The physical aspects of energy transduction in biological systems

Biological thermodynamics: Ervin Bauer and the unification of life sciences and physics

Biological systems operate toward the maximization of their self-maintenance and adaptability. This is achieved through the establishment of robust self-maintaining configurations acting as attractors resistant to external and internal perturbations. Ervin Bauer (1890-1938) was the first who formulated this essential thermodynamic constraint in the operation of biological systems, which he defined as the stable non-equilibrium state. The latter appears as the basic attractor relative to which biological organization is established. The stable non-equilibrium state represents a generalized cell energy status corresponding to efficient spatiotemporal organization of the fluxes of matter and energy and constantly reproducing the conditions of self-maintenance of metabolism and controlling the rates of major metabolic fluxes that follow thermodynamically and kinetically defined computational principles. This state is realized in the autopoietic structures having closed loops of causation based on the operation of biological codes. The principle of thermodynamic buffering determines the conditions for optimization of the fluxes of load and consumption in metabolism establishing the conditions of metabolic stable non-equilibrium. In developing and evolving biological systems, the principle of stable non-equilibrium is transformed into the principle of increasing external work, which is grounded in the hyper-restorative non-equilibrium dynamics. Bauer's concept of the stable non-equilibrium state puts thermodynamics into the frames of the internal biological causality governing self-maintenance and development of living systems. It can be defined as a relational theory of biological thermodynamics since the standard to which it refers represents the actual biological function rather than the abstract state of thermodynamic equilibrium.

Toward the Relational Formulation of Biological Thermodynamics

Classical thermodynamics employs the state of thermodynamic equilibrium, characterized by maximal disorder of the constituent particles, as the reference frame from which the Second Law is formulated and the definition of entropy is derived. Non-equilibrium thermodynamics analyzes the fluxes of matter and energy that are generated in the course of the general tendency to achieve equilibrium. The systems described by classical and non-equilibrium thermodynamics may be heuristically useful within certain limits, but epistemologically, they have fundamental problems in the application to autopoietic living systems. We discuss here the paradigm defined as a relational biological thermodynamics. The standard to which this refers relates to the biological function operating within the context of particular environment and not to the abstract state of thermodynamic equilibrium. This is defined as the stable non-equilibrium state, following Ervin Bauer. Similar to physics, where abandoning the absolute space-time resulted in the application of non-Euclidean geometry, relational biological thermodynamics leads to revealing the basic iterative structures that are formed as a consequence of the search for an optimal coordinate system by living organisms to maintain stable non-equilibrium. Through this search, the developing system achieves the condition of maximization of its power via synergistic effects.

Molecular-level understanding of biological energy coupling and transduction: Response to "Chemiosmotic misunderstandings"

In a recent paper entitled "Chemiosmotic misunderstandings", it is claimed that "enough shortcomings in Mitchell's chemiosmotic theory have not been found and that a novel paradigm that offers at least as much explanatory power as chemiosmosis is not ready." This view is refuted by a wealth of molecular-level experimental data and strong new theoretical and computational evidence. It is shown that the chemiosmotic theory was beset with a large number of major shortcomings ever since the time when it was first proposed in the 1960s. These multiple shortcomings and flaws of chemiosmosis were repeatedly pointed out in incisive critiques by biochemical authorities of the late 20th century. All the shortcomings and flaws have been shown to be rectified by a quantitative, unified molecular-level theory that leads to a deeper and far more accurate understanding of biological energy coupling and ATP synthesis. The new theory is shown to be consistent with pioneering X-ray and cryo-EM structures and validated by state-of-the-art single-molecule techniques. Several new biochemical experimental tests are proposed and constructive ways for providing a revitalizing conceptual background and theory for integration of the available experimental information are suggested.

Simulation of coherent energy transfer in an alpha-helical peptide by Fermi resonance

A mechanism by which NH stretching quanta are coherently transported along a chain of hydrogen bonded peptide groups is demonstrated by classical simulation of a section of the alpha-helical peptide poly(L-alanine). Vibrational motion takes place on a complex energy surface constructed from earlier ab initio and empirical surfaces. A speculative hypothesis of the biological role of this mechanism is presented, and the critical parameters governing the dynamics are identified and discussed.

Physical mechanism of ATP formation in biomembranes

Membrane-bound and isolated H+ ATPases of various origin are able to synthesize ATP from ADP and Pi after a jump-like pH increase. In the course of this increase the pH of solution (or suspension) must cross a value corresponding to pK of certain acid groups in the catalytic component of ATPase. In the case of isolated soluble enzymes it is possible to obtain up to 10 ATP molecules per one pH jump per one enzyme molecule. A physical mechanism of this phenomenon as well as of oxidative and photosynthetic phosphorylation is suggested.

Microscopic imaging of cells

The microworld was revealed to investigators through a glass bead or a hanging water droplet long before optics was understood. The cellular structure of plants was well resolved by such simple magnifying glasses, van Leeuwenhoek, the Dutch merchant and amateur microscopist, was the first to report to the English Royal Society his observations of bacteria with his single-lens microscope in 1665.

Protein states and proteinquakes

After photodissociation of carbon monoxide bound to myoglobin, the protein relaxes to the deoxy equilibrium structure in a quake-like motion. Investigation of the proteinquake and of related intramolecular equilibrium motions shows that states and motions have a hierarchical glass-like structure.

Intermediate and stable redox states of cytochrome c studied by low temperature resonance Raman spectroscopy

Stabilized intermediate redox states of cytochrome c are generated by radiolytic reduction of initially oxidized enzyme in glass matrices at liquid nitrogen temperature. In the intermediate states the heme group is reduced by hydrated electrons, whereas the protein conformation is restrained close to its oxidized form by the low-temperature glass matrix. The intermediate and stable redox states of cytochrome c at neutral and alkaline pH are studied by low-temperature resonance Raman spectroscopy using excitations in resonance with the B (Soret) and Q1 (beta) optical transitions. The assignments of the cytochrome c resonance Raman bands are discussed. The observed spectral characteristics of the intermediate states as well as of the alkaline transition in the oxidized state are interpreted in terms of oxidation-state marker modes, spin-state marker modes, heme iron--axial ligand stretching modes, totally symmetric in-plane porphyrin modes, nontotally symmetric in-plane modes, and out-of-plane modes.

PH-jump-induced ADP phosphorylation in mitochondria

Mitochondria, uncoupled by aging or by freeze-thaw treatment, are able to synthesize ATP from ADP and Pi after a fast increase (but not decrease) in the external pH. The maximal ATP yield (approx. 2.5 ATP molecules/electron-transport chain per pH jump) can be obtained under the following conditions: (1) the pH change during the jump must exceed 0.7 pH units; (2) in the course of this change, the pH of the mitochondrial suspension must cross the pH 8.1-8.3 value. This pH-jump-induced ATP synthesis is completely inhibited by oligomycin.

Infrared spectroscopy of photodissociated carboxymyoglobin at low temperatures

We have studied the infrared spectra of the bound and photodissociated states of Mb-12CO and Mb-13CO from 5.2 to 300 K. The absorbance peaks seen between 1800 and 2200 cm-1 correspond to CO stretching vibrations. In the bound state of Mb-12CO, the known lines A0 at 1969, A1 at 1945, and A2 at 1927 cm-1, have center frequencies, widths, and absorbances that are independent of temperature between 5.2 and 160 K. Above 160 K, A2 gradually shifts to 1933 cm-1. The low-temperature photodissociated state (Mb) shows three lines (B0, B1, B2) at 2144, 2131, and 2119 cm-1 for 12CO. The absorbances of the three lines depend on temperature. B0 is tentatively assigned to free CO in the heme pocket and B1 and B2, to CO weakly bound to the heme or heme pocket wall. The data are consistent with a model in which photodissociation of MbCO leads to B1 and B2. B2 decays thermally to B1 above 13 K; rebinding to A occurs from B1. The barriers between B2 and B1 and between B1 and A are described by activation enthalpy spectra. Heme and the central metal atom in state Mb have near-infrared, EPR, and Mössbauer spectra that differ slightly from those of deoxyMb. The observation of essentially free CO in state B implies that the difference between Mb and deoxyMb is not due to an interaction of the flashed-off ligand with the protein but is caused by an incomplete relaxation of the protein structure at low temperatures.

Continuous flow-resonance Raman spectroscopy of an intermediate redox state of cytochrome C

An intermediate redox state of cytochrome c at alkaline pH, generated upon rapid reduction by sodium dithionite, has been observed by resonance Raman (RR) spectroscopy in combination with the continuous flow technique. The RR spectrum of the intermediate state is reported for excitation both in the (alpha, beta) and the Soret optical absorption band. The spectra of the intermediate state are more like those of the stable reduced form than those of the stable oxidized form. For excitation of 514.5 nm, the most prominent indication of an intermediate state is the wave-number shift of one RR band from 1,562 cm-1 in the stable oxidized state through 1,535 cm-1 in the intermediate state to 1,544 cm-1 in the stable reduced state. For excitation at 413.1 nm, a band, present at 1,542 cm-1 in the stable reduced state but not present in the stable oxidized state, is absent in the intermediate state. We interpret the intermediate species as the state where the heme iron is reduced but the protein remains in the conformation of the oxidized state, with methionine-80 displaced as sixth ligand to the heme iron, before relaxing to the conformation of the stable reduced state, with methionine-80 returned as sixth ligand.

Time-resolved resonance Raman spectroscopy of cytochrome c reduced by pulse radiolysis

The first investigation of the dynamics of a redox transition of an electron-transfer enzyme by time-resolved resonance Raman spectroscopy in combination with pulse-radiolytic reduction is described by an application to cytochrome c. A long-lived transient state is observed upon reduction of the alkaline form of cytochrome c as a distinct frequency shift of one resonance Raman band. From the frequency in the stable oxidized state, 1567 cm(-1), this particular resonance Raman band shifts within less than 1 microsecond to 1533 cm(-1) in the transient reduced state, which has a lifetime longer than 20 ms but shorter than a few seconds. Finally, in the stable reduced state, this band is located at 1547 cm(-1). According to a previous normal coordinate analysis, this resonance Raman band can be assigned predominantly to a stretching mode of the outermost C-C bonds in the four pyrrole rings of porphyrin. This vibrational mode is influenced by the protein most directly through the covalent thioether linkages of two cysteines to porphyrin. We interpret the long lifetime of the transient state as due to the slow return of Met-80 as sixth ligand to the heme iron upon reduction of the alkaline form of cytochrome c.

Electron tunneling process and the segment mobility of macromolecules

New experimental data [Berg, A. I., Noks, P. P., Kononenko, A. A., Frolov, E. N., Khrymova, I. N., Rubin A. B., Likhtenstein, G. I., Goldanskii, V. I., Parak, F., Bukl, M. & Mössbauer, R. (1979) Mol. Biol. (USSR) 13, 81-89; Berg, A. I., Noks, P. P., Kononenko, A. A., Frolov, E. N., Uspenskaya, N. Y., Khrymova, I. N., Rubin, A. B., Likhtenstein, G. I. & Hideg, K. (1979) Mol. Biol (USSR) 13, 469-477] provide evidence that the electron tunneling process is connected to a special type of conformational transition (segmental transition) protein macromolecules in photosynthetic membranes. This problem is investigated with a simple mechanical model. It is shown that the segmental degree of freedom can play the role of the strongly interacting accepting mode for the electron tunneling process. The temperature dependences of the electron tunneling rate and the recoilless gamma-ray absorption of membrane-bound 57Fe, as an indicator of the intramolecular mobility, are calculated. The problem of energy storage in proteins is also discussed.

Photo-induced electron transport and water state in Rhodospirillum rubrum chromatophores

It is shown that in bacterial chromatophores the pronounced changes in the free water content with a proton spin-spin relaxation time (T2) of 10(-3)--10(-2) s does not influence the efficiency of electron transfer from the photosynthetic reaction centre to the membrane pool of secondary acceptors. An abrupt inhibition of this process occurs only after the loss of the water with faster proton spin-spin relaxation time (T2 of 10(-4) s). The process is reversible. The water fraction in question is obviously bound to the chromatophore proteins and forms the primary hydration layer.