Femtosecond processes in proteins

Individual heme a and heme a3 contributions to the Soret absorption spectrum of the reduced bovine cytochrome c oxidase

Bovine cytochrome c oxidase (CcO) contains two hemes, a and a₃, chemically identical but differing in coordination and spin state. The Soret absorption band of reduced aa₃-type cytochrome c oxidase consists of overlapping bands of the hemes a²⁺ and a₃²⁺. It shows a peak at ∼444 nm and a distinct shoulder at ∼425 nm. However, attribution of individual spectral lineshapes to hemes a²⁺ and a₃²⁺ in the Soret is controversial. In the present work, we characterized spectral contributions of hemes a²⁺ and a₃²⁺ using two approaches. First, we reconstructed bovine CcO heme a²⁺ spectrum using a selective Ca²⁺-induced spectral shift of the heme a²⁺. Second, we investigated photobleaching of the reduced Thermus thermophilus ba₃- and bovine aa₃-oxidases in the Soret induced by femtosecond laser pulses in the Q-band. The resolved spectra show splitting of the electronic B_0x-, B_0y-transitions of both reduced hemes. The heme a²⁺ spectrum is shifted to the red relative to heme a₃²⁺ spectrum. The ∼425 nm shoulder is mostly attributed to heme a₃²⁺.

Hidden vibronic and excitonic structure and vibronic coherence transfer in the bacterial reaction center

We report two-dimensional electronic spectroscopy (2DES) experiments on the bacterial reaction center (BRC) from purple bacteria, revealing hidden vibronic and excitonic structure. Through analysis of the coherent dynamics of the BRC, we identify multiple quasi-resonances between pigment vibrations and excitonic energy gaps, and vibronic coherence transfer processes that are typically neglected in standard models of photosynthetic energy transfer and charge separation. We support our assignment with control experiments on bacteriochlorophyll and simulations of the coherent dynamics using a reduced excitonic model of the BRC. We find that specific vibronic coherence processes can readily reveal weak exciton transitions. While the functional relevance of such processes is unclear, they provide a spectroscopic tool that uses vibrations as a window for observing excited state structure and dynamics elsewhere in the BRC via vibronic coupling. Vibronic coherence transfer reveals the upper exciton of the “special pair” that was weakly visible in previous 2DES experiments.

The voltage dependent sidedness of the reprotonation of the retinal Schiff base determines the unique inward pumping of Xenorhodopsin

The new class of microbial rhodopsins, called xenorhodopsins (XeRs) (1), extends the versatility of this family by inward H + pumps (2-4). These pumps are an alternative optogenetic tool to the light-gated ion channels (e.g. ChR1,2), because the activation of electrically excitable cells by XeRs is independent from the surrounding physiological conditions. In this work we functionally and spectroscopically characterized XeR from Nanosalina ( Ns XeR) (1). The photodynamic behavior of Ns XeR was investigated on the ps to s time scale elucidating the formation of the J and K and a previously unknown long-lived intermediate. The pH dependent kinetics reveal that alkalization of the surrounding medium accelerates the photocycle and the pump turnover. In patch-clamp experiments the blue-light illumination of Ns XeR in the M state shows a potential-dependent vectoriality of the photocurrent transients, suggesting a variable accessibility of reprotonation of the retinal Schiff base. Insights on the kinetically independent switching mechanism could furthermore be obtained by mutational studies on the putative intracellular H + acceptor D220.

Low-Frequency Protein Motions Coupled to Catalytic Sites

This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.

Mimicking Natural Photosynthesis: Designing Ultrafast Photosensitized Electron Transfer into Multiheme Cytochrome Protein Nanowires

Efficient nanomaterials for artificial photosynthesis require fast and robust unidirectional electron transfer (ET) from photosensitizers through charge-separation and accumulation units to redox-active catalytic sites. We explored the ultrafast time-scale limits of photo-induced charge transfer between a Ru(II)tris(bipyridine) derivative photosensitizer and PpcA, a 3-heme c-type cytochrome serving as a nanoscale biological wire. Four covalent attachment sites (K28C, K29C, K52C, and G53C) were engineered in PpcA enabling site-specific covalent labeling with expected donor-acceptor (DA) distances of 4-8 Å. X-ray scattering results demonstrated that mutations and chemical labeling did not disrupt the structure of the proteins. Time-resolved spectroscopy revealed three orders of magnitude difference in charge transfer rates for the systems with otherwise similar DA distances and the same number of covalent bonds separating donors and acceptors. All-atom molecular dynamics simulations provided additional insight into the structure-function requirements for ultrafast charge transfer and the requirement of van der Waals contact between aromatic atoms of photosensitizers and hemes in order to observe sub-nanosecond ET. This work demonstrates opportunities to utilize multi-heme c-cytochromes as frameworks for designing ultrafast light-driven ET into charge-accumulating biohybrid model systems, and ultimately for mimicking the photosynthetic paradigm of efficiently coupling ultrafast, light-driven electron transfer chemistry to multi-step catalysis within small, experimentally versatile photosynthetic biohybrid assemblies.

Characterization of Vibrational Coherence in Monomeric Bacteriochlorophyll a by Two-Dimensional Electronic Spectroscopy

Bacteriochlorophyll a (BChla) is the most abundant pigment found in the Bacterial Reaction Center (BRC) and light-harvesting proteins of photosynthetic purple and green bacteria. Recent two-dimensional electronic spectroscopy (2DES) studies of photosynthetic pigment-protein complexes including the BRC and the Fenna-Matthews-Olson (FMO) complex have shown oscillatory signals, or coherences, whose physical origin has been hotly debated. To better understand the observations of coherence in larger photosynthetic systems, it is important to carefully characterize the spectroscopic signatures of the monomeric pigments. Prior spectroscopic studies of BChla have differed significantly in their observations, with some studies reporting little to no coherence. Here we present evidence of strong coherences in monomeric BChla in isopropanol using 2DES at 77 K. We resolve many modes with frequencies that correspond well with known vibrational modes. We confirm their vibrational origin by comparing the 2D spectroscopic signatures with expectations based on a purely vibrational model.

Excitation-dependent electron exchange energy and electron transfer dynamics in a series of covalently tethered N,N-bis(4'-tert-butylbiphenyl-4-yl)aniline - [C60] fullerene dyads via varying π-conjugated spacers

Femtosecond time-resolved fluorescence and transient absorption studies are reported for three newly synthesized covalently linked N,N-bis(4'-tert-butylbiphenyl-4-yl)aniline (BBA) and pyrrolidinofullerenes (C60)-based donor-π conjugated bridge-acceptor dyads (D-B-A) as functions of the bridge length (7.1, 9.5 and 11.2 Å for Dyad-1, Dyad-2 and Dyad-3), dielectric constants of the medium and pump wavelengths. In polar solvent, ultrafast fluorescence quenching (kEET ≥ 2 × 1012 s-1) of the BBA moiety upon excitation of the BBA moiety (320 nm) is observed in the dyads and is assigned to a mechanism involving electron exchange energy transfer (EET) from 1BBA* to C60 followed by electron transfer from BBA to 1C60*. Cohesive rise and decay dynamics of conjugated BBA˙+-C60˙- anion pairs confirm the involvement of a distance independent adiabatic charge-separation (CS) process (kCS ≥ 2.2 × 1011 s-1) with near unity quantum efficiency (φCS ≥ 99.7%) and a distance-dependent non-adiabatic charge-recombination (CR) process [kCR ∼ (1010-108) s-1]. In contrast, excitation of the C60 moiety (λex = 430 to 700 nm) illustrates photoinduced electron transfer from BBA to 1C60*, involving non-adiabatic (diabatic) and distance-dependent CS (kCS in the range of 0.59-1.78 × 1011 s-1) with 98.86-99.6% (Dyad-3-Dyad-1) quantum efficiency and a CR process with kCR values [kCR ∼ (1010-108) s-1] up to three orders greater than kCS of the respective dyads. Both the processes, CS and CR, upon C60 excitation and the CR process upon BBA excitation show distance dependent rate constants with exponential factor β ≤ 0.5 Å-1, and electron transfer is concluded to occur through a covalently linked conjugated π bridge. Global and target analysis of fsTA data reveal the occurrence of two closely lying CS states, thermally hot (CShot) and thermally relaxed (CSeq) states, and two CR processes with two orders of different rate constants. Careful analysis of the kinetic and thermodynamic data allowed us to estimate the total reorganization energy and electronic coupling matrix (V), which decrease exponentially with distance. These novel features of the distance independent adiabatic CS process and the distance-dependent diabatic CR process upon donor excitation are due to extending the π-conjugation between BBA and C60. The demonstrated results may provide a benchmark in the design of light-harvesting molecular devices where ultrafast CS processes and long-lived CS states are essential requirements.

Vibronic Wavepackets and Energy Transfer in Cryptophyte Light-Harvesting Complexes

Determining the key features of high-efficiency photosynthetic energy transfer remains an ongoing task. Recently, there has been evidence for the role of vibronic coherence in linking donor and acceptor states to redistribute oscillator strength for enhanced energy transfer. To gain further insights into the interplay between vibronic wavepackets and energy-transfer dynamics, we systematically compare four structurally related phycobiliproteins from cryptophyte algae by broad-band pump-probe spectroscopy and extend a parametric model based on global analysis to include vibrational wavepacket characterization. The four phycobiliproteins isolated from cryptophyte algae are two "open" structures and two "closed" structures. The closed structures exhibit strong exciton coupling in the central dimer. The dominant energy-transfer pathway occurs on the subpicosecond timescale across the largest energy gap in each of the proteins, from central to peripheral chromophores. All proteins exhibit a strong 1585 cm^-1 coherent oscillation whose relative amplitude, a measure of vibronic intensity borrowing from resonance between donor and acceptor states, scales with both energy-transfer rates and damping rates. Central exciton splitting may aid in bringing the vibronically linked donor and acceptor states into better resonance resulting in the observed doubled rate in the closed structures. Several excited-state vibrational wavepackets persist on timescales relevant to energy transfer, highlighting the importance of further investigation of the interplay between electronic coupling and nuclear degrees of freedom in studies on high-efficiency photosynthesis.

FRAME: femtosecond videography for atomic and molecular dynamics

Many important scientific questions in physics, chemistry and biology require effective methodologies to spectroscopically probe ultrafast intra- and inter-atomic/molecular dynamics. However, current methods that extend into the femtosecond regime are capable of only point measurements or single-snapshot visualizations and thus lack the capability to perform ultrafast spectroscopic videography of dynamic single events. Here we present a laser-probe-based method that enables two-dimensional videography at ultrafast timescales (femtosecond and shorter) of single, non-repetitive events. The method is based on superimposing a structural code onto the illumination to encrypt a single event, which is then deciphered in a post-processing step. This coding strategy enables laser probing with arbitrary wavelengths/bandwidths to collect signals with indiscriminate spectral information, thus allowing for ultrafast videography with full spectroscopic capability. To demonstrate the high temporal resolution of our method, we present videography of light propagation with record high 200 femtosecond temporal resolution. The method is widely applicable for studying a multitude of dynamical processes in physics, chemistry and biology over a wide range of time scales. Because the minimum frame separation (temporal resolution) is dictated by only the laser pulse duration, attosecond-laser technology may further increase video rates by several orders of magnitude.

Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations

The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. In this perspective we discuss how quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations can synergistically converge to gain insight into the migration mechanism of ligands. We show how the evaluation of the free energy landscape for ligand diffusion based on the outcome of computational techniques can assist the definition of sound reaction schemes, leading to a comprehensive understanding of the broad range of chemical events and time scales that encompass the transport of small ligands in hemeproteins.

Primary processes in heme-based sensor proteins

A wide and still rapidly increasing range of heme-based sensor proteins has been discovered over the last two decades. At the molecular level, these proteins function as bistable switches in which the catalytic activity of an enzymatic domain is altered mostly by binding or dissociation of small gaseous ligands (O2, NO or CO) to the heme in a sensor domain. The initial "signal" at the heme level is subsequently transmitted within the protein to the catalytic site, ultimately leading to adapted expression levels of specific proteins. Making use of the photolability of the heme-ligand bond that mimics thermal dissociation, early processes in this intra-protein signaling pathway can be followed using ultrafast optical spectroscopic techniques; they also occur on timescales accessible to molecular dynamics simulations. Experimental studies performed over the last decade on proteins including the sensors FixL (O2), CooA (CO) and soluble guanylate cyclase (NO) are reviewed with an emphasis on emerging general mechanisms. After heme-ligand bond breaking, the ligand can escape from the heme pocket and eventually from the protein, or rebind directly to the heme. Remarkably, in all sensor proteins the rebinding, specifically of the sensed ligand, is highly efficient. This "ligand trap" property possibly provides means to smoothen the effects of fast environmental fluctuations on the switching frequency. For 6-coordinate proteins, where exchange between an internal heme-bound residue and external gaseous ligands occurs, the study of early processes starting from the unliganded form indicates that mobility of the internal ligand may facilitate signal transfer. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.

Electromagnetic field of microtubules: effects on transfer of mass particles and electrons

Biological polar molecules and polymer structures with energy supply (such as microtubules in the cytoskeleton) can get excited and generate an endogenous electromagnetic field with strong electrical component in their vicinity. The endogenous electrical fields through action on charges, on dipoles and multipoles, and through polarization (causing dielectrophoretic effect) exert forces and can drive charges and particles in the cell. The transport of mass particles and electrons is analyzed as a Wiener-Lévy process with inclusion of deterministic force (validity of the Bloch theorem is assumed for transport of electrons in molecular chains too). We compare transport driven by deterministic forces (together with an inseparable thermal component) with that driven thermally and evaluate the probability to reach the target. Deterministic forces can transport particles and electrons with higher probability than forces of thermal origin only. The effect of deterministic forces on directed transport is dominant.

Dynamical theory of primary processes of charge separation in the photosynthetic reaction center

A dynamical theory has been developed for primary separation of charges in the course of photosynthesis. The theory deals with both hopping and superexchange transfer mechanisms. Dynamics of electron transfer from dimeric bacteriochlorophyll to quinone has been calculated. The results obtained agree with experimental data and provide a unified explanation of both the hierarchy of the transfer time in the photosynthetic reaction center and the phenomenon of coherent oscillations accompanying the transfer process.

Following ligand migration pathways from picoseconds to milliseconds in type II truncated hemoglobin from Thermobifida fusca

CO recombination kinetics has been investigated in the type II truncated hemoglobin from Thermobifida fusca (Tf-trHb) over more than 10 time decades (from 1 ps to ∼100 ms) by combining femtosecond transient absorption, nanosecond laser flash photolysis and optoacoustic spectroscopy. Photolysis is followed by a rapid geminate recombination with a time constant of ∼2 ns representing almost 60% of the overall reaction. An additional, small amplitude geminate recombination was identified at ∼100 ns. Finally, CO pressure dependent measurements brought out the presence of two transient species in the second order rebinding phase, with time constants ranging from ∼3 to ∼100 ms. The available experimental evidence suggests that the two transients are due to the presence of two conformations which do not interconvert within the time frame of the experiment. Computational studies revealed that the plasticity of protein structure is able to define a branched pathway connecting the ligand binding site and the solvent. This allowed to build a kinetic model capable of describing the complete time course of the CO rebinding kinetics to Tf-trHb.

Enhancement of vibrational coherence by femtosecond degenerate four-wave-mixing for a chromophore in 1-propanol glass

The enhancement effect of vibrational coherence by femtosecond degenerate four-wave-mixing (DFWM) technique was investigated with a dye, NK-2990, doped in low temperature 1-propanol glass. The strongest enhancement was observed with the delay between the first and the second pulses, t(13), set at about quarter of the oscillation period, which does not coincide with the theoretical prediction of half the period. One of the enhanced vibrational modes at ca. 90 cm(-1) became significantly broader below the glass transition temperature, indicating its sensitivity towards microscopic viscosity of the environment.

Excited-state vibrational coherence in methanol solution of Zn(II) tetrakis(N-methylpyridyl)porphyrin: charge-dependent intermolecular mode frequencies and implications for electron-transfer dynamics in photosynthetic reaction centers

The nature of the intermolecular vibrational modes between the redox-active chromophores and the protein medium in the photosynthetic reaction center is central to an understanding of the structural origin of the quantum efficiency of the light-driven charge-separation reactions that result in storage of solar energy. In recent work on this issue, we have characterized the low-frequency vibrational coherence of Zn(II) meso-tetrakis(N-methylpyridyl)porphyrin (ZnTMPyP) and compared it to that from bacteriochlorophyll a in polar solution and in the small light-harvesting subunits B820 and B777. The charge-transfer character of ZnTMPyP's π* excited states afford us the opportunity to characterize how the intermolecular vibrational modes and potential with the surrounding medium are affected by the charge on the porphyrin macrocycle. The excited-state vibrational coherence observed with Q-band (S(1) state) excitation at 625 nm of ZnTMPyP in methanol solution contains dominant contributions from a pair of rapidly damped (effective damping time γ < 400 fs) components that are assigned to the hindered translational and librational porphyrin-solvent intermolecular modes. The 256 cm(-1) mean frequency of the intermolecular modes is significantly higher than that observed previously in the ground state, 79 cm(-1), with Soret-band excitation at 420 nm [Dillman et al., J. Phys. Chem. B. 2009, 113, 6127-6139]. The increased mode frequency arises from the activation of the ion-dipole and ion-induced-dipole terms in the intermolecular potential. In the ground state, the π-electron density of ZnTMPyP is mostly confined to the region of the porphyrin macrocycle. In the excited state, the π-electron density is extensively delocalized from the porphyrin out to two of the peripheral N-methylpyridyl rings, each of which carries a single formal charge. The charge-dependent terms contribute to a significant stabilization of the equilibrium geometry of the porphyrin-solvent complex in the excited state. In the photosynthetic reaction center, these terms will play an important role in trapping the charged products of the forward, charge-separation reactions, and the location of the bacteriopheophytin acceptor in a nonpolar region of the structure enhances the rate of the secondary charge-separation reaction.

Energetics of bacterial photosynthesis

We report the results of extensive numerical simulations and theoretical calculations of electronic transitions in the reaction center of Rhodobacter sphaeroides photosynthetic bacterium. The energetics and kinetics of five electronic transitions related to the kinetic scheme of primary charge separation have been analyzed and compared to experimental observations. Nonergodic formulation of the reaction kinetics is required for the calculation of the rates due to a severe breakdown of the system ergodicity on the time scale of primary charge separation, with the consequent inapplicability of the standard canonical prescription to calculate the activation barrier. Common to all reactions studied is a significant excess of the charge-transfer reorganization energy from the width of the energy gap fluctuations over that from the Stokes shift of the transition. This property of the hydrated proteins, breaking the linear response of the thermal bath, allows the reaction center to significantly reduce the reaction free energy of near-activationless electron hops and thus raise the overall energetic efficiency of the biological charge-transfer chain. The increase of the rate of primary charge separation with cooling is explained in terms of the temperature variation of induction solvation, which dominates the average donor-acceptor energy gap for all electronic transitions in the reaction center. It is also suggested that the experimentally observed break in the Arrhenius slope of the primary recombination rate, occurring near the temperature of the dynamical transition in proteins, can be traced back to a significant drop of the solvent reorganization energy close to that temperature.

Control of retinal isomerization in bacteriorhodopsin in the high-intensity regime

A learning algorithm was used to manipulate optical pulse shapes and optimize retinal isomerization in bacteriorhodopsin, for excitation levels up to 1.8 x 10(16) photons per square centimeter. Below 1/3 the maximum excitation level, the yield was not sensitive to pulse shape. Above this level the learning algorithm found that a Fourier-transform-limited (TL) pulse maximized the 13-cis population. For this optimal pulse the yield increases linearly with intensity well beyond the saturation of the first excited state. To understand these results we performed systematic searches varying the chirp and energy of the pump pulses while monitoring the isomerization yield. The results are interpreted including the influence of 1-photon and multiphoton transitions. The population dynamics in each intermediate conformation and the final branching ratio between the all-trans and 13-cis isomers are modified by changes in the pulse energy and duration.

The petite purple photosynthetic powerpack

Photoreaction centres are Nature's solar batteries. These nanometre-scale power producers are responsible for transducing the energy of sunlight into a form that can be used by biological systems, thereby powering most of the biological activity on the planet. Although to the layman the word 'photosynthesis' is usually associated with green plants, much of our understanding of the molecular basis of biological transduction of light energy has come from studies of purple photosynthetic bacteria. Their RCs (reaction centres) and attendant light-harvesting complexes have been subjected to an intensive spectroscopic scrutiny, coupled with genetic manipulation and structural studies, that has revealed many of the molecular and mechanistic details of biological energy transfer, electron transfer and coupled proton translocation. This review provides a short overview of the structure and mechanism of the purple bacterial RC, focusing in the main on the most heavily studied complex from Rhodobacter sphaeroides.

Low-frequency mode activity of heme: femtosecond coherence spectroscopy of iron porphine halides and nitrophorin

The low-frequency mode activity of metalloporphyrins has been studied for iron porphine-halides (Fe(P)(X), X = Cl, Br) and nitrophorin 4 (NP4) using femtosecond coherence spectroscopy (FCS) in combination with polarized resonance Raman spectroscopy and density functional theory (DFT). It is confirmed that the mode symmetry selection rules for FCS are the same as for Raman scattering and that both Franck-Condon and Jahn-Teller mode activities are observed for Fe(P)(X) under Soret resonance conditions. The DFT-calculated low-frequency (20-400 cm (-1)) modes, and their frequency shifts upon halide substitution, are in good agreement with experimental Raman and coherence data, so that mode assignments can be made. The doming mode is located at approximately 80 cm (-1) for Fe(P)(Cl) and at approximately 60 cm (-1) for Fe(P)(Br). NP4 is also studied with coherence techniques, and the NO-bound species of ferric and ferrous NP4 display a mode at approximately 30-40 cm (-1) that is associated with transient heme doming motion following NO photolysis. The coherence spectra of three ferric derivatives of NP4 with different degrees of heme ruffling distortion are also investigated. We find a mode at approximately 60 cm (-1) whose relative intensity in the coherence spectra depends quadratically on the magnitude of the ruffling distortion. To quantitatively account for this correlation, a new "distortion-induced" Raman enhancement mechanism is presented. This mechanism is unique to low-frequency "soft modes" of the molecular framework that can be distorted by environmental forces. These results demonstrate the potential of FCS as a sensitive probe of dynamic and functionally important nonplanar heme vibrational excitations that are induced by the protein environmental forces or by the chemical reactions in the aqueous phase.

Energetics and kinetics of primary charge separation in bacterial photosynthesis

We report the results of molecular dynamics (MD) simulations and formal modeling of the free-energy surfaces and reaction rates of primary charge separation in the reaction center of Rhodobacter sphaeroides. Two simulation protocols were used to produce MD trajectories. Standard force-field potentials were employed in the first protocol. In the second protocol, the special pair was made polarizable to reproduce a high polarizability of its photoexcited state observed by Stark spectroscopy. The charge distribution between covalent and charge-transfer states of the special pair was dynamically adjusted during the simulation run. We found from both protocols that the breadth of electrostatic fluctuations of the protein/water environment far exceeds previous estimates, resulting in about 1.6 eV reorganization energy of electron transfer in the first protocol and 2.5 eV in the second protocol. Most of these electrostatic fluctuations become dynamically frozen on the time scale of primary charge separation, resulting in much smaller solvation contributions to the activation barrier. While water dominates solvation thermodynamics on long observation times, protein emerges as the major thermal bath coupled to electron transfer on the picosecond time of the reaction. Marcus parabolas were obtained for the free-energy surfaces of electron transfer by using the first protocol, while a highly asymmetric surface was obtained in the second protocol. A nonergodic formulation of the diffusion-reaction electron-transfer kinetics has allowed us to reproduce the experimental results for both the temperature dependence of the rate and the nonexponential decay of the population of the photoexcited special pair.

Coherent oscillations in ultrafast fluorescence of photoactive yellow protein

The ultrafast photoinduced dynamics of photoactive yellow protein in aqueous solution were studied at room temperature by femtosecond fluorescence spectroscopy using an optical Kerr-gate technique. Coherent oscillations of the wave packet were directly observed in the two-dimensional time-energy map of ultrafast fluorescence with 180 fs time resolution and 5 nm spectral resolution. The two-dimensional map revealed that four or more oscillatory components exist within the broad bandwidth of the fluorescence spectrum, each of which is restricted in the respective narrow spectral region. Typical frequencies of the oscillatory modes are 50 and 120 cm(-1). In the landscape on the map, the oscillatory components were recognized as the ridges which were winding and descending with time. The amplitude of the oscillatory and winding behaviors is a few hundred cm(-1), which is the same order as the frequencies of the oscillations. The mean spectral positions of the oscillatory components in the two-dimensional map are well explained by considering the vibrational energies of intramolecular modes in the electronic ground state of the chromophore. The entire view of the wave packet oscillations and broadening in the electronic excited state, accompanied by fluorescence transitions to the vibrational sublevels belonging to the electronic ground state, was obtained.

Investigations of vibrational coherence in the low-frequency region of ferric heme proteins

Femtosecond coherence spectroscopy is applied to a series of ferric heme protein samples. The low-frequency vibrational spectra that are revealed show dominant oscillations near 40 cm(-1). MbCN is taken as a typical example of a histidine-ligated, six-coordinate, ferric heme and a comprehensive spectroscopic analysis is carried out. The results of this analysis reveal a new heme photoproduct species, absorbing near 418 nm, which is consistent with the photolysis of the His(93) axial ligand. The photoproduct undergoes subsequent rebinding/recovery with a time constant of approximately 4 ps. The photoproduct lineshapes are consistent with a photolysis quantum yield of 75-100%, although the observation of a relatively strong six-coordinate heme coherence near 252 cm(-1) (assigned to nu(9) in the MbCN Raman spectrum) suggests that the 75% lower limit is much more likely. The phase and amplitude excitation profiles of the low-frequency mode at 40 cm(-1) suggest that this mode is strongly coupled to the MbCN photoproduct species and it is assigned to the doming mode of the transient penta-coordinated material. The absolute phase of the 40 cm(-1) mode is found to be pi/2 on the red side of 418 nm and it jumps to 3pi/2 as excitation is tuned to the blue side of 418 nm. The absolute phase of the 40 cm(-1) signal is not explained by the standard theory for resonant impulsive stimulated Raman scattering. New mechanisms that give a dominant momentum impulse to the resonant wavepacket, rather than a coordinate displacement, are discussed. The possibilities of heme iron atom recoil after photolysis, as well as ultrafast nonradiative decay, are explored as potential ways to generate the strong momentum impulse needed to understand the phase properties of the 40 cm(-1) mode.

Ultrafast dynamics of ligands within heme proteins

Physiological bond formation and bond breaking events between proteins and ligands and their immediate consequences are difficult to synchronize and study in general. However, diatomic ligands can be photodissociated from heme, and thus in heme proteins ligand release and rebinding dynamics and trajectories have been studied on timescales of the internal vibrations of the protein that drive many biochemical reactions, and longer. The rapidly expanding number of characterized heme proteins involved in a large variety of functions allows comparative dynamics-structure-function studies. In this review, an overview is given of recent progress in this field, and in particular on initial sensing processes in signaling proteins, and on ligand and electron transfer dynamics in oxidases and cytochromes.

Low frequency spectral density of ferrous heme: perturbations induced by axial ligation and protein insertion

Femtosecond coherence spectroscopy is used to probe low frequency (20-400 cm(-1)) modes of the ferrous heme group in solution, with and without 2-methyl imidazole (2MeIm) as an axial ligand. The results are compared to heme proteins (CPO, P450(cam), HRP, Mb) where insertion of the heme into the protein results in redistribution of the low frequency spectral density and in (approximately 60%) longer damping times for the coherent signals. The major effect of imidazole ligation to the ferrous heme is the "softening" of the low frequency force constants by a factor of approximately 0.6 +/- 0.1. The functional consequences of imidazole ligation are assessed and it is found that the enthalpic CO rebinding barrier is increased significantly when imidazole is bound. The force constant softening analysis, combined with the kinetics results, indicates that the iron is displaced by only approximately 0.2 A from the heme plane in the absence of the imidazole ligand, whereas it is displaced by approximately 0.4 A when imidazole (histidine) is present. This suggests that binding of imidazole (histidine) as an axial ligand, and the concomitant softening of the force constants, leads to an anharmonic distortion of the heme group that has significant functional consequences.

Role of the middle residue in the triple tryptophan electron transfer chain of DNA photolyase: ultrafast spectroscopy of a Trp-->Phe mutant

Photoreduction of the semi-reduced flavin adenine dinucleotide cofactor FADH* in DNA photolyase from Escherichia coli into FADH- involves three tryptophan (W) residues that form a closely spaced electron-transfer chain FADH*-W382-W359-W306. To investigate this process, we have constructed a mutant photolyase in which W359 is replaced by phenylalanine (F). Monitoring its photoproducts by femtosecond spectroscopy, the excited-state FADH* was found to decay in approximately 30 ps, similar as in wild type (WT) photolyase. In contrast to WT, however, in W359F mutant photolyase the ground-state FADH* fully recovered virtually concomitantly with the decay of its excited state and, despite the presence of the primary electron donor W382, no measurable flavin reduction was observed at any time. Thus, W359F photolyase appears to behave like many other flavoproteins, where flavin excited states are quenched by very short-lived oxidation of aromatic residues. Our analysis indicates that both charge recombination of the primary charge separation state FADH-W382*+ and (in WT) electron transfer from W359 to W382*+ occur with time constants <4 ps, considerably faster than the initial W382-->FADH* electron-transfer step. Our results provide a first experimental indication that electron transfer between aromatic residues can take place on the time scale of approximately 10(-12) s.

Accommodation of NO in the active site of mammalian and bacterial cytochrome c oxidase aa3

Following different reports on the stoichiometry and configuration of NO binding to mammalian and bacterial reduced cytochrome c oxidase aa(3) (CcO), we investigated NO binding and dynamics in the active site of beef heart CcO as a function of NO concentration, using ultrafast transient absorption and EPR spectroscopy. We find that in the physiological range only one NO molecule binds to heme a(3), and time-resolved experiments indicate that even transient binding to Cu(B) does not occur. Only at very high (approximately 2 mM) concentrations a second NO is accommodated in the active site, although in a different configuration than previously observed for CcO from Paracoccus denitrificans [E. Pilet, W. Nitschke, F. Rappaport, T. Soulimane, J.-C. Lambry, U. Liebl and M.H. Vos. Biochemistry 43 (2004) 14118-14127], where we proposed that a second NO does bind to Cu(B). In addition, in the bacterial enzyme two NO molecules can bind already at NO concentrations of approximately 1 microM. The unexpected differences highlighted in this study may relate to differences in the physiological relevance of the CcO-NO interactions in both species.

Ultrafast Dynamics of Photoactive Yellow Protein via the Photoexcitation and Emission Processes†

Pump-dump fluorescence spectroscopy was performed for photoactive yellow protein (PYP) at room temperature. The effect of the dump pulse on the population of the potential energy surface of the electronic excited state was examined as depletion in the stationary fluorescence intensity. The dynamic behavior of the population in the electronic excited state was successfully probed in the various combinations of the pump-dump delay, the dump-pulse wavelength, the dump-pulse energy and the observation wavelength. The experimental results were compared with the results obtained by the femtosecond time-resolved fluorescence spectroscopy.

Analysis of cross peaks in two-dimensional electronic photon-echo spectroscopy for simple models with vibrations and dissipation

The recently developed efficient method for the calculation of four-wave mixing signals [M. F. Gelin et al., J. Chem. Phys. 123, 164112 (2005)] is employed for the calculation of two-dimensional electronic photon-echo spectra. The effect of the explicit treatment of vibrations coupled to the electronic transitions is systematically analyzed. The impact of pulse durations, optical dephasing, and temperature on the spectra is investigated. The study aims at an understanding of the mechanisms which may give rise to cross peaks in the two-dimensional electronic spectra and at clarifying the conditions of their detection.

Femtosecond quantum control of molecular dynamics in the condensed phase

We review the progress in controlling quantum dynamical processes in the condensed phase with femtosecond laser pulses. Due to its high particle density the condensed phase has both high relevance and appeal for chemical synthesis. Thus, in recent years different methods have been developed to manipulate the dynamics of condensed-phase systems by changing one or multiple laser pulse parameters. Single-parameter control is often achieved by variation of the excitation pulse's wavelength, its linear chirp or its temporal subpulse separation in case of pulse sequences. Multiparameter control schemes are more flexible and provide a much larger parameter space for an optimal solution. This is realized in adaptive femtosecond quantum control, in which the optimal solution is iteratively obtained through the combination of an experimental feedback signal and an automated learning algorithm. Several experiments are presented that illustrate the different control concepts and highlight their broad applicability. These fascinating achievements show the continuous progress on the way towards the control of complex quantum reactions in the condensed phase.

Ligand Dynamics in an Electron Transfer Protein

Substitution of the heme coordination residue Met-80 of the electron transport protein yeast iso-1-cytochrome c allows external ligands like CO to bind and thus increase the effective redox potential. This mutation, in principle, turns the protein into a quasi-native photoactivable electron donor. We have studied the kinetic and spectral characteristics of geminate recombination of heme and CO in a series of single M80X (X = Ala, Ser, Asp, Arg) mutants, using femtosecond transient absorption spectroscopy. In these proteins, all geminate recombination occurs on the picosecond and early nanosecond time scale, in a multiphasic manner, in which heme relaxation takes place on the same time scale. The extent of geminate recombination varies from >99% (Ala, Ser) to approximately 70% (Arg), the latter value being in principle low enough for electron injection studies. The rates and extent of the CO geminate recombination phases are much higher than in functional ligand-binding proteins like myoglobin, presumably reflecting the rigid and hydrophobic properties of the heme environment, which are optimized for electron transfer. Thus, the dynamics of CO recombination in cytochrome c are a tool for studying the heme pocket, in a similar way as NO in myoglobin. We discuss the differences in the CO kinetics between the mutants in terms of the properties of the heme environment and strategies to enhance the CO escape yield. Experiments on double mutants in which Phe-82 is replaced by Asp or Gly as well as the M80D substitution indicate that such steric changes substantially increase the motional freedom-dissociated CO.

Enhancement and Suppression of Vibrational Coherence in Degenerate Four-Wave-Mixing Signal Generated from Dye-Doped Polymer Films

Vibrational coherence in the degenerate four-wave-mixing (DFWM) signal generated from polymer films doped with a dye, oxazine 4 (Ox4), at 10 K was investigated. It was found that the amplitudes of some low-frequency oscillations (<400 cm(-1)) were enhanced when the delay between the first and second femtosecond pulses was set out of phase with the oscillation period. Frequency and reorganization energy dependence was investigated by computer simulation based on the response function formalism which considers all the possible Liouville space pathways for the DFWM signal. It was revealed that low-frequency oscillations with weak coupling to the optical transition can be enhanced in the stimulated photon echo signal compared to the transient grating signal.