Biogenic isoprene emission as expression of dissipativity,a fundamental cell property

Energy dynamics of isoprene biosynthesis and the mechanism of isoprene emission are discussed in view of their fundamental role in dissipativity of living cells. The significance of basic principles of colloidal chemistry for biological energy conversion is emphasized. The idea is put forward of the existence in living cells of the universal energy-dynamic structural unit, termed “biological micelle,” that accounts for the transport and distribution of protons over the cell volume. This unit is responsible for the creation and maintenance of physiological pH at any metabolically active site within the cell. Particular attention is paid to the involvement of F-type ATPase in the active proton transport from the thylakoid interior to the F1 domain of ATP-synthase and to recycling of protons from the outer cell surface to the thylakoid lumen due to H+-pumping activity of the thylakoid ATPase. The mechanism responsible for the outflow of entropy deS through the production of isoprene by protonation of dimethylallyl pyrophosphate (DMAPP) has been found. The stable steady-state condition of any thermodynamic system, including the living system, is correlated with the maximum entropy production. The rate of isoprene emission increases with temperature, which compensates for the decrease in outflow of thermal entropy deS. When the ambient temperature is increased, the sum of deS removed as heat and deS removed with isoprene emission remains constant. Thus, photobiosynthesis of isoprene is a special case of the entropy deS dissipation that provides a stable stationary state to the cell.     

Biogenic Isoprene (A Review)

Biogenic isoprene was discovered in the mid-1950s as a component of volatile substances emitted from leaves. In plant species emitting isoprene under illumination, this process is closely related to photosynthesis. Thus, a photobiological phenomenon termed isoprene effect or isoprene emission (IE) was discovered. Subsequent studies showed that leaves are capable of releasing isoprene also in darkness, though at a rate two orders of magnitude lower than that in illuminated leaves. It is presently known that the isoprene is emitted not by all plant species from various taxonomic groups, whereas the dark release of isoprene occurs in cells of all living organisms. This review presents a brief historical account of studies dealt with IE. A special emphasis is placed on the roles of light as an energy source and of CO₂ as a carbon source; these factors create the energy–metabolite flow that runs through the green photosynthesizing cell. The data available suggest that IE can be considered as a manifestation of excretory function of the leaf. An attempt is made to describe IE from the standpoint of thermodynamics of irreversible processes. It is shown that the cell represents a dissipative structure whose organization and stability is provided by irreversible processes running far from equilibrium. General view on isoprene emission is that it results from regulated conversions of carbon and free energy in a series of photosynthetic reactions under stressful conditions caused by CO₂ deficit inside illuminated autotrophic cells. This stress generates the energy overflow, far in excess of the energy-consuming capacity. The necessity of discharging this energy excess is dictated by the fact that the living cell is a dissipative structure.     

The strategy of ecosystem development: specific dissipation as an indicator of ecosystem maturity

The ratio of entropy generation rate to entropy embodied in structures relatively to the surroundings can be considered as an indicator of the ability of a self-organizing dissipative system to maintain itself far from equilibrium by pumping out entropy. The higher the ratio (which may be called the specific entropy production or the specific dissipation of a system), the lower the capacity of a system to convert the incoming low-entropy energy into internal organization. It appears that the ratio attains special significance for interpreting the evolution of biological systems, as the maximum expression of self-organizing systems, from the sub-cellular to the ecosystem scale. This paper proposes specific dissipation, written as the ratio of biological entropy production to exergy stored in the living biomass, as a thermodynamic orientor as well as an indicator of the development state of ecological systems. After having presented a method for estimating the specific dissipation in lakes, the adequacy of the proposed indicator is discussed and also tested by comparing its response to those of some classical ecological attributes (successional sequences of species, biodiversity, individual body size, structural organization and generation time of organisms) throughout the seasonal progression of the plankton community in Lake Trasimeno (Umbria, Italy). The results support the hypothesis that the minimization of specific dissipation is a primary criterion of evolution of ecological systems and also sustain the use of specific dissipation as an indicator of ecological maturity.     

Thermodynamic stability of ecosystems

The stability of ecosystems during periods of stasis in their macro-evolutionary trajectory is studied from a non-equilibrium thermodynamic perspective. Individuals of the species are considered as units of entropy production and entropy exchange in an open thermodynamic system. Within the framework of the classical theory of irreversible thermodynamics, and under the condition of constant external constraints, such a system will naturally evolve toward a globally stable thermodynamic stationary state. It is thus suggested that the ecological steady state, or stasis, is a particular case of the thermodynamic stationary state, and that the evolution of community stability through natural selection is a manifestation of non-equilibrium thermodynamic directives. Furthermore, it is argued that punctuation of stasis leading to ecosystem succession, may be a manifestation of non-equilibrium "phase transitions" brought on by a change of external constraints through a thermodynamic critical point.     

Non-equilibrium thermodynamics of temporally oscillating chemical reactions.

Two thermodynamic quantities are introduced: the entropy change due to a variation of chemical affinity from a steady, state. to some other state and the corresponding entropy production. The entropy change is always negative definite except at the steady state and is capable of being a Liapunov function. The phase-plane behaviour of the entropy production along the trajectory generated by kinetic equations is investigated in connection with the stability of steady state. The examples taken on that occasion are the Volterra-Lotka and Prigogine-Lefever models. The non-equilibrium thermodynamic properties common to the oscillating reactions in two-variable system are in general considered with an emphasis on the thermodynamic analysis for the direction of rotation of the trajectory generated by the two-variable kinetic equations.     

Macroecology: the organizing forces

The fundamental problem in ecology is the relationship between organisms and the physical world. This question is approached through the study of ecosystems as wholes. Pristine, autonomous Arctic lakes provide an invaluable starting point for such investigations. Studies on these lakes, initiated in 1958, indicate that the dominant fish populations assume a recognizable and repeatable structure, which if not disturbed by external forces, is maintained indefinitely. The observable characteristics are high biomass, large individual size, great age, uniformity of individuals despite great variation in age, and relatively few juveniles. This configuration expresses a state of least specific energy dissipation or least specific entropy production and may be regarded as a standing wave in the energy flow. Similar characteristics were found in the dominant species in a wide range of ecosystems worldwide. A state of least dissipation develops when two energy transport processes interfere with each other in the vicinity of thermodynamic equilibrium. Thus it is postulated that living organisms originated through the agonistic interaction between two energy transport processes within materials, initially occurring in an environment close to thermodynamic equilibrium. These two processes, fundamental to energy transfer, are recognized as the principle of least action and its diametrical opposite, the principle of most action. Each force dominates system behavior in a different time frame: most action in the short-term (ecological time) and least action over the long-term (evolutionary time). Interaction between the countervailing forces provides an understanding of a wide range of emergent ecological generalities such as succession, r- and K-selection, the stability and diversity of ecosystems, and the directionality of evolutionary change.     

Ozone Quenching Properties of Isoprene and Its Antioxidant Role in Leaves

Isoprene is formed in and emitted by plants and the reason for this apparent carbon waste is still unclear. It has been proposed that isoprene stabilizes cell and particularly chloroplast thylakoid membranes. We tested if membrane stabilization or isoprene reactivity with ozone induces protection against acute ozone exposures. The reduction of visible, physiological, anatomical, and ultrastructural (chloroplast) damage shows that clones of plants sensitive to ozone and unable to emit isoprene become resistant to acute and short exposure to ozone if they are fumigated with exogenous isoprene, and that isoprene-emitting plants that are sensitive to ozone do not suffer damage when exposed to ozone. Isoprene-induced ozone resistance is associated with the maintenance of photochemical efficiency and with a low energy dissipation, as indicated by fluorescence quenching. This suggests that isoprene effectively stabilizes thylakoid membranes. However, when isoprene reacts with ozone within the leaves or in a humid atmosphere, it quenches the ozone concentration to levels that are less or non-toxic for plants. Thus, protection from ozone in plants fumigated with isoprene may be due to a direct ozone quenching rather than to an induced resistance at membrane level. Irrespective of the mechanism, isoprene is one of the most effective antioxidants in plants.     

Structure and function in the excretory systems of some terrestrial prosobranch snails (Cyclophoridae)

The excretory systems of terrestrial prosobranch snails of the family Cyclophoridae, collected in Jamaica, Costa Rica and South Africa, have been examined physiologically and as regards their gross and fine structure. The process of urine formation commences in the heart, where fluid is filtered across the wall of the ventricle. Filtration through the auricular wall is believed to be negligible. The kidney, which contains three types of cell, modifies the composition of the filtrate. One type of resorptive cell, characterized by basal infoldings associated with mitochondria, takes up salts. Another type, with basal subcellular spaces, may be responsible for taking up water. The third type of cell is secretory, producing concretions of uric acid and phospholipid which are liberated into the kidney lumen when the cell degenerates.
The rate and mechanism of urine production have been investigated using injections of inulin. The filtration rate at 25°C is 0.5 μl/g/min, and in 100% R.H. the average rate of urine production is 0–39 μl/g/min.
An accessory excretory organ has been developed from the hypobranchial gland of aquatic forms. It is composed of groups of subepithelial tubular glands opening into the mantle cavity by one or a series of pores, and secreting purines, phospholipids and mucus. There is evidence that this organ becomes progressively more complex in forms occupying drier habitats.
The systems of excretion and osmoregulation in the Cyclophoridae are considered to be very similar to those in their aquatic relatives, the Viviparidae and Ampullariidae. Certainly the cyclophorids are not as well adapted to a terrestrial life as are the Pulmonata, and in many respects they may be considered "aquatic" snails living on land.     

On the relationship between dissipation and the rate of spontaneous entropy production from linear irreversible thermodynamics

When systems are far from equilibrium, the temperature, the entropy and the thermodynamic entropy production are not defined and the Gibbs entropy does not provide useful information about the physical properties of a system. Furthermore, far from equilibrium, or if the dissipative field changes in time, the spontaneous entropy production of linear irreversible thermodynamics becomes irrelevant. In 2000 we introduced a definition for the dissipation function and showed that for systems of arbitrary size, arbitrarily near or far from equilibrium, the time integral of the ensemble average of this quantity can never decrease. In the low-field limit, its ensemble average becomes equal to the spontaneous entropy production of linear irreversible thermodynamics. We discuss how these quantities are related and why one should use dissipation rather than entropy or entropy production for non-equilibrium systems.     

Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium

The principles of thermodynamics apply to both equilibrium and nonequilibrium biochemical systems. The mathematical machinery of the classic thermodynamics, however, mainly applies to systems in equilibrium. We introduce a thermodynamic formalism for the study of metabolic biochemical reaction (open, nonlinear) networks in both time-dependent and time-independent nonequilibrium states. Classical concepts in equilibrium thermodynamics-enthalpy, entropy, and Gibbs free energy of biochemical reaction systems-are generalized to nonequilibrium settings. Chemical motive force, heat dissipation rate, and entropy production (creation) rate, key concepts in nonequilibrium systems, are introduced. Dynamic equations for the thermodynamic quantities are presented in terms of the key observables of a biochemical network: stoichiometric matrix Q, reaction fluxes J, and chemical potentials of species mu without evoking empirical rate laws. Energy conservation and the Second Law are established for steady-state and dynamic biochemical networks. The theory provides the physiochemical basis for analyzing large-scale metabolic networks in living organisms.     

Induction of a longer term component of isoprene release in darkened aspen leaves: origin and regulation under different environmental conditions

After darkening, isoprene emission continues for 20 to 30 min following biphasic kinetics. The initial dark release of isoprene (postillumination emission), for 200 to 300 s, occurs mainly at the expense of its immediate substrate, dimethylallyldiphosphate (DMADP), but the origin and controls of the secondary burst of isoprene release (dark-induced emission) between approximately 300 and 1,500 s, are not entirely understood. We used a fast-response gas-exchange system to characterize the controls of dark-induced isoprene emission by light, temperature, and CO(2) and oxygen concentrations preceding leaf darkening and the effects of short light pulses and changing gas concentrations during dark-induced isoprene release in hybrid aspen (Populus tremula × Populus tremuloides). The effect of the 2-C-methyl-D-erythritol-4-phosphate pathway inhibitor fosmidomycin was also investigated. The integral of postillumination isoprene release was considered to constitute the DMADP pool size, while the integral of dark-induced emission was defined as the "dark" pool. Overall, the steady-state emission rate in light and the maximum dark-induced emission rate responded similarly to variations in preceding environmental drivers and atmospheric composition, increasing with increasing light, having maxima at approximately 40 °C and close to the CO(2) compensation point, and were suppressed by lack of oxygen. The DMADP and dark pool sizes were also similar through their environmental dependencies, except for high temperatures, where the dark pool significantly exceeded the DMADP pool. Isoprene release could be enhanced by short lightflecks early during dark-induced isoprene release, but not at later stages. Fosmidomycin strongly suppressed both the isoprene emission rates in light and in the dark, but the dark pool was only moderately affected. These results demonstrate a strong correspondence between the steady-state isoprene emission in light and the dark-induced emission and suggest that the dark pool reflects the total pool size of 2-C-methyl-d-erythritol-4-phosphate pathway metabolites upstream of DMADP. These metabolites are converted to isoprene as soon as ATP and NADPH become available, likely by dark activation of chloroplastic glycolysis and chlororespiration.     

Metamorphosis of the excretory system of Paragonimus ohirai (Trematoda), with special reference to its functional significance

The fine structure of the excretory system was studied in metacercariae and juveniles of Paragonimus ohirai. The former were in vitro excysted, and the latter were collected from the abdominal cavity of a rat 24 hours postinfection. The terminal organs of the excretory system were composed of a flame cell and the first cell of a tubule. In the excysted metacercaria, there was no space between these cells to allow the passage of fluid. This suggests that the terminal organs of P. ohirai may be inactive in this stage. The excretory bladder was formed of epithelial cells which contained numerous lipid droplets and a large amount of glycogen in the cytoplasm. The bladder of the metacercaria seems to function as a storage area for nutrients and other materials. These characteristics of the metacercaria are considered to be related to the enclosed conditions created by encystment. Excretory organs had undergone cytomorphosis in the juveniles and appear to possess active excretory function. The periflagellar space in the terminal organs was formed, and lipids and concretions were excreted from a thin layer of the excretory epithelia into the lumen.     

Does microbial life always feed on negative entropy? Thermodynamic analysis of microbial growth.

Schr?dinger stated in his landmark book, What is Life?, that life feeds on negative entropy. In this contribution, the validity of this statement is discussed through a careful thermodynamic analysis of microbial growth processes. In principle, both feeding on negative entropy, i.e. yielding products of higher entropy than the substrates, and generating heat can be used by microorganisms to rid themselves of internal entropy production resulting from maintenance and growth processes. Literature data are reviewed in order to compare these two mechanisms. It is shown that entropy-neutral, entropy-driven, and entropy-retarded growth exist. The analysis of some particularly interesting microorganisms shows that enthalpy-retarded microbial growth may also exist, which would signify a net uptake of heat during growth. However, the existence of endothermic life has never been demonstrated in a calorimeter. The internal entropy production in live cells also reflects itself in the Gibbs energy dissipation accompanying growth, which is related quantitatively to the biomass yield. An empirical correlation of the Gibbs energy dissipation in terms of the physico-chemical nature of the growth substrate has been proposed in the literature and can be used to predict the biomass yield approximately. The ratio of enthalpy change and Gibbs energy change can also be predicted since it is shown to be approximately equal to the same ratio of the relevant catabolic process alone.     

The Critical Roles of Information and Nonequilibrium Thermodynamics in Evolution of Living Systems

Living cells are spatially bounded, low entropy systems that, although far from thermodynamic equilibrium, have persisted for billions of years. Schrödinger, Prigogine, and others explored the physical principles of living systems primarily in terms of the thermodynamics of order, energy, and entropy. This provided valuable insights, but not a comprehensive model. We propose the first principles of living systems must include: (1) Information dynamics, which permits conversion of energy to order through synthesis of specific and reproducible, structurally-ordered components; and (2) Nonequilibrium thermodynamics, which generate Darwinian forces that optimize the system. Living systems are fundamentally unstable because they exist far from thermodynamic equilibrium, but this apparently precarious state allows critical response that includes: (1) Feedback so that loss of order due to environmental perturbations generate information that initiates a corresponding response to restore baseline state. (2) Death due to a return to thermodynamic equilibrium to rapidly eliminate systems that cannot maintain order in local conditions. (3) Mitosis that rewards very successful systems, even when they attain order that is too high to be sustainable by environmental energy, by dividing so that each daughter cell has a much smaller energy requirement. Thus, nonequilibrium thermodynamics are ultimately responsible for Darwinian forces that optimize system dynamics, conferring robustness sufficient to allow continuous existence of living systems over billions of years.     

Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity

Given the three-dimensional structure of a protein, its thermodynamic properties are calculated using a recently introduced distance constraint model (DCM) within a mean-field treatment. The DCM is constructed from a free energy decomposition that partitions microscopic interactions into a variety of constraint types, i.e., covalent bonds, salt-bridges, hydrogen-bonds, and torsional-forces, each associated with an enthalpy and entropy contribution. A Gibbs ensemble of accessible microstates is defined by a set of topologically distinct mechanical frameworks generated by perturbing away from the native constraint topology. The total enthalpy of a given framework is calculated as a linear sum of enthalpy components over all constraints present. Total entropy is generally a nonadditive property of free energy decompositions. Here, we calculate total entropy as a linear sum of entropy components over a set of independent constraints determined by a graph algorithm that builds up a mechanical framework one constraint at a time, placing constraints with lower entropy before those with greater entropy. This procedure provides a natural mechanism for enthalpy-entropy compensation. A minimal DCM with five phenomenological parameters is found to capture the essential physics relating thermodynamic response to network rigidity. Moreover, two parameters are fixed by simultaneously fitting to heat capacity curves for histidine binding protein and ubiquitin at five different pH conditions. The three free parameter DCM provides a quantitative characterization of conformational flexibility consistent with thermodynamic stability. It is found that native hydrogen bond topology provides a key signature in governing molecular cooperativity and the folding-unfolding transition.     

The thermodynamics of protein-ligand interaction and solvation: insights for ligand design

Isothermal titration calorimetry is able to provide accurate information on the thermodynamic contributions of enthalpy and entropy changes to free energies of binding. The Structure/Calorimetry of Reported Protein Interactions Online database of published isothermal titration calorimetry studies and structural information on the interactions between proteins and small-molecule ligands is used here to reveal general thermodynamic properties of protein-ligand interactions and to investigate correlations with changes in solvation. The overwhelming majority of interactions are found to be enthalpically favoured. Synthetic inhibitors and biological ligands form two distinct subpopulations in the data, with the former having greater average affinity due to more favourable entropy changes on binding. The greatest correlation is found between the binding free energy and apolar surface burial upon complex formation. However, the free-energy contribution per unit area buried is only 30-50% of that expected from earlier studies of transfer free energies of small molecules. A simple probability-based estimator for the maximal affinity of a binding site in terms of its apolar surface area is proposed. Polar surface area burial also contributes substantially to affinity but is difficult to express in terms of unit area due to the small variation in the amount of polar surface buried and a tendency for cancellation of its enthalpic and entropic contributions. Conventionally, the contribution of apolar desolvation to affinity is attributed to gain of entropy due to solvent release. Although data presented here are supportive of this notion, because the correlation of entropy change with apolar surface burial is relatively weak, it cannot, on present evidence, be confidently considered to be correct. Further, thermodynamic changes arising from small differences between ligands binding to individual proteins are relatively large and, in general, uncorrelated with changes in solvation, suggesting that trends identified across widely differing proteins are of limited use in explaining or predicting the effects of ligand modifications.     

Protein heat capacity: inconsistencies in the current view of cold denaturation

The present study shows on the basis of the thermodynamic stability criterion (partial differential S/partial differential T)p>0 that partitioning of the entropy of cold-unfolding of a protein into independent positive conformational and negative hydrational contributions is incorrect. Furthermore it provides a new microscopic interpretation of protein heat capacity that takes into account the significant fluctuations in energy and entropy which result from the small size of these macromolecules.     

Two-dimensional differential scanning calorimetry: simultaneous resolution of intrinsic protein structural energetics and ligand binding interactions by global linkage analysis.

A general theoretical development for the design and analysis of two-dimensional thermal stability surfaces of proteins is presented. The surfaces are generated from multiple excess heat capacity profiles ( vs T) obtained at varying concentrations of an interacting ligand. The energetics of both the intrinsic protein stability and the protein-ligand interaction are simultaneously resolved by employing statistical thermodynamic models in global linkage analysis. This formalism allows resolution of the intrinsic protein folding-unfolding parameters (enthalpy, entropy, and heat capacity changes) as well as the ligand interaction parameters (binding stoichiometry, enthalpy, entropy, and heat capacity changes). The theory has been applied to the case of ribonuclease A and its interaction with cytidine-2'-monophosphate. The accuracy of the thermodynamic parameters obtained by this approach compares within error with those parameters that can be obtained by direct measurements.     

Translocons, thermodynamics, and the folding of membrane proteins

Recent three-dimensional structures of helical membrane proteins present new challenges for the prediction of structure from amino acid sequence. Membrane proteins reside stably in a thermodynamic free energy minimum after release into the membrane's bilayer fabric from the translocon complex. This means that structure prediction is primarily a problem of physical chemistry. But the folding processes within the translocon must also be considered. A distilled overview of the physical principles of membrane protein stability is presented, and extended to encompass translocon-assisted folding.