Protein conformational dynamics probed by single-molecule electron transfer

Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.     

Ultrafast electron localization dynamics following photo-induced charge transfer

Molecular dynamics occurring in the earliest stages following photo-induced charge transfer were investigated. Femtosecond time-resolved absorption anisotropy measurements on [Ru(bpy)(3)](2+), where bpy is 2,2'-bipyridine, reveal a time dependence in nitrile solutions attributed to initial delocalization of the excited state over all three ligands followed by charge localization onto a single ligand. The localization process is proposed to be coupled to nondiffusive solvation dynamics. In contrast, measurements sampling population dynamics show spectral evolution associated with wave packet motion on the excited state surface that is independent of solvent. The results therefore reveal two important contributions to the evolution of charge transfer states in condensed phase, one that is strongly coupled to the surrounding environment and another that follows a potential internal to the molecule.     

Molecular dynamics of a cytochrome c-cytochrome b5 electron transfer complex

Cytochrome c and cytochrome b5 form an electrostatically associated electron transfer complex. Computer models of this and related complexes that were generated by docking the x-ray structures of the individual proteins have provided insight into the specificity and mechanism of electron transfer reactions. Previous static modeling studies were extended by molecular dynamics simulations of a cytochrome c-cytochrome b5 intermolecular complex. The simulations indicate that electrostatic interactions at the molecular interface results in a flexible association complex that samples alternative interheme geometries and molecular conformations. Many of these transient geometries appear to be more favorable for electron transfer than those formed in the initial model complex. Of particular interest is a conformational change that occurred in phenylalanine 82 of cytochrome c that allowed the phenyl side chain to bridge the two cytochrome heme groups.     

Dynamics affecting the primary charge transfer in photosynthesis

Analysis of a 60-picosecond molecular dynamics trajectory of the reaction center of Rhodopseudomonas viridis provides an understanding of observations concerning vibrational coherence and the nonexponential kinetics of the primary charge transfer in photosynthesis. Complex kinetics arises from energy gap correlations that persist beyond 1 picosecond.     

Coherence dynamics in photosynthesis: protein protection of excitonic coherence

The role of quantum coherence in promoting the efficiency of the initial stages of photosynthesis is an open and intriguing question. We performed a two-color photon echo experiment on a bacterial reaction center that enabled direct visualization of the coherence dynamics in the reaction center. The data revealed long-lasting coherence between two electronic states that are formed by mixing of the bacteriopheophytin and accessory bacteriochlorophyll excited states. This coherence can only be explained by strong correlation between the protein-induced fluctuations in the transition energy of neighboring chromophores. Our results suggest that correlated protein environments preserve electronic coherence in photosynthetic complexes and allow the excitation to move coherently in space, enabling highly efficient energy harvesting and trapping in photosynthesis.     

Protein catalysis of the retinal subpicosecond photoisomerization in the primary process of bacteriorhodopsin photosynthesis

The rate of retinal photoisomerization in wild-type bacteriorhodopsin (wt bR) is compared with that in a number of mutants in which a positively charged (Arg(82)), a negatively charged (Asp(85) or Asp(212)), or neutral hydrogen bonding (Asp(115) or Tyr(185)) amino acid residue known to be functionally important within the retinal cavity is replaced by a neutral, non-hydrogen bonding one. Only the replacements of the charged residues reduced the photoisomerization rate of the 13-cis and all-trans isomers present in these mutants by factors of approximately 1/4 and approximately 1/20, respectively. Retinal photo- and thermal isomerization catalysis and selectivity in wt bR by charged residues is discussed in terms of the known protein structure, the valence-bond wave functions of the ground and excited state of the retinal, and the electrostatic stabilization interactions within the retinal cavity.     

Vibrational promotion of electron transfer

By using laser methods to prepare specific quantum states of gas-phase nitric oxide molecules, we examined the role of vibrational motion in electron transfer to a molecule from a metal surface free from the complicating influence of solvation effects. The signature of the electron transfer process is a highly efficient multiquantum vibrational relaxation event, where the nitrogen oxide loses hundreds of kilojoules per mole of energy on a subpicosecond time scale. These results cannot be explained simply on the basis of Franck-Condon factors. The large-amplitude vibrational motion associated with molecules in high vibrational states strongly modulates the energetic driving force of the electron transfer reaction. These results show the importance of molecular vibration in promoting electron transfer reactions, a class of chemistry important to molecular electronics devices, solar energy conversion, and many biological processes.     

Long-range electron transfer in heme proteins

Kinetic experiments have conclusively shown that electron transfer can take place over large distances (greater than 10 angstroms) through protein interiors. Current research focuses on the elucidation of the factors that determine the rates of long-range electron-transfer reactions in modified proteins and protein complexes. Factors receiving experimental and theoretical attention include the donor-acceptor distance, changes in geometry of the donor and acceptor upon electron transfer, and the thermodynamic driving force. Recent experimental work on heme proteins indicates that the electron-transfer rate falls off exponentially with donor-acceptor distance at long range. The rate is greatly enhanced in proteins in which the structural changes accompanying electron transfer are very small.     

Intramolecular long-distance electron transfer in organic molecules

Intramolecular long-distance electron transfer (EI) has been actively studied in recent years in order to test existing theories in a quantitative way and to provide the necessary constants for predicting ET rates from simple structural parameters. Theoretical predictions of an "inverted region," where increasing the driving force of the reaction will decrease its rate, have begun to be experimentally confirmed. A predicted nonlinear dependence of ET rates on the polarity of the solvent has also been confirmed. This work has implications for the design of efficient photochemical charge-separation devices. Other studies have been directed toward determining the distance dependence of ET reactions. Model studies on different series of compounds give similar distance dependences. When different stereochemical structures are compared, it becomes apparent that geometrical factors must be taken into account. Finally, the mechanism of coupling between donor and acceptor in weakly interacting systems has become of major importance. The theoretical and experimental evidence favors a model in which coupling is provided by the interaction with the orbitals of the intervening molecular fragments, although more experimental evidence is needed.     

西南喀斯特典型树种光合特性的季节变化及主要影响因子

为了解喀斯特典型植物光合作用季节变化特征,应用LI-6400便携式光合作用测定系统,对滇南安息香(Styrax benzoinoides Craib)、女贞(Ligustrum lucidum)和岩樟(Cinnamomum saxatile)3种喀斯特典型植物在自然生境中的光合季节动态及主要影响因子进行研究。结果表明:女贞和岩樟的光合速率季节变化表现为4月、7月较高而1月、10月低,滇南安息香的光合速率季节变化则不明显;3种植物都出现了光合"午休"现象,但不同树种的变化曲线不同;不同季节影响3种植物的净光合速率(Pn)的因子不同:1月和10月,3种植物共同的主要影响因子为光强(PAR)和蒸腾速率(Tr),4月3种植物的主要影响因子各不相同,胞间CO2含量(Ci)和光强(PAR)是影响女贞的主要影响因子,光强(PAR)和蒸腾速率(Tr)是影响岩樟的主要影响因子,而各因子对滇南安息香的影响不显著。7月影响3种植物净光合速率的因子主要是气孔导度(Gs)和胞间CO2含量(Ci)。光强是不同季节影响3种植物净光合速率最为主要的因子。通过对3种植物光合作用季节变化特征分析,女贞和岩樟能较好的与西南喀斯特环境相适应,而滇南安息香对西南喀斯特环境适应性较差。     

Femtosecond dynamics of electron localization at interfaces

The dynamics of two-dimensional small-polaron formation at ultrathin alkane layers on a silver(111) surface have been studied with femtosecond time- and angle-resolved two-photon photoemission spectroscopy. Optical excitation creates interfacial electrons in quasi-free states for motion parallel to the interface. These initially delocalized electrons self-trap as small polarons in a localized state within a few hundred femtoseconds. The localized electrons then decay back to the metal within picoseconds by tunneling through the adlayer potential barrier. The energy dependence of the self-trapping rate has been measured and modeled with a theory analogous to electron transfer theory. This analysis determines the inter- and intramolecular vibrational modes of the overlayer responsible for self-trapping as well as the relaxation energy of the overlayer molecular lattice. These results for a model interface contribute to the fundamental picture of electron behavior in weakly bonded solids and can lead to better understanding of carrier dynamics in many different systems, including organic light-emitting diodes.     

Photoprotection by carotenoids during photosynthesis: motional dependence of intramolecular energy transfer

A new carotenoporphyrin has been prepared in which a synthetic carotenoid is joined to a tetraarylporphyrin through a flexible trimethylene linkage. This molecule exists primarily in an extended conformation with the carotenoid chromophore far from the porphyrin pi-electron system. In benzene solution, where large-amplitude molecular motions are rapid, the molecule can momentarily assume less stable conformations which favor triplet energy transfer, and quenching of the porphyrin triplet by the carotenoid is fast. In a polystyrene matrix or frozen glass such motions are slow, and energy transfer cannot compete with other pathways for depopulating the triplet state. These observations help establish the requirements for biological photoprotection.     

Efficient multistep photoinitiated electron transfer in a molecular pentad

A synthetic five-part molecular device has been prepared that uses a multistep electron transfer strategy similar to that of photosynthetic organisms to capture light energy and convert it to chemical potential in the form of long-lived charge separation. It consists of two covalently linked porphyrin moieties, one containing a zinc ion (P(Zn)) and the other present as the free base (P). The metailated porphyrin bears a carotenoid polyene (C) and the other a diquinone species (Q(A)-Q(B)). Excitation of the free-base porphyrin in a chloroform solution of the pentad yields an initial charge-separated state, C-P(Zn)-P(.+).-Q(A)(-)-Q(B), with a quantum yield of 0.85. Subsequent electron transfer steps lead to a final charge-separated state, C(.+)-P(Zn)-P-Q(A)-Q(B)(.-), which is formed with an overall quantum yield of 0.83 and has a lifetime of 55 microseconds. Irradiation of the free-base form of the pentad, C-P-P-Q(A)-Q(B), gives a similar charge-separated state with a lower quantum yield (0.15 in dichloromethane), although the lifetime is increased to approximately 340 microseconds. The artificial photosynthetic system preserves a significant fraction ( approximately 1.0 electron volt) of the initial excitation energy (1.9 electron volts) in the long-lived, charge-separated state.     

Polychlorinated biphenyls: transfer from microparticulates to marine phytoplankton and the effects on photosynthesis

Polychlorinated biphenyls (PCB's) initially associated with microparticulates are incorporated into marine diatom cells. The time course of transfer is rapid; equilibrium is attained within several hours. Assays with chlorophyll a fluorescence in vivo indicate that the transferred PCB's reach sites in the photosynthetic machinery that are sensitive to the effects of these compounds.     

Dispersed polaron simulations of electron transfer in photosynthetic reaction centers

A microscopic method for simulating quantum mechanical, nuclear tunneling effects in biological electron transfer reactions is presented and applied to several electron transfer steps in photosynthetic bacterial reaction centers. In this "dispersed polaron" method the fluctuations of the protein and the electron carriers are projected as effective normal modes onto an appropriate reaction coordinate and used to evaluate the quantum mechanical rate constant. The simulations, based on the crystallographic structure of the reaction center from Rhodopseudomonas viridis, focus on electron transfer from a bacteriopheophytin to a quinone and the subsequent back-reaction. The rates of both of these reactions are almost independent of temperature or even increase with decreasing temperature. The simulations reproduce this unusual temperature dependence in a qualitative way, without the use of adjustable parameters for the protein's Franck-Condon factors. The observed dependence of the back-reaction on the free energy of the reaction also is reproduced, including the special behavior in the "inverted region."     

Vibrational modes and the dynamic solvent effect in electron and proton transfer

This article primarily reviews recent work on ultrafast experiments on excited state intramolecular electron and proton transfer, with an emphasis on experiments on chemical systems that have been analyzed theoretically. In particular, those systems that have been quantitatively characterized by static spectroscopy, which provides detailed information about the reaction potential energy surface and about other parameters that are necessary to make a direct comparison to theoretical predictions, are described.     

The dependence of electron transfer efficiency on the conformational order in organic monolayers

The electron transfer through an organized organic monolayer of alkyl chains adsorbed on a silicon wafer has been studied. The silicon was used as an electrode in a three-electrode electrochemical cell, and the current versus voltage response was measured. The results show that when the chains in the monolayer are in the "all trans" configuration, the charge transfer efficiency is higher than when the chains have a "gauche" configuration. A mechanism rationalizing all the observations is suggested.