations such as in glycolysis, especially in anaerobic cells.     

Some problems in the usage of Gibbs free energy in biochemistry

The usage of Gibbs free energy (G) in biochemistry is examined critically. The textbook formulation of the Second Law of Thermodynamics as applied to chemically-reacting systems is reviewed. Cognizance of the established theory and terminology of chemical thermodynamics leads to the conclusion that the symbol "delta G", as used in most biochemical calculations of free-energy change (e.g. in freeze-clamp study of steady-state metabolic processes), is erroneous. The instantaneous change, symbolized by the expression (delta G/delta xi) (with xi the degree of advancement of the reaction), is seen to be the correct form for describing the thermodynamic quality of the reactions of cell metabolism. Mathematical and graphical analysis of a sample reaction demonstrates the fundamental difference between delta G and (delta G/delta xi). Some problems in the application and interpretation of free-energy change in biochemical systems are reviewed: (1) Advances in protein dynamics have revealed the free-energy linkage properties of the enzyme molecule in binding/catalytic events of catalysis, demanding that we view the thermodynamics of elementary enzyme reactions with a finer eye. (2) The reality of metabolic microenvironments in vivo leads to equivocation in the significance of free-energy changes measured under macroscopic conditions in vitro. (3) The physicochemical character of reaction dynamics in the living cell may in some cases exceed the domain of validity of such thermodynamic state functions as Gibbs free energy.     

Kinetic studies on human lactate dehydrogenase isoenzyme-catalyzed lactate-to-pyruvate reaction

In order to evaluate the functional differences that may exist in human lactate dehydrogenase (LDH) isoenzymes widely used for clinical examination the kinetic and thermodynamic properties of the lactate to pyruvate reaction that they catalize were examined. Small but significant differences in the kinetic properties of the three isoenzymes were observed. The difference in the rate constants might affect the activity measurement of the individual isoenzyme as the initial velocity for the L-P reaction catalyzed will not be the same for an equal amount of enzyme. Equilibrium constants for the overall reaction in the presence and absence of pyruvate have been determined. On the basis of transition-state theory, the standard enthalpy and free-energy changes for formation of ternary activated complex were positive, while the standard entropy change was negative. Although the standard free-energy change was the same for activation by the three isoenzymes, the enthalpy and entropy changes for the LDH-3-catalyzed reaction were different from the respective values for others. A large positive value for the free-energy change and a negative value for the entropy change indicated unfavorable production of the activated complex (K _infeq. ^sup╪ =1.89×10^-16). The enzyme appears to stabilize and retain the activated complex until it dissociates into the products.     

An alternate method of calculating the heat of growth of Escherichia coli K-12 on succinic acid

The DeltaH(f) (0) unit weight of a complex substance such as a biological macromolecule is almost always obtained by means of combustion analysis. In theory, this can also be done by summing the DeltaH(f) (0) values for the monomers comprising the macromolecule plus the enthalpic energies involved in their polymerization. The enthalpy of formation of one unit-carbon formula weight of dried Escherichia coli K-12 cells was determined by summing the values of the enthalpies of formation of the quantities of monomers in the major classes of macromolecules substances comprising the cellular biomass and the enthalpic energies involved in their polymerizations. To this value was added the enthalpy of formation of the cellular ions in their aqueous standard states, per unit-carbon formula weight of cellular substance and the enthalpy change with respect to the ionization of the protein amino acid side chains. If it is assumed that the cellular fabric is insoluble and that the ions are soluble, the sum of the enthalpies of formation of all the cellular components should closely approximate the enthalpy of formation of one unit-carbon formula weight equivalent of living cells. Using this value, a calculation of the enthalpy change accompanying anabolism shows this latter to be effectively zero, indicating that the heat of growth (anabolism plus catabolism) is equal to that calculated for catabolism alone. This conclusion is in accord with those of several investigators who have used manometry or direct calorimetry.     

Sucrose utilization by Zymomonas mobilis: formation of a levan

1. Molar growth-yield coefficients of Zymomonas mobilis for glucose, fructose, glucose plus fructose, and sucrose are reported. Yield coefficients for sucrose are appreciably lower than those for the equivalent concentrations of glucose plus fructose. 2. Only 2.6% of [U-(14)C]glucose supplied in the growth medium is incorporated into cell substance by Z. mobilis utilizing glucose as the energy source. 3. During growth on sucrose a levan is formed. It has been characterized and shown to resemble other bacterial levans. 4. Levan formation from sucrose could be demonstrated with both washed cell suspensions and cell extracts of Z. mobilis. 5. Sucrose phosphorylase could not be demonstrated in extracts of the organism.     

Thermodynamics of the control of metabolism

A theory is presented, describing the control analysis of metabolic systems in terms of Gibbs free energies, extending earlier work of Kacser and Burns (25), and Heinrich and Rapoport (29). It is shown that relationships exist between flux control coefficients (the degree to which enzymes control steady-state fluxes) and free-energy elasticity coefficients, defined as the fractional change in the rate of a reaction induced by a standard change in one free-energy difference, while all the other free-energy differences are kept constant. Application of this extended control analysis to some biochemical reactions, including proton translocation, demonstrates that

1. Problems arising in the control analysis because of conservation (sum concentration of substrate and product constant) can be circumvented.
2. Although free-energy elasticity coefficients are maximal when the reaction is close to equilibrium, they can also be significant when the reaction is not close to equilibrium.
3. Problems in the control analysis caused by compartmentation can be resolved by defining control parameters that refer to the organelle as a whole.
4. These latter control parameters obey the above-mentioned relationships.

     

Fluorescence energy transfer between the primer and the beta subunit of the DNA polymerase III holoenzyme.

We report here our initial success in using fluorescence energy transfer to map the position of the subunits of the DNA polymerase III holoenzyme within initiation complexes formed on primed DNA. Using primers containing a fluorescent derivative 3 nucleotides from the 3'-terminus and acceptors of fluorescence energy transfer located on Cys333 of the beta subunit, a donor-acceptor distance of 65 A was measured. Coupling this distance with other information enabled us to propose a model for the positioning of beta within initiation complexes. Examination of the fluorescence properties of a labeled primer with the unlabeled beta subunit and other assemblies of DNA polymerase III holoenzyme subunits allowed us to distinguish all of the known intermediates of the holoenzyme-catalyzed reaction. Specific fluorescence changes could be assigned for primer annealing, Escherichia coli single-stranded DNA-binding protein binding, 3'----5' exonucleolytic hydrolysis of the primer, DNA polymerase III* binding, initiation complex formation upon the addition of beta in the presence of ATP, and DNA elongation. These fluorescence changes are sufficiently large to support future detailed kinetic studies. Particularly interesting was the difference in fluorescence changes accompanying initiation complex formation as compared to binding of DNA polymerase III holoenzyme subunit assemblies. Initiation complex formation resulted in a strong fluorescence enhancement. Binding of DNA polymerase III* led to a fluorescence quenching, and transfer of beta to primed DNA by the gamma delta complex did not change the fluorescence. This demonstrates a rearrangement of subunits accompanying initiation complex formation. Monitoring fluorescence changes with labeled beta, we have determined that beta binds with a stoichiometry of one monomer/primer terminus.     

Adaptation of metabolic enzyme activities of Trypanosoma brucei promastigotes to growth rate and carbon regimen.

The insect stage of Trypanosoma brucei adapted the activities of 16 metabolic enzymes to growth rate and carbon source. Cells were grown in chemostats with glucose, rate limiting or in excess, or high concentrations of proline as carbon and energy sources. At each steady state, samples were collected for measurements of substrate and end product concentrations, cellular parameters, and enzyme activities. Correlation coefficients were calculated for all parameters and used to analyze the data set. Rates of substrate consumption and end product formation increased with increasing growth rate. Acetate and succinate were the major nonvolatile end products, but measurable quantities of alanine were also produced. More acetate than succinate was formed during growth on glucose, but growth on proline yielded an equimolar ratio. Growth rate barely affected the relative amounts of end products formed. The end products accounted for the glucose consumed during glucose-limited growth and growth at high rates on excess glucose. A discrepancy, indicating production of CO2, occurred during slow growth on excess glucose and, even more pronounced, in cells growing on proline. The activities of the metabolic enzymes varied by factors of 2 to 40. There was no single enzyme that correlated with consumption of substrate and/or end product formation in all cases. A group of enzymes whose activities rigorously covaried could also not be identified. These findings indicate that T. brucei adapted the activities of each of the metabolic enzymes studied separately. The results of this complex manner of adaptation were more or less constant ratios of the end products and a very efficient energy metabolism.     

Evidence for new factors in the coordinate regulation of energy metabolism in Escherichia coli. Effects of hypoxia, chloramphenicol succinate, and 2,4-dinitrophenol on glucose utilization, glycogen synthesis, adenylate energy charge, and hexose phosphates during the first two periods of nitrogen starvation.

We studied the effects of decreased aeration, chloramphenicol succinate, and 2,4-dinitrophenol on the cellular rates of glycogen synthesis and glucose utilization and on the cellular concentrations of adenine nucleotides, glucose 6-phosphate, fructose 1,6-diphosphate, and phosphoenolpyruvate during the first two periods of nitrogen starvation of Escherichia coli W4597(K). A quantitative relationship between the changes in the rates and the accompanying changes in the hexose phosphates is demonstrated. However, the relationship for glycogen synthesis is different in different sets of metabolic conditions. We suggest that this difference reflects a change in the steady state level of a previously unknown effector of ADP-glucose synthetase (glucose 1-phosphate adenylyltransferase, EC 2.7.7.27) the rate-limiting enzyme of bacterial glycogen synthesis. We show that the properties of the hypothetical in vivo effector are consistent with the inhibitory effects of ppGpp (guanosine 3'-diphosphate 5'-diphosphate) and pppGpp (guanosine 3'-diphosphate 5'-triphosphate) on this enzyme in vitro. In addition, tetracycline, an inhibitor of the synthesis of these nucleotides, apparently prevents the change in the quantitative relationship. The relationship between glucose utilization and the hexose phosphates is altered at the transition to Period II of nitrogen starvation. We propose that this change reflects the alteration of the cellular steady state level of an unknown effector of the glucose phosphotransferase system. In contrast to the ATP-hexose phosphate system of shared regulatory effects, the specific effects of the unknown effectors allow the rates of glucose utilization and glycogen synthesis to be altered independently of each other and independently of changes in the rate of glycolysis. This independence allows a greater latitude of response for the individual pathways in more severe metabolic stress or in accommodating the metabolic changes necessary for long term survival.     

The equilibrium of the reaction catalysed by citrate oxaloacetate-lyase

1. A method of preparation and purification of citrate oxaloacetate-lyase (EC 4.1.3.6) from Aerobacter aerogenes is described. 2. The equilibrium of this reaction has been determined at pH 8·4 and 25°. It has been shown that K, i.e. [citrate³⁻]/[oxaloacetate_keto²⁻][acetate ⁻], is 3·08±0·72, but that K_app., i.e. [total citrate]/[total oxaloacetate][total acetate], is markedly affected by the initial concentrations of the reactants and magnesium. 3. The free-energy change during the cleavage of citrate has been calculated and compared with data from other sources. 4. The free energy of hydrolysis of acetyl-CoA has been evaluated from the present data. 5. A detailed knowledge of the interactions of the reactants with metal ions has been shown to be important in the calculation of the equilibrium constant and related thermodynamic functions.     

Changes in redox potentials during transitional processes in pure and mixed cultures of Escherichia coli and Serratia marcescens

There were studied transitional processes accompanying the beginning of growth under glucose addition and stopping of growth under glucose exhaustion in pure and mixed aerobic cultures of Escherichia coli and Serratia marcescens. Continued record of Eh, pH, and CO2 showed that these processes sharply differ from each other in their character in pure and mixed cultures, it is particularly related to the changes of the redox potential. There is no characteristic change in the redox potential in pure culture of E. coli at growth termination in the case when S. marcescens cells are present in the culture.     

Activation of the insulin receptor's kinase domain changes the rate-determining step of substrate phosphorylation

The insulin receptor and many other protein kinases are activated by relief of intrasteric inhibition that is regulated by reversible phosphorylation. The changes accompanying activation of the insulin receptor's kinase domain were analyzed using steady-state kinetics, viscometric analysis, and equilibrium binding measurements. Peptide phosphorylation catalyzed by the unphosphorylated basal-state kinase is limited by a slow rate of the chemical step, and the activated enzyme is limited by product release rates. Underlying these changes were a 36-fold increase in the rate constant for the chemical step of the enzyme-catalyzed reaction, a 5-fold increase in the affinity for MgATP, and an 8-fold increase in the affinity for peptide substrate. This results in binding of substrates that is 2.2 kcal/mol more favorable and a free energy barrier for transition state formation that is lowered by 2.1 kcal/mol in the activated enzyme. Therefore, the change in conformational free energy inherent in the protein after autophosphorylation [Bishop, S. M., Ross, J. B. A., and Kohanski, R. A. (1999) Biochemistry 38, 3079-3089] is equally distributed between formation of the substrate ternary complex and formation of the transition state complex.     

Resolvability of free energy changes for oxygen binding and subunit association by human hemoglobin.

Probability distributions of the free energy changes for oxygen binding, subunit association, and quaternary enhancement by human hemoglobin were obtained from Monte Carlo simulations performed on two independent sets of variable protein concentration equilibrium oxygen-binding data. Uncertainties in unliganded and fully liganded dimer to tetramer association free energy changes (0 delta G'2 and 4 delta G'2) were accounted for in the simulations. Distributions of the dimer to tetramer association free energy changes for forming singly and triply liganded tetramers (1 delta G'2 and 3 delta G'2) are well defined and quite symmetric, whereas that for forming doubly liganded tetramers (2 delta G'2) is poorly defined and highly asymmetric. The distribution of the dimer stepwise oxygen-binding free-energy change (delta g'2i) is well defined and quite symmetric as are those of the tetramer stepwise oxygen-binding free-energy changes for binding the first and last oxygens to tetramers (delta g'41 and delta g'44). Distributions of the intermediate tetramer stepwise oxygen-binding free-energy changes (delta g'42 and delta g'43) are poorly defined and highly asymmetric, but are compensatory in that their sum (delta g'4[2 + 3]) is again well defined and nearly symmetric. Distributions of the free energy changes corresponding to the tetramer product Adair oxygen binding constants (delta G'4i) are well defined and quite symmetric for i = 1, 3, 4 but not for i = 2. The distribution of delta g'44 - delta g'2i (the quaternary enhancement free energy change) is relatively narrow, nearly symmetric, and confined to the negative free-energy domain. This suggests that the quaternary enhancement free energy change (a) may be resolved with good confidence from this data and (b) is finite and negative under the conditions of these experiments. Our results also suggest two different four-state combinatorial switch models that provide accurate characterization of hemoglobin's functional behavior.     

Energy coupling in Saccharomyces cerevisiae: selected opportunities for metabolic engineering

Free-energy (ATP) conservation during product formation is crucial for the maximum product yield that can be obtained, but often overlooked in metabolic engineering strategies. Product pathways that do not yield ATP or even demand input of free energy (ATP) require an additional pathway to supply the ATP needed for product formation, cellular maintenance, and/or growth. On the other hand, product pathways with a high ATP yield may result in excess biomass formation at the expense of the product yield. This mini-review discusses the importance of the ATP yield for product formation and presents several opportunities for engineering free-energy (ATP) conservation, with a focus on sugar-based product formation by Saccharomyces cerevisiae. These engineering opportunities are not limited to the metabolic flexibility within S.?cerevisiae itself, but also expression of heterologous reactions will be taken into account. As such, the diversity in microbial sugar uptake and phosphorylation mechanisms, carboxylation reactions, product export, and the flexibility of oxidative phosphorylation via the respiratory chain and H(+) -ATP synthase can be used to increase or decrease free-energy (ATP) conservation. For product pathways with a negative, zero or too high ATP yield, analysis and metabolic engineering of the ATP yield of product formation will provide a promising strategy to increase the product yield and simplify process conditions.     

Role of Galactose or Glucose-1-Phosphate in Preventing the Lysis of Streptococcus diacetilactis

Cells of Streptococcus diacetilactis DRCI grown at 32 C in media containing glucose as the energy source were osmotically fragile and began to lyse immediately after growth was stopped (by the action of chloramphenicol or the exhaustion of glucose), unless they were then stabilized by hypertonic medium or spermine or by storage at low pH or low temperature, or both. In media containing excess glucose, with growth limited by exhaustion of some nutrient other than the energy source, the appearance of lysis was masked by the occurrence of a balance between lysis and synthesis. The osmotic fragility apparently resulted from inability of the organism to use glucose as an adequate precursor of galactosamine, and conditions of temperature and pH that promoted rapid growth on glucose were particularly conducive to the formation of cells that lysed readily. Growing the organism in media containing galactose, lactose, maltose, or glucose (at 17 C) as energy source resulted in the formation of cells that were resistant to lysis and richer in galactosamine than unstable cells formed on glucose at 32 C. The results indicate that the organism phosphorolyzes maltose to glucose plus beta-glucose-1-phosphate, and suggest that it can use the beta-glucose-1-phosphate in place of alpha-glucose-1-phosphate in the formation of cell materials.     

Membrane catalysis: synchronous multielectron reactions at the interface between two liquid phases. Bioenergetic mechanisms

Kinetics of multi-electron reactions at the interface between two immiscible liquids are considered. Calculations of the energy of solvent reorganization, of the work required to bring reactants and reaction products together, and of the electrostatic contributions to the Gibbs free energy of the reaction during electron transfer between reactants which are in different dielectric media are reported. Conditions under which the free energy of activation of the interfacial reaction of electron transfer decreases are established. The influence of the distance between reactants and of the dielectric permittivity of the non-aqueous phase on the solvent reorganization energy value is studied. Conditions under which multielectron reactions at the interface proceed are discussed. The biophysics and biochemistry of photosynthesis and respiration are considered as examples of multielectron processes.     

The role of ATP and free ADP in metabolic coupling during fuel-stimulated insulin release from islet beta-cells in the isolated perfused rat pancreas.

The isolated perfused rat pancreas was used to test the hypothesis that total cellular ATP or the ratio of ATP/free ADP plays the primary role in coupling intermediary metabolism to the biophysical events that are the basis of glucose-stimulated insulin release. The pancreas was preperfused for 20 min with 4.0 mM of a physiological mixture of 20 amino acids plus 4.2 mM glucose, and insulin release was then stimulated for 150 s by suddenly increasing the glucose to 8.3 mM. The pancreas was sampled at 24, 48, 72, and 150 s after the switch. The content of total ATP, ADP, AMP, Pi, phosphocreatine, and creatine were measured in beta-cell enriched cores of pancreatic islets microdissected from freeze-dried pancreas cryostat sections. Metabolites were measured by quantitative histochemical enzymatic cycling techniques. Modeling studies were carried out to assess the impact of biochemical analytical results on the membrane potential of the beta-cells. The level of free ADP was calculated using the creatine kinase equilibrium reaction and an intracellular pH of 7.2. First phase insulin release was stimulated at least 10-fold with the maximum reached 45 s after adding high glucose. The biochemical analytical data demonstrate that the total cellular level of the putative coupling factor ATP and of the ratios ATP/free ADP and ATP/free ADP x Pi are not significantly influenced by a glucose level change that causes a more than 10-fold surge of insulin release. The strength and limitations of the present experimental strategy and the implications of the results for our understanding of metabolic coupling in glucose-stimulated insulin release are discussed.