A molecular mechanism of conformational gating of electron transfer in photosynthetic reaction centra

Improved dechlorination and mineralization of 4-chlorophenol in a sequential biocathode-bioanode bioelectrochemical system with mixed photosynthetic bacteria

A new approach that improved the dechlorination and mineralization of 4-chlorophenol (4-CP) was demonstrated in a sequential biocathode-bioanode bioelectrochemical system (BES) with mixed photosynthetic bacteria (PSB). The biocathode with additional PSB inoculation showed higher 4-CP dechlorination efficiency (DE) and maximum current (81.8 ± 2.9%, 0.021 ± 0.002A) than that at abiotic cathode (45.3 ± 3.7%, 0.011 ± 0.002A) (P<0.005). Light response in biocathode BES with or without PSB ascertained the important role of PSB played in the dechlorination and current generation. Dechlorination and mineralization of 4-CP was achieved in the sequential biocathode-bioanode BES, which could be further enhanced with PSB inoculation in both cathode chamber and anode chamber. 4-CP DE in the cathode chamber was improved from 55.0 ± 2.0% to 78.8 ± 4.9%, and the phenol degradation in the anode chamber was improved from 65.3 ± 2.1% to 71.3 ± 1.4%. This study directed a new way for improving dechlorination at biocathode and product degradation at bioanode with PSB inoculation in BES.

A synthetic picture of intramolecular dynamics of proteins. Towards a contemporary statistical theory of biochemical processes

An increasing body of experimental evidence indicates the slow character of internal dynamics of native proteins. The important consequence of this is that theories of chemical reactions, used hitherto, appear inadequate for description of most biochemical reactions. Construction of a contemporary, truly advanced statistical theory of biochemical processes will need simple but realistic models of microscopic dynamics of biomolecules. In this review, intended to be a contribution towards this direction, three topics are considered. First, an intentionally simplified picture of dynamics of native proteins which emerges from recent investigations is presented. Fast vibrational modes of motion, of periods varying from 10(-14) to 10(-11) s, are contrasted with purely stochastic conformational transitions. Significant evidence is adduced that the relaxation time spectrum of the latter spreads in the whole range from 10(-11) to 10(5) s or longer, and up to 10(-7) s it is practically quasi-continuous. Next, the essential ideas of the theory of reaction rates based on stochastic models of intramolecular dynamics are outlined. Special attention is paid to reactions involving molecules in the initial conformational substrates confirmed to the transition state, which is realized in actual experimental situations. And finally, the two best experimentally justified classes of models of conformational transition dynamics, symbolically referred to as "protein glass" and "protein machine", are described and applied to the interpretation of a few simple biochemical processes, perhaps the most important result reported is the demonstration of the possibility of predominance of the short initial condition-dependent stage of protein involved reactions over the main stage described by the standard kinetics. This initial stage, and not the latter, is expected to be responsible for the coupling of component reactions in the complete enzymatic cycles as well as more complex processes of biological free energy transduction.

Low-temperature electron transfer from cytochrome to the special pair in Rhodopseudomonas viridis: role of the L162 residue

Electron transfer from the tetraheme cytochrome c to the special pair of bacteriochlorophylls (P) has been studied by flash absorption spectroscopy in reaction centers isolated from seven strains of the photosynthetic purple bacterium Rhodopseudomonas viridis, where the residue L162, located between the proximal heme c-559 and P, is Y (wild type), F, W, G, M, T, or L. Measurements were performed between 294 K and 8 K, under redox conditions in which the two high-potential hemes of the cytochrome were chemically reduced. At room temperature, the kinetics of P+ reduction include two phases in all of the strains: a dominant very fast phase (VF), and a minor fast phase (F). The VF phase has the following t(1/2): 90 ns (M), 130 ns (W), 135 ns (F), 189 ns (Y; wild type), 200 ns (G), 390 ns (L), and 430 ns (T). These data show that electron transfer is fast whatever the nature of the amino acid at position L162. The amplitudes of both phases decrease suddenly around 200 K in Y, F, and W. The effect of temperature on the extent of fast phases is different in mutants G, M, L, and T, in which electron transfer from c-559 to P+ takes place at cryogenic temperatures in a substantial fraction of the reaction centers (T, 48%; G, 38%; L, 23%, at 40 K; and M, 28%, at 60 K), producing a stable charge separated state. In these nonaromatic mutants the rate of VF electron transfer from cytochrome to P+ is nearly temperature-independent between 294 K and 8 K, remaining very fast at very low temperatures (123 ns at 60 K for M; 251 ns at 40 K for L; 190 ns at 8 K for G, and 458 ns at 8 K for T). In all cases, a decrease in amplitudes of the fast phases is paralleled by an increase in very slow reduction of P+, presumably by back-reaction with Q(A)-. The significance of these results is discussed in relation to electron transfer theories and to freezing at low temperatures of cytochrome structural reorganization.

Protein machine model of enzymatic reactions gated by enzyme internal dynamics

The slow character of conformational transition dynamics in native proteins, recently becoming more and more apparent, makes conventional theories of chemical reactions inapplicable for the description of enzymatic reactions. Any contemporary statistical theory of biochemical processes has to be based on a possibly simple but realistic model of microscopic dynamics of participating biomolecules. In a model considered in this paper the dynamics of enzymatic protein is approximated by a quasi-continuous diffusive motion of its solid-like structural elements relative to each other. The enzymatic reaction is assumed to involve three steps (a covalent tranformation preceded and followed by association-dissociation processes with the substrate and the product), each step being gated by conformational diffusion. In general, the reaction proceeds in three stages: initial, transient and steady-state. Carefully approximated analytical formulae describing the kinetics in each stage are derived. In the limit of the fast internal dynamics of the enzyme, when compared to the local chemical transformations, the initial stage of reaction, dependent on the initial distribution of enzyme conformations, is absent and all the formulae describing the remaining two stages simplify to those provided by the classical theory of Haldane. However, following recent studies, the rule seems to be that it is the conformational dynamics of the enzyme, and not the details of chemical mechanism, that affects the rate of enzymatic reaction. Apart from the possibility of the initial inhomogeneous kinetics, the important result obtained in the limit of slow conformational dynamics is that the kinetic mechanisms of a reaction differ in general between the transient and steady-state stages. Possibilities of carrying out an experimentum crucis directly discrediting the conventional approach are considered.

Interaction between cytochrome c and the photosynthetic reaction center of purple bacteria: behaviour at low temperature

In purple photosynthetic bacteria the electron donor to the special pair, after its oxidation by a light-induced reaction, is a c-type cytochrome: either a soluble monoheme cytochrome which forms a transitory complex with the reaction center, or a tetraheme cytochrome which remains permanently bound to the reaction center. The effects of low temperatures on electron transfer in the complex are presented and discussed. They provide estimates for the reorganization energy. The most prominent effect of low temperature is that a dominant fast phase of electron transfer becomes impossible at a temperature of around 250 K (monoheme cytochrome) or located between 250 K and 80 K according to the redox state (tetraheme cytochrome). This inhibition is attributed to a freezing-like transition of pools of water molecules which blocks structural changes of the protein which are normally associated with the cytochrome oxidation.