Femtosecond time-resolved fluorescence spectroscopy of bacteriorhodopsin: Direct observation of excited state dynamics in the primary step of the proton pump cycle

Insights into excited-state and isomerization dynamics of bacteriorhodopsin from ultrafast transient UV absorption

A visible-pump/UV-probe transient absorption is used to characterize the ultrafast dynamics of bacteriorhodopsin with 80-fs time resolution. We identify three spectral components in the 265- to 310-nm region, related to the all-trans retinal, tryptophan (Trp)-86 and the isomerized photoproduct, allowing us to map the dynamics from reactants to products, along with the response of Trp amino acids. The signal of the photoproduct appears with a time delay of approximately 250 fs and is characterized by a steep rise ( approximately 150 fs), followed by additional rise and decay components, with time scales characteristic of the J intermediate. The delayed onset and the steep rise point to an impulsive formation of a transition state on the way to isomerization. We argue that this impulsive formation results from a splitting of a wave packet of torsional modes on the potential surface at the branching between the all-trans and the cis forms. Parallel to these dynamics, the signal caused by Trp response rises in approximately 200 fs, because of the translocation of charge along the conjugate chain, and possible mechanisms are presented, which trigger isomerization.

Twisting Dynamics in the Excited Singlet State of Michler's Ketone

Ultrafast relaxation dynamics of the excited singlet (S(1)) state of Michler's ketone (MK) has been investigated in different kinds of solvents using a time-resolved absorption spectroscopic technique with 120 fs time resolution. This technique reveals that conversion of the locally excited (LE) state to the twisted intramolecular charge transfer (TICT) state because of twisting of the N,N-dimethylanilino groups with respect to the central carbonyl group is the major relaxation process responsible for the multi-exponential and probe-wavelength-dependent transient absorption dynamics of the S1 state of MK, but solvation dynamics does not have a significant role in this process. Theoretical optimization of the ground-state geometry of MK shows that the dimethylanilino groups attached to the central carbonyl group are at a dihedral angle of about 51 degrees with respect to each other because of steric interaction between the phenyl rings. Following photoexcitation of MK to its S1 state, two kinds of twisting motions have been resolved. Immediately after photoexcitation, an ultrafast "anti-twisting" motion of the dimethylanilino groups brings back the pretwisted molecule to a near-planar geometry with high mesomeric interaction and intramolecular charge transfer (ICT) character. This motion is observed in all kinds of solvents. Additionally, in solvents of large polarity, the dimethylamino groups undergo further twisting to about 90 degrees with respect to the phenyl ring, to which it is attached, leading to the conversion of the ICT state to the TICT state. Similar characteristics of the absorption spectra of the TICT state and the anion radical of MK establish the nearly pure electron transfer (ET) character of the TICT state. In aprotic solvents, because of the steep slope of the potential energy surface near the Franck-Condon (FC) or LE state region, the LE state is nearly nonemissive at room temperature and fluorescence emission is observed from only the ICT and TICT states. Alternatively, in protic solvents, because of an intermolecular hydrogen-bonding interaction between MK and the solvent, the LE region is more flat and stimulated emission from this state is also observed. However, a stronger hydrogen-bonding interaction between the TICT state and the solvent as well as the closeness between the two potential energy surfaces due to the TICT and the ground states cause the nonradiative coupling between these states to be very effective and, hence, cause the TICT state to be weakly emissive. The multi-exponentiality and strong wavelength-dependence of the kinetics of the relaxation process taking place in the S1 state of MK have arisen for several reasons, such as strong overlapping of transient absorption and stimulated emission spectra of the LE, ICT, and TICT states, which are formed consecutively following photoexcitation of the molecule, as well as the fact that different probe wavelengths monitor different regions of the potential energy surface representing the twisting motion of the excited molecule.

(Sub)-Picosecond Spectral Evolution of Fluorescence in Photoactive Proteins Studied with a Synchroscan Streak Camera System

The spectral evolution of three photoactive proteins has been investigated by measuring the fluorescence with good temporal and wavelength resolution and a high signal-to-noise ratio. Upon excitation at 400 nm wild-type (wt) PYP both at neutral pH and in the low-pH blueshifted pBdark state exhibited a strong quenching of the fluorescence, the major part of which could be described by lifetimes of about 1.7 and 7.7 ps. The remaining fluorescence decay occurred multiexponentially with lifetimes between 30 and 125 ps. Additionally, in wtPYP at neutral pH, a dynamic Stokes shift was found to occur with a time constant of about 0.25 ps. In a PYP preparation that was reconstituted with the chromophore 7-hydroxy-coumarin-3- carboxylic acid rather than the native coumaric acid, and which is therefore not capable of performing the cis-trans-isomerization that initiates the photocycle in wtPYP, the fluorescence was found to decay multiexponentially with lifetimes of 51 ps, 0.33 and 3.77 ns. Additionally, dynamic Stokes shifts were observed with time constants of about 0.1 and 3.5 ps. Upon comparison of the dynamics of this preparation with that of wtPYP the multiexponential decay with lifetimes of 1.7 and 7.7 ps found in wtPYP was attributed to photochemistry of the p-coumaric-acid chromophore. The emission from bacteriorhodopsin mutant D85S upon excitation at 635 nm decays biexponentially with estimated lifetimes of 5.2 and 19.1 ps. No dynamic Stokes shift was observed here. Four lifetimes were needed to describe the decay of the emission from the A* state in the green fluorescent protein. From a target analysis it was concluded that the longer lifetimes are accompanied by a decreasing probability of forming I*, which approaches zero with the longest A* lifetime of 1.5 ns. These observations may be explained by heterogeneity of A and by relaxation of A*. In all three systems studied, multiexponential decay of emission was present, suggesting that heterogeneity is a common feature of these chromophore protein complexes.

Ultrafast excited state dynamics of the protonated Schiff base of all-trans retinal in solvents

We present a comparative study of the ultrafast photophysics of all-trans retinal in the protonated Schiff base form in solvents with different polarities and viscosities. Steady-state spectra of retinal in the protonated Schiff base form show large absorption-emission Stokes shifts (6500-8100 cm(-1)) for both polar and nonpolar solvents. Using a broadband fluorescence up-conversion experiment, the relaxation kinetics of fluorescence is investigated with 120 fs time resolution. The time-zero spectra already exhibit a Stokes-shift of approximately 6000 cm(-1), indicating depopulation of the Franck-Condon region in < or =100 fs. We attribute it to relaxation along skeletal stretching. A dramatic spectral narrowing is observed on a 150 fs timescale, which we assign to relaxation from the S(2) to the S(1) state. Along with the direct excitation of S(1), this relaxation populates different quasistationary states in S(1), as suggested from the existence of three distinct fluorescence decay times with different decay associated spectra. A 0.5-0.65 ps decay component is observed, which may reflect the direct repopulation of the ground state, in line with the small isomerization yield in solvents. Two longer decay components are observed and are attributed to torsional motion leading to photo-isomerization. The various decay channels show little or no dependence with respect to the viscosity or dielectric constant of the solvents. This suggests that in the protein, the bond selectivity of isomerization is mainly governed by steric effects.

Excited-state dynamics of bacteriorhodopsin probed by broadband femtosecond fluorescence spectroscopy

The impact of varying excitation densities (approximately 0.3 to approximately 40 photons per molecule) on the ultrafast fluorescence dynamics of bacteriorhodopsin has been studied in a wide spectral range (630-900 nm). For low excitation densities, the fluorescence dynamics can be approximated biexponentially with time constants of <0.15 and approximately 0.45 ps. The spectrum associated with the fastest time constant peaks at 650 nm, while the 0.45 ps component is most prominent at 750 nm. Superimposed on these kinetics is a shift of the fluorescence maximum with time (dynamic Stokes shift). Higher excitation densities alter the time constants and their amplitudes. These changes are assigned to multi-photon absorptions.

Contrasting the excited-state dynamics of the photoactive yellow protein chromophore: protein versus solvent environments

Wavelength- and time-resolved fluorescence experiments have been performed on the photoactive yellow protein, the E46Q mutant, the hybrids of these proteins containing a nonisomerizing "locked" chromophore, and the native and locked chromophores in aqueous solution. The ultrafast dynamics of these six systems is compared and spectral signatures of isomerization and solvation are discussed. We find that the ultrafast red-shifting of fluorescence is associated mostly with solvation dynamics, whereas isomerization manifests itself as quenching of fluorescence. The observed multiexponential quenching of the protein samples differs from the single-exponential lifetimes of the chromophores in solution. The locked chromophore in the protein environment decays faster than in solution. This is due to additional channels of excited-state energy dissipation via the covalent and hydrogen bonds with the protein environment. The observed large dispersion of quenching timescales observed in the protein samples that contain the native pigment favors both an inhomogeneous model and an excited-state barrier for isomerization.

Membrane lateral mobility obstructed by polymer-tethered lipids studied at the single molecule level

Obstructed long-range lateral diffusion of phospholipids (TRITC-DHPE) and membrane proteins (bacteriorhodopsin) in a planar polymer-tethered 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer is studied using wide-field single molecule fluorescence microscopy. The obstacles are well-controlled concentrations of hydrophobic lipid-mimicking dioctadecylamine moieties in the polymer-exposed monolayer of the model membrane. Diffusion of both types of tracer molecules is well described by a percolating system with different percolation thresholds for lipids and proteins. Data analysis using a free area model of obstructed lipid diffusion indicates that phospholipids and tethered lipids interact via hard-core repulsion. A comparison to Monte Carlo lattice calculations reveals that tethered lipids act as immobile obstacles, are randomly distributed, and do not self-assemble into large-scale aggregates for low to moderate tethering concentrations. A procedure is presented to identify anomalous subdiffusion from tracking data at a single time lag. From the analysis of the cumulative distribution function of the square displacements, it was found that TRITC-DHPE and W80i show normal diffusion at lower concentrations of tethered lipids and anomalous diffusion at higher ones. This study may help improve our understanding of how lipids and proteins in biomembranes may be obstructed by very small obstacles comprising only one or very few molecules.

Femtosecond primary events in bacteriorhodopsin and its retinal modified analogs: Revision of commonly accepted interpretation of electronic spectra of transient intermediates in the bacteriorhodopsin photocycle

Femtosecond primary events in bacteriorhodopsin (BR) and its retinal modified analogs are discussed. Ultrafast time resolved electronic spectra of the primary intermediates induced in the BR photocycle are discussed along with spectral and kinetic inconsistencies of the previous models proposed in the literature. The theoretical model proposed in this paper based on vibrational coupling between the electronic transition of the chromophore and intramolecular vibrational modes allows us to calculate the equilibrium electronic absorption band shape and the hole burning profiles. The model is able to rationalize the complex pattern of behavior for the primary events in BR and explain the origin of the apparent inconsistencies between the experiment and the previous theoretical models. The model presented in the paper is based on the anharmonic coupling assumption in the adiabatic approximation using the canonical transformation method for diagonalization of the vibrational Hamiltonian instead of the commonly used perturbation theory. The electronic transition occurs between the Born-Oppenheimer potential energy surfaces with the electron involved in the transition being coupled to the intramolecular vibrational modes of the molecule (chromophore). The relaxation of the excited state occurs by indirect damping (dephasing) mechanisms. The indirect dephasing is governed by the time evolution of the anharmonic coupling constant driven by the resonance energy exchange between the intramolecular vibrational mode and the bath. The coupling with the intramolecular vibrational modes results in the Franck-Condon progression of bands that are broadened due to the vibrational dephasing mechanisms. The electronic absorption line shape has been calculated based on the linear response theory whereas the third order nonlinear response functions have been used to analyze the hole burning profiles obtained from the pump-probe time-resolved measurements. The theoretical treatment proposed in this paper provides a basis for a substantial revision of the commonly accepted interpretation of the primary events in the BR photocycle that exists in the literature.

Femtosecond and picosecond fluorescence of native bacteriorhodopsin and a nonisomerizing analog

The spectrally and temporally resolved fluorescence properties of native bacteriorhodopsin (bR) and bR reconstituted with a nonisomerizing analog of the retinal Schiff base (bR5.12) are examined. The first attempt to experimentally monitor the excited state relaxation processes in both type of pigments using ultrafast fluorescence spectroscopy is reported. The fluorescence is emitted from retinal molecules in an all-trans configuration. Substantial energy relaxation involves very fast intramolecular and intermolecular vibrational modes and these are shown to occur on a time scale faster than isomerization. The possible contribution of dielectric interaction between the retinal Schiff base and the protein environment for the excited state energy relaxation is discussed.

Real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization

Real-time investigations of the rearrangement of bonds during chemical transformations require femtosecond temporal resolution, so that the atomic vibrations within the reacting molecules can be observed. Following the development of lasers capable of emitting ultrashort laser flashes on this timescale, chemical reactions involving relatively simple molecules have been monitored in detail, revealing the transient existence of intermediate species as reactants are transformed into products. Here we report the direct observation of nuclear motion in a complex biological system, the retinal chromophore of bacteriorhodopsin (bR568), as it undergoes the trans-cis photoisomerization that is fundamental to the vision process. By using visible-light pulses of less than 5 femtosecond in duration, we are able to monitor changes in the vibrational spectra of the transition state and thus show that despite photoexcitation of the anti-bonding molecular orbital involved, isomerization does not occur instantly, but involves transient formation of a so-called 'tumbling state'. Our observations thus agree with growing experimental and ab initio evidence for a three-state photoisomerization model and firmly discount the initially suggested two-state model for this process.

Examples of hula-twist in photochemical cis- trans isomerization

ALiu and Hammond recently reasoned that the hula-twist (HT), a volume-conserving cis-trans isomerization mechanism, is involved in reactions of confined systems. We now show that HT can be applied to various reported photochemical isomerization of chromophores (small organic systems as well as photoactive bio-pigments). The results, when taken as a whole, argue powerfully that HT is a common supramolecular photoisomerization reaction mechanism.

Closing in on bacteriorhodopsin: progress in understanding the molecule

Bacteriorhodopsin is the best understood ion transport protein and has become a paradigm for membrane proteins in general and transporters in particular. Models up to 2.5 A resolution of bacteriorhodopsin's structure have been published during the last three years and are basic for understanding its function. Thus one focus of this review is to summarize and to compare these models in detail. Another focus is to follow the protein through its catalytic cycle in summarizing more recent developments. We focus on literature published since 1995; a comprehensive series of reviews was published in 1995 (112).

Chemical dynamics in proteins: the photoisomerization of retinal in bacteriorhodopsin

Chemical dynamics in proteins are discussed, with bacteriorhodopsin serving as a model system. Ultrafast time-resolved methods used to probe the chemical dynamics of retinal photoisomerization in bacteriorhodopsin are discussed, along with future prospects for ultrafast time-resolved crystallography. The photoisomerization of retinal in bacteriorhodopsin is far more selective and efficient than in solution, the origins of which are discussed in the context of a three-state model for the photoisomerization reaction coordinate. The chemical dynamics are complex, with the excited-state relaxation exhibiting a multiexponential decay with well-defined rate constants. Possible origins for the two major components are also discussed.

The photoisomerization of retinal in bacteriorhodospin: experimental evidence for a three-state model

The primary events in the all-trans to 13-cis photoisomerization of retinal in bacteriorhodopsin have been investigated with femtosecond time-resolved absorbance spectroscopy. Spectra measured over a broad range extending from 7000 to 22,400 cm-1 reveal features whose dynamics are inconsistent with a model proposed earlier to account for the highly efficient photoisomerization process. Emerging from this work is a new three-state model. Photoexcitation of retinal with visible light accesses a shallow well on the excited state potential energy surface. This well is bounded by a small barrier, arising from an avoided crossing that separates the Franck-Condon region from the nearby reactive region of the photoisomerization coordinate. At ambient temperatures, the reactive region is accessed with a time constant of approximately 500 fs, whereupon the retinal rapidly twists and encounters a second avoided crossing region. The protein mediates the passage into the second avoided crossing region and thereby exerts control over the quantum yield for forming 13-cis retinal. The driving force for photoisomerization resides in the retinal, not in the surrounding protein. This view contrasts with an earlier model where photoexcitation was thought to access directly a reactive region of the excited-state potential and thereby drive the retinal to a twisted conformation within 100-200 fs.

Protein fluorescence, dynamics and function: exploration of analogy between electronically excited and biocatalytic transition states

With the advent and development of time-resolved spectroscopic techniques and substantial progress in understanding of photophysical and photochemical phenomena, a new goal may be achieved: modeling of biochemical reaction or its elementary step by a photochemical event occurring within the probe, bound to a protein molecule. The probe may be located in a well-determined site of the protein matrix and report on the modulation of the reaction rate by the matrix and by the surrounding solvent, or by interactions in multiprotein complexes and in biomembranes. The advantages of this approach are obvious: in contrast to ordinary biochemical reaction, the excited-state reaction may be started by a short light pulse, and its kinetics may be observed directly with high resolution in time. In addition, if the reaction rate is influenced by the dynamics of the protein matrix, these dynamics may be studied simultaneously with the reaction, by using the same or a similar probe and within the same time range. In this review, the prospects for application of probes exhibiting electron transfer, proton transfer, molecular rotations and isomerizations are presented and discussed. The general problem of photochemical modeling of biochemical reactions is discussed. This modeling may result in deeper understanding of enzyme catalyzed reaction mechanisms.