Metabolic "channeling" and cellular physiology.
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Cell Compartmentation↗
Biomedical subjects
G R Welch
Publications and source records attributed to G R Welch.
Lipopolysaccharide, tumor necrosis factor-alpha, and IL-1 beta prevent programmed cell death (apoptosis) in human peripheral blood monocytes.
Human peripheral blood monocytes progressively lose viability when cultured in the absence of serum, cytokines, or other stimuli. In this study, we investigated whether monocyte death results from membrane damage (i.e., necrosis) or internally regulated processes [i.e., programmed cell death (PCD) or apoptosis]. Our results clearly indicated that monocytes die by PCD when cultured without stimulation. Death was associated with fragmentation of DNA into integer multiples of approximately 200 bp, a decrease in cell size, condensation of the nucleus and cytoplasmic organelles, and membrane blebbing, all of which are cardinal features of PCD. Monocytes exposed to nonphysiologic conditions such as acidic media (pH 4.2), 56 degrees C for 30 min, or freezing and thawing were killed without concomitant DNA fragmentation, indicating that DNA fragmentation was not a result of cell death per se. Addition of Escherichia coli LPS, a potent monocyte activating agent, in concentrations as low as 0.1 ng/ml caused a marked increase in monocyte survival and prevented DNA fragmentation. Moreover, exogenous human rTNF-alpha or IL-1 beta also prevented PCD, suggesting that PCD is regulated by certain cytokines released from LPS-stimulated monocytes. The results indicate that in the absence of appropriate stimulation, monocytes are programmed to undergo a sequence of molecular events leading to cell death. Regulation of PCD may be an important homeostatic mechanism for controlling the number of monocytes available to respond to infection, wound healing, and tumor growth.
Cell Survival↗
Thermodynamics and living systems: problems and paradigms.
The utility of thermodynamic laws in biological systems is reviewed. The joint historical development of thermodynamics and of respiratory physiology in the 19th century is surveyed. From first principles of thermodynamics, problems are noted in their application to physiological calorimetry.
Calorimetry↗
Selective induction of Fc gamma RIII on human monocytes by transforming growth factor-beta.
Transforming growth factor-beta (TGF-beta) is a polypeptide that participates in morphogenesis, inflammation, and would repair. Emerging as an important immunomodulatory molecule, TGF-beta may also regulate the phenotype and function of mononuclear cells within an inflammatory site. In this study TGF-beta is shown to induce expression of the gp50-65 receptor for Fc gamma RIII on otherwise negative peripheral blood monocytes. Circulating monocytes express Fc gamma RI and Fc gamma RII, but not Fc gamma RIII, and no inducing agent for Fc gamma RIII has previously been identified. Within hours after exposure of freshly isolated peripheral blood monocytes to picomolar concentrations of TGF-beta 1 or TGF-beta 2, mRNA specific for Fc gamma RIII is detectable followed by expression of the receptors on the cell surface. Neutralizing antibodies to TGF-beta completely inhibit the TGF-beta-induced up-regulation of Fc gamma RIII. In contrast to TGF-beta, other cytokines involved in the inflammatory response are ineffective in regulating Fc gamma RIII expression on human monocytes. Thus, the early release of TGF-beta by platelets in an inflammatory site may foster enhanced immunophagocytosis and contribute to host defense by inducing monocyte Fc gamma RIII expression.
Antigens, Differentiation↗
Cooperative effect of fructose bisphosphate and glyceraldehyde-3-phosphate dehydrogenase on aldolase action.
The combination of binding and kinetic approaches is suggested to study (i) the mechanism of substrate-modulated dynamic enzyme associations; (ii) the specificity of enzyme interactions. The effect of complex formation between aldolase and glyceraldehyde-3-phosphate dehydrogenase (D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating), EC 1.2.1.12) on aldolase catalysis was investigated under pseudo-first-order conditions. No change in kcat but a significant increase in KM of fructose 1,6-bisphosphate for aldolase was found when both enzymes were obtained from muscle. In contrast, kcat rather than KM changed if dehydrogenase was isolated from yeast. Next, the conversion of fructose 1-phosphate was not affected by interactions between enzyme couples isolated from muscle. The influence of fructose phosphates on the enzyme-complex formation was studied by means of covalently attached fluorescent probe. We found that the interaction ws not perturbed by the presence of fructose 1-phosphate; however, fructose 1,6-bisphosphate altered the dissociation constant of the enzyme complex. A molecular model for fructose 1,6-bisphosphate-modulated enzyme interaction has been evaluated which suggests that high levels of fructose bisphosphate would drive the formation of the 'channelling' complex between aldolase and glyceraldehyde-3-phosphate dehydrogenase.
Animals↗
Transient-time analysis of substrate-channelling in interacting enzyme systems.
The kinetics of dynamically interacting enzyme systems is examined, in the light of increasing evidence attesting to the widespread occurrence of this mode of organization in vivo. The transient time, a key phenomenological parameter for the coupled reaction, is expressed as a function of the lifetime of the intermediate substrate. The relationships between the transient time and the pseudo-first-order rate constants for the coupled reaction by the complexed and uncomplexed enzyme species are indicative of the mechanism of intermediate transfer ('channelling'). In a dynamically interacting enzyme system these kinetic parameters are composite functions of those for the processes catalysed by the complex and by the separated enzymes. The mathematical paradigm can be extended to a linear sequence of N coupled reactions catalysed by dynamically (pair-wise) interacting enzymes.
Kinetics↗
Of men, molecules, and (ir)reducibility.
The subject of (ir)reducibility in biochemistry has resurfaced recently in the literature. Along with it comes a renewed emphasis on the organizational complexity of the living state and, more broadly, concern over the unity of the sciences.
Biochemical Phenomena↗
The perfection of substrate-channelling in interacting enzyme systems: energetics and evolution.
Some implications of substrate channelling in interacting enzyme systems are considered, with regard to the energetics and evolution of enzyme action. The transient time, a key analytical parameter relating to the phenomenon of channelling, is the basis of our kinetic study. Bounds on the kinetics of multienzyme complexes are established using (apparent) rate constants emanating from the transient-time formulation of coupled reactions. From a transition state representation of the rate process, it is shown how dynamically and statically organized enzyme systems lead to the modification of current ideas on the evolutionary optimization of the energy profile of enzyme catalysis in situ.
Biological Evolution↗
Evidence that stimulation of gluconeogenesis by fatty acid is mediated through thermodynamic mechanisms.
We have studied the stimulatory effects of palmitate on the rate of glucose synthesis from lactate in isolated hepatocytes. Control of the metabolic flow was achieved by modulating the activity of enolase using graded concentrations of fluoride. Unexpectedly, palmitate stimulated gluconeogenesis even when enolase was rate-limiting. This stimulation was also observed when the activities of phosphoenolpyruvate carboxykinase and aspartate aminotransferase were modulated using graded concentrations of quinolinate and aminooxyacetate, respectively. Linear force-flow relationships were found between the rate of gluconeogenesis and indicators of cellular energy status (i.e. mitochondrial membrane and redox potentials and cellular phosphorylation potential). These findings suggest that the fatty acid stimulation of glucose synthesis is in part mediated through thermodynamic mechanisms.
Aminooxyacetic Acid↗
The control of cell metabolism for homogeneous vs. heterogeneous enzyme systems.
Metabolic control theories, based on such parameters as "elasticity coefficients" and "flux-control coefficients", have emerged in recent years. These offer a potentially unifying, holistic paradigm for understanding the regulation of cell metabolism. Much of the foundation relies on the supposition that the system is a homogeneous bulk-phase solution of individual enzymes. We examine some of the tenets of such theories, in the light of increasing knowledge of enzyme organization in vivo. We cast the control parameters into a more general form applicable to the linear kinetic regime, using a newly defined unit--the kinetic power, which allows complete specification in terms of any and all factors which bear upon the conversion of free substrate to free product in situ. Extending the control theory to heterogeneous states of enzyme organization, we make a formal distinction between "solution connectivity" and "structural connectivity" in a multienzyme system. The use of "structural" rate expressions leads to the definition of a flux-control coefficient which specifies the interdependence of the individual rate processes in an organized system. The problems and limitations in applying the control theory to experimental analysis of real systems in situ are discussed. "We have arrived at last at a point which comes rather close to what might be defined as 'molecular control of cellular activity', only to discover that the 'controlling' molecules have themselves acquired their specific configurations, which are the key to their power of control, by virtue of their membership in the population of an organized cell, hence under 'cellular control'." (Weiss, 1963).
Enzymes↗
Biophysics: whence it came, where it's going.
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Biophysics↗
Linear relationships between mitochondrial forces and cytoplasmic flows argue for the organized energy-coupled nature of cellular metabolism.
We have studied rates of formation of glucose, urea and lactate by isolated hepatocytes incubated with a variety of inhibitors of energy transduction. Linear relationships have been found between these metabolic rates and mitochondrial forces (membrane, redox and phosphorylation potentials). The findings are suggestive of extensive enzyme organization within these metabolic pathways.
Animals↗
Quantitation of the interaction between citrate synthase and malate dehydrogenase.
Formation of a bienzyme complex of pig heart mitochondrial malate dehydrogenase and citrate synthase in a buffered system is demonstrated by means of a covalently attached fluorescent probe to citrate synthase. Assuming 1:1 stoichiometry of the enzymes in the complex, an apparent dissociation constant of 10(-6) M was calculated from fluorescence anisotropy measurements. The effect of various metabolites on the interaction was tested. NAD+, oxalacetate, citrate, ATP, and L(-)- or D(+)-malate had no effect on the association of the two enzymes, whereas alpha-ketoglutarate increased and NADH decreased it. The interaction of mitochondrial citrate synthase with cytosolic malate dehydrogenase was found to be much weaker, whereas interaction of citrate synthase with another cytosolic enzyme, aldolase, could not be detected. In kinetic experiments, the activation of malate dehydrogenase by citrate synthase was observed. The effect of pyridine nucleotides and alpha-ketoglutarate is discussed in relation to the direction of the metabolic flow of oxalacetate.
Adenosine Triphosphate↗
A double-quenching method for studying protein dynamics: separation of the fluorescence quenching parameters characteristic of solvent-exposed and solvent-masked fluorophors.
A novel experimental method, suitable for separate analysis of the quenching parameters characteristic of solvent-exposed and solvent-masked fluorophors of macromolecules, is described. The method is based on the modified Stern-Volmer analysis and requires simultaneous application of two kinds of quencher: one that can selectively quench the emission of exposed fluorophors (e.g., ionic quenchers) and another that is nonselective (e.g., oxygen or, in many cases, acrylamide), capable of quenching the fluorescence of both exposed and masked groups. In order to examine the accuracy of the model, a computer simulation was performed. The results showed that the errors are comparable to those arising from the conventional quenching experiments. The method is applicable to phosphorescence quenching as well and is extendable to time-resolved measurements (by replacing fluorescence intensities with lifetimes). The method was applied to resolve the quenching parameters of lysozyme fluorescence by the use of iodide as selective and acrylamide as nonselective quenchers. The determination of the acrylamide quenching constant associated with the internal fluorophor, Trp-108 (Kq = 3.5 M-1), permits specific studies on the dynamics of internal regions of the protein. The quenching constant determined for the more exposed residue Trp-62 (Kq = 1.6 M-1) provides local information about the surface independent of the electrostatic effects observed when an ionic quencher is used.
Animals↗
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.
Biochemical Phenomena↗
The evolution of enzyme kinetic power.
Evolution of the kinetic potential of enzyme reactions is discussed. Quantitative assessment of the evolution of enzyme action has usually focused on optimization of the parametric ratio kcat./Km, which is the apparent second-order rate constant for the reaction of free substrate with free enzyme to give product. We propose that the general form kcat.[E]T/Km (where [E]T is total enzyme concentration), which is designated the 'kinetic power', is the real measure of kinetic/catalytic potential in situ. The standard paradigm of 'perfection' dictates the evolutionary maximum of 'kinetic power' to be k+s[E]T/2, where k+s is the diffusion-controlled rate constant for formation of the ES complex (and, hence, for the overall enzyme reaction). We discuss the role of protein conformational mobility in determining this state of 'perfection', via gating of substrate binding and determination of the catalytic configuration. Going beyond the level of the individual enzyme, we indicate the manner by which the organizational features of enzyme action in vivo may enhance the 'kinetic power'. Through evolutionary 'perfection' of the microenvironment, one finds that the 'kinetic power' of enzymes can be affected by alteration of [E]T as well as the unitary rate constants. At this level of complexity, we begin to realize that the 'kinetic' description of cell metabolism must be supplemented with thermodynamic concepts.
Biological Evolution↗
The dynamic basis of energy transduction in enzymes.
The most important idea underlying our treatment herein is the unity of the enzyme molecule and the medium. Appreciation of this relationship is vital, if enzymology is to graduate from its present reductionistic status to a more holistic posture. Enzymes are biological entities firstly, and isolated objects of physicochemical analysis secondly. Perhaps the most crucial 'biological lesson', particularly apropos of enzymes in intermediary metabolism, concerns the 'cytosociology' of enzyme action in vivo [94,128]. The natural habitat of many enzymes in the living cell is far different from that in bulk aqueous solution in vitro. In order to obtain a real grasp of the nature of enzyme function, one must ultimately couch enzymology in concepts emerging from contemporary cell biology [95]. Notwithstanding, analysis precedes synthesis; and one must needs begin with the individual enzyme molecule. The trenchant efforts of the physical chemist and the organic chemist have produced a wealth of information on the nature of the binding and catalytic events at the enzyme active site. While it is not yet possible to explain precisely the complete sequence of events in the catalytic process, nevertheless, the basic mechanisms by which enzymes effect catalysis (i.e., reduce activation energy) now seem apparent [81,129]. The new frontier is to be found, in exploring the dynamic role of the protein matrix [17]. Not only does the protein provide the 3-D scaffolding for active-site processes, but, more importantly, it serves as the local solvent for the bound chemical subsystem. Thus, the dynamical aspects of enzyme catalysis (for thermally based systems) must arise from the fluctuational properties of the protein molecule. This notion is the common denominator in all of the models in subsection IIC. It is the anisotropic nature of this fluctuational behavior, which would characterize the energy-transduction phenomenon leading to localized catalytic events at the active-site. In Section III we attempted to show that all of the various enzyme models contribute pieces to a single, all-embracing jig-saw puzzle. Some models focus on the dynamical properties of the protein per se, whereas others deal with the stochastic aspects of protein-solvent interaction. The two approaches are complementary, as are mutually interlocking pieces of a puzzle. The ultimate picture depicted by this 'jig-saw puzzle' is still somewhat vague--owing to the present paucity of empirical information on protein motions.(ABSTRACT TRUNCATED AT 400 WORDS)
Binding Sites↗
Förster-type energy transfer as a probe for changes in local fluctuations of the protein matrix.
Much evidence, on both theoretical and experimental sides, indicates the importance of local fluctuations (in energy levels, conformational substates, etc.) of the macromolecular matrix in the biological activity of proteins. We describe here a novel application of the Förster-type energy-transfer process capable of monitoring changes both in local fluctuations and in conformational states of macromolecules. A new energy-transfer parameter, f, is defined as an average transfer efficiency, [E], normalized by the actual average quantum efficiency of the donor fluorescence, [phi D]. A simple oscillator model (for a one donor-one acceptor system) is presented to show the sensitivity of this parameter to changes in amplitudes of local fluctuations. The different modes of averaging (static, dynamic, and intermediate cases) occurring for a given value of the average transfer rate, [kt], and the experimental requirements as well as limitations of the method are also discussed. The experimental tests were performed on the ribonuclease T1-pyridoxamine 5'-phosphate conjugate (a one donor-one acceptor system) by studying the change of the f parameter with temperature, an environmental parameter expectedly perturbing local fluctuations of proteins. The parameter f increased with increasing temperature as expected on the basis of the oscillator model, suggesting that it really reflects changes of fluctuation amplitudes (significant changes in the orientation factor, k2, as well as in the spectral properties of the fluorophores can be excluded by anisotropy measurements and spectral investigations). Possibilities of the general applicability of the method are also discussed.
Energy Transfer↗