▪ Abstract Proton-coupled electron transfer (PCET) is an important mechanism for charge transfer in a wide variety of systems including biology- and materials-oriented venues. We review several are...

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Proton-Coupled Electron Transfer

Molecular recognition is central to all biological processes. For the past 50 years, Koshland's 'induced fit' hypothesis has been the textbook explanation for molecular recognition events. However, recent experimental evidence supports an alternative mechanism. 'Conformational selection' postulates that all protein conformations pre-exist, and the ligand selects the most favored conformation. Following binding the ensemble undergoes a population shift, redistributing the conformational states. Both conformational selection and induced fit appear to play roles. Following binding by a primary conformational selection event, optimization of side chain and backbone interactions is likely to proceed by an induced fit mechanism. Conformational selection has been observed for protein-ligand, protein-protein, protein-DNA, protein-RNA and RNA-ligand interactions. These data support a new molecular recognition paradigm for processes as diverse as signaling, catalysis, gene regulation and protein aggregation in disease, which has the potential to significantly impact our views and strategies in drug design, biomolecular engineering and molecular evolution.

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The role of dynamic conformational ensembles in biomolecular recognition

Increases in ultraviolet radiation at the Earth's surface due to the depletion of the stratospheric ozone layer have recently fuelled interest in the mechanisms of various effects it might have on organisms. DNA is certainly one of the key targets for UV-induced damage in a variety of organisms ranging from bacteria to humans. UV radiation induces two of the most abundant mutagenic and cytotoxic DNA lesions such as cyclobutane–pyrimidine dimers (CPDs) and 6–4 photoproducts (6–4PPs) and their Dewar valence isomers. However, cells have developed a number of repair or tolerance mechanisms to counteract the DNA damage caused by UV or any other stressors. Photoreactivation with the help of the enzyme photolyase is one of the most important and frequently occurring repair mechanisms in a variety of organisms. Excision repair, which can be distinguished into base excision repair (BER) and nucleotide excision repair (NER), also plays an important role in DNA repair
in several organisms with the help of a number of glycosylases and polymerases, respectively. In addition, mechanisms such as mutagenic repair or dimer bypass, recombinational repair, cell-cycle checkpoints, apoptosis and certain alternative repair pathways are also operative in various organisms. This review deals with UV-induced DNA damage and the associated repair mechanisms as well as methods of detecting DNA damage and its future perspectives.

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UV-induced DNA damage and repair: a review

The genetic and biochemical networks which underlie such things as homeostasis in metabolism and the developmental programs of living cells, must withstand considerable variations and random perturbations of biochemical parameters These occur as transient changes in, for example, transcription, translation, and RNA and protein degradation The intensity and duration of these perturbations differ between cells in a population The unique state of cells, and thus the diversity in a population, is owing to the different environmental stimuli the individual cells experience and the inherent stochastic nature of biochemical processes (for example, refs 5 and 6) It has been proposed, but not demonstrated, that autoregulatory, negative feedback loops in gene circuits provide stability, thereby limiting the range over which the concentrations of network components fluctuate Here we have designed and constructed simple gene circuits consisting of a regulator and transcriptional repressor modules in Escherichia coli and we show the gain of stability produced by negative feedback

Engineering stability in gene networks by autoregulation

Striving for new solar fuels, the water oxidation reaction currently is considered to be a bottleneck, hampering progress in the development of applicable technologies for the conversion of light into storable fuels. This review compares and unifies viewpoints on water oxidation from various fields of catalysis research. The first part deals with the thermodynamic efficiency and mechanisms of electrochemical water splitting by metal oxides on electrode surfaces, explaining the recent concept of the potential-determining step. Subsequently, novel cobalt oxide-based catalysts for heterogeneous (electro)catalysis are discussed. These may share structural and functional properties with surface oxides, multinuclear molecular catalysts and the catalytic manganese–calcium complex of photosynthetic water oxidation. Recent developments in homogeneous water-oxidation catalysis are outlined with a focus on the discovery of mononuclear ruthenium (and non-ruthenium) complexes that efficiently mediate O2 evolution from water. Water oxidation in photosynthesis is the subject of a concise presentation of structure and function of the natural paragon—the manganese–calcium complex in photosystem II—for which ideas concerning redox-potential leveling, proton removal, and OO bond formation mechanisms are discussed. The last part highlights common themes and unifying concepts.

The Mechanism of Water Oxidation: From Electrolysis via Homogeneous to Biological Catalysis

Multicolour near-infrared femtosecond experiments of a genetically modified bacterial reaction centre show that the phase of two excited-state vibrational modes is conserved for a period of picoseconds over a large range of temperatures. The direct visualization of low-frequency nuclear vibrations in this protein, which is embedded in its natural membrane, implicates coherent nuclear motion in the primary electron transfer reaction in functional reaction centres.

Visualization of coherent nuclear motion in a membrane protein by femtosecond spectroscopy

Amino-acid radicals play key roles in many enzymatic reactions. Catalysis often involves transfer of a radical character within the protein, as in class I ribonucleotide reductase where radical transfer occurs over 35 A, from a tyrosyl radical to a cysteine. It is currently debated whether this kind of long-range transfer occurs by electron transfer, followed by proton release to create a neutral radical, or by H-atom transfer, that is, simultaneous transfer of electrons and protons. The latter mechanism avoids the energetic cost of charge formation in the low dielectric protein, but it is less robust to structural changes than is electron transfer. Available experimental data do not clearly discriminate between these proposals. We have studied the mechanism of photoactivation (light-induced reduction of the flavin adenine dinucleotide cofactor) of Escherichia coli DNA photolyase using time-resolved absorption spectroscopy. Here we show that the excited flavin adenine dinucleotide radical abstracts an electron from a nearby tryptophan in 30 ps. After subsequent electron transfer along a chain of three tryptophans, the most remote tryptophan (as a cation radical) releases a proton to the solvent in about 300 ns, showing that electron transfer occurs before proton dissociation. A similar process may take place in photolyase-like blue-light receptors.

Intraprotein radical transfer during photoactivation of DNA photolyase.

It is shown that vibrational coherence modulates the femtosecond kinetics of stimulated emission and absorption of reaction centers of purple bacteria. In the DLL mutant of Rhodobacter capsulatus, which lacks the bacteriopheophytin electron acceptor, oscillations with periods of approximately 500 fs and possibly also of approximately 2 ps were observed, which are associated with formation of the excited state. The kinetics, which reflect primary processes in Rhodobacter sphaeroides R-26, were modulated by oscillations with a period of approximately 700 fs at 796 nm and approximately 2 ps at 930 nm. In the latter case, at 930 nm, where the stimulated emission of the excited state, P*, is probed, oscillations could only be resolved when a sufficiently narrow (10 nm) and concomitantly long pump pulse was used. This may indicate that the potential energy surface of the excited state is anharmonic or that low-frequency oscillations are masked when higher frequency modes are also coherently excited, or both. The possibility is discussed that the primary charge separation may be a coherent and adiabatic process coupled to low-frequency vibrational modes.

https://www.pnas.org/content/pnas/88/20/8885.full.pdf

Direct Observation of Vibrational Coherence in Bacterial Reaction Centers Using Femtosecond Absorption Spectroscopy

The temporal evolution of the near-infrared stimulated emission band of the special pair excited state (P*) in the reaction center of Rhodobacter sphaeroides has been studied in intracytoplasmic membranes of the antenna-deficient RCO1 mutant at 10 K with a resolution of 30 fs. On the 100-fs time scale the emission band gradually shifts to longer wavelengths. After 150 fs the band shifts back to shorter wavelengths and continues to develop on the picosecond time scale in a damped oscillatory manner (most prominent fundamental frequencies around 15 cm-1 and at 92, 122, and 153 cm-1). These phenomena are shown to be due to low-frequency vibrational motions in the P* excited state that conserve their phase on the time scale of electron transfer. These results imply that the vibrational manifold of P* is not thermalized during the electron-transfer reaction in functional reaction centers. The initial Stokes shift dynamics are largely determined by the modes in the 90-160-cm-1 frequency range, which probably involve motions of several chromophores, including the bacteriopheophytin electron acceptor HL.

Marten H. Vos

Papers

Visualization of coherent nuclear motion in a membrane protein by femtosecond spectroscopy

Intraprotein radical transfer during photoactivation of DNA photolyase.

Direct Observation of Vibrational Coherence in Bacterial Reaction Centers Using Femtosecond Absorption Spectroscopy

Coherent dynamics during the primary electron-transfer reaction in membrane-bound reaction centers of Rhodobacter sphaeroides.

Femtosecond processes in proteins