Subpicosecond spectroscopy of bacteriorhodopsin

Ultrafast photochemistry of anabaena sensory rhodopsin: experiment and theory

Light induced isomerization of the retinal chromophore activates biological function in all retinal protein (RP) driving processes such as ion-pumping, vertebrate vision and phototaxis in organisms as primitive as archea, or as complex as mammals. This process and its consecutive reactions have been the focus of experimental and theoretical research for decades. The aim of this review is to demonstrate how the experimental and theoretical research efforts can now be combined to reach a more comprehensive understanding of the excited state process on the molecular level. Using the Anabaena Sensory Rhodopsin as an example we will show how contemporary time-resolved spectroscopy and recently implemented excited state QM/MM methods consistently describe photochemistry in retinal proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.

Experimental evidence for secondary protein-chromophore interactions at the Schiff base linkage in bacteriorhodopsin: Molecular mechanism for proton pumping

Resonance Raman spectroscopy of the retinylidene chromophore in various isotopically labeled membrane environments together with spectra of isotopically labeled model compounds demonstrates that a secondary protein interaction is present at the protonated Schiff base linkage in bacteriorhodopsin. The data indicate that although the interaction is present in all protonated bacteriorhodopsin species it is absent in unprotonated intermediates. Furthermore, kinetic resonance Raman spectroscopy has been used to monitor the dynamics of Schiff base deprotonation as a function of pH. All our results are consistent with lysine as the interacting group. A structure for the interaction is proposed in which the interacting protein group in an unprotonated configuration is complexed through the Schiff base proton to the Schiff base nitrogen. These data suggest a molecular mechanism for proton pumping and ion gate molecular regulation. In this mechanism, light causes electron redistribution in the retinylidene chromophore, which results in the deprotonation of an amino acid side chain with pK >10.2 +/- 0.3 (e.g., arginine). This induces subsequent retinal and protein conformational transitions which eventually lower the pK of the Schiff base complex from >12 before light absorption to 10.2 +/- 0.3 in microseconds after photon absorption. Finally, in this low pK state the complex can reprotonate the proton-deficient high pK group generated by light, and the complex is then reprotonated from the opposite side of the membrane.

Early picosecond events in the photocycle of bacteriorhodopsin

The primary processes of the photochemical cycle of light-adapted bacteriorhodopsin (BR) were studied by various experimental techniques with a time resolution of 5 x 10(-13) s. The following results were obtained. (a) After optical excitation the first excited singlet state S(1) of bacteriorhodopsin is observed via its fluorescence and absorption properties. The population of the excited singlet state decays with a lifetime tau(1) of approximately 0.7 ps (430 +/- 50 fs) (52). (b) With the same time constant the first ground-state intermediate J builds up. Its absorption spectrum is red-shifted relative to the spectrum of BR by approximately 30 nm. (c) The second photoproduct K, which appears with a time constant of tau(2) = 5 ps shows a red-shift of 20 nm, relative to the peak of BR. Its absorption remains constant for the observation time of 300 ps. (d) Upon suspending bacteriorhodopsin in D(2)O and deuterating the retinal Schiff base at its nitrogen (lysine 216), the same photoproducts J and K are observed. The relaxation time constants tau(1) and tau(2) remain unchanged upon deuteration within the experimental accuracy of 20%.

Nanosecond photolytic interruption of bacteriorhodopsin photocycle: K-590 --> BR-570 reaction

The molecular processes comprising the room temperature bacteriorhodopsin (BR) photocycle are examined through the properties of the photo-induced reverse reaction, K-590 + hnu --> BR-570 (K --> BR). Two sequential pumping pulses, each of 10-ns duration, are used, respectively, to initiate the photocycle via the forward BR-570 + hnu --> K-590 (BR --> K) reaction (532 nm) and to photolytically interrupt the thermal BR photocycle after a 20-ns delay via K --> BR (620-700 nm). The ground-state BR-570 population, monitored by 633-nm absorption 200 mus after the photocycle begins, provides a quantitative measure of the efficiency with which K --> BR interrupts the photocycle to reform BR-570. The quantum yield (Phi) for K --> BR is found to be 1.6 +/- 0.1 times larger than that for BR --> K which, when compared to a Phi of 0.64 for BR --> K, suggests that Phi for K --> BR is approximately 1.0. The significance of such a high efficiency K --> BR reaction with respect to mechanistic descriptions of the BR photocycle is discussed.

Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics

Following a survey of 2D IR principles, this article describes recent experiments on the hydrogen-bond dynamics of small ions, amide-I modes, nitrile probes, peptides, reverse transcriptase inhibitors, and amyloid fibrils.

Bioenergetics of the Archaea

In the late 1970s, on the basis of rRNA phylogeny, Archaea (archaebacteria) was identified as a distinct domain of life besides Bacteria (eubacteria) and Eucarya. Though forming a separate domain, Archaea display an enormous diversity of lifestyles and metabolic capabilities. Many archaeal species are adapted to extreme environments with respect to salinity, temperatures around the boiling point of water, and/or extremely alkaline or acidic pH. This has posed the challenge of studying the molecular and mechanistic bases on which these organisms can cope with such adverse conditions. This review considers our cumulative knowledge on archaeal mechanisms of primary energy conservation, in relationship to those of bacteria and eucarya. Although the universal principle of chemiosmotic energy conservation also holds for Archaea, distinct features have been discovered with respect to novel ion-transducing, membrane-residing protein complexes and the use of novel cofactors in bioenergetics of methanogenesis. From aerobically respiring Archaea, unusual electron-transporting supercomplexes could be isolated and functionally resolved, and a proposal on the organization of archaeal electron transport chains has been presented. The unique functions of archaeal rhodopsins as sensory systems and as proton or chloride pumps have been elucidated on the basis of recent structural information on the atomic scale. Whereas components of methanogenesis and of phototrophic energy transduction in halobacteria appear to be unique to Archaea, respiratory complexes and the ATP synthase exhibit some chimeric features with respect to their evolutionary origin. Nevertheless, archaeal ATP synthases are to be considered distinct members of this family of secondary energy transducers. A major challenge to future investigations is the development of archaeal genetic transformation systems, in order to gain access to the regulation of bioenergetic systems and to overproducers of archaeal membrane proteins as a prerequisite for their crystallization.

Applications of ultrafast laser spectroscopy for the study of biological systems

The discovery of mode-locked laser operation now nearly two decades ago has started a development which enables researchers to probe the dynamics of ultrafast physical and chemical processes at the molecular level on shorter and shorter time scales. Naturally the first applications were in the fields of photophysics and photochemistry where it was then possible for the first time to probe electronic and vibrational relaxation processes on a sub-nanosecond timescale. The development went from lasers producing pulses of many picoseconds to the shortest pulses which are at present just a few femtoseconds long. Soon after their discovery ultrashort pulses were applied also to biological systems which has revealed a wealth of information contributing to our understanding of a broadrange of biological processes on the molecular level.It is the aim of this review to discuss the recent advances and point out some future trends in the study of ultrafast processes in biological systems using laser techniques. The emphasis will be mainly on new results obtained during the last 5 or 6 years. The term ultrafast means that I shall restrict myself to sub-nanosecond processes with a few exceptions.

Picosecond time-resolved fluorescence spectroscopy of K-590 in the bacteriorhodopsin photocycle

The fluorescence spectrum of a distinct isometric and conformational intermediate formed on the 10(-11) s time scale during the bacteriorhodopsin (BR) photocycle is observed at room temperature using a two laser, pump-probe technique with picosecond time resolution. The BR photocycle is initiated by pulsed (8 ps) excitation at 565 nm, whereas the fluorescence is generated by 4-ps laser pulses at 590 nm. The unstructured fluorescence extends from 650 to 880 nm and appears in the same general spectral region as the fluorescence spectrum assigned to BR-570. The transient fluorescence spectrum can be distinguished from that assigned to BR-570 by a larger emission quantum yield (approximately twice that of BR-570) and by a maximum intensity near 731 nm (shifted 17 nm to higher energy from the maximum of the BR-570 fluorescence spectrum). The fluorescence spectrum of BR-570 only is measured with low energy, picosecond pulsed excitation at 590 nm and is in good agreement with recent data in the literature. The assignment of the transient fluorescence spectrum to the K-590 intermediate is based on its appearance at time delays longer than 40 ps. The K-590 fluorescence spectrum remains unchanged over the entire 40-100-ps interval. The relevance of these fluorescence data with respect to the molecular mechanism used to model the primary processes in the BR photocycle also is discussed.

Direct observation of the femtosecond excited-state cis-trans isomerization in bacteriorhodopsin

Femtosecond optical measurement techniques have been used to study the primary photoprocesses in the light-driven transmembrane proton pump bacteriorhodopsin. Light-adapted bacteriorhodopsin was excited with a 60-femtosecond pump pulse at 618 nanometers, and the transient absorption spectra from 560 to 710 nanometers were recorded from -50 to 1000 femtoseconds by means of 6-femtosecond probe pulses. By 60 femtoseconds, a broad transient hole appeared in the absorption spectrum whose amplitude remained constant for about 200 femtoseconds. Stimulated emission in the 660- to 710-nanometer region and excited-state absorption in the 560- to 580-nanometer region appeared promptly and then shifted and decayed from 0 to approximately 150 femtoseconds. These spectral features provide a direct observation of the 13-trans to 13-cis torsional isomerization of the retinal chromophore on the excited-state potential surface. Absorption due to the primary ground-state photoproduct J appears with a time constant of approximately 500 femtoseconds.

A time-resolved spectral study of the K and KL intermediates of bacteriorhodopsin

Nanosecond time-resolved absorption measurements on the photolysis products of bacteriorhodopsin (BR) in intact membranes are reported. At room temperature in fluid solution a single intermediate (KL) is seen 10 ns after excitation. Both spectral and kinetic results are consistent with the KL intermediate converting to the L intermediate by a single first order reaction. The observed temperature-dependent rate has the Arrhenius parameters: Ea = 10.5 kcal/mol, A = 5 x 10(13) s-1. The precursor to the KL intermediate is also observed. Its spectral character is consistent with the K intermediate which has been previously reported. The current data is consistent with a linear sequence in the BR photocycle for K, KL, and L in room temperature fluid solution. Differences in the spectral characteristics of the K intermediates described here and elsewhere are discussed in terms of differences in the microenvironment around the retinal moiety and the affect this may have on the conformation of the chromophore.

Fourier transform infrared spectroscopic evidence for the existence of two conformations of the bacteriorhodopsin primary photoproduct at low temperature

Fourier transform infrared difference spectroscopy of bacteriorhodopsin at low temperature reveals at least two stable forms of bacteriorhodopsin570 and the K photoproduct. In the case of bacteriorhodopsin570, warming from 81 to 135 K causes a reduction in absorption of several chromophore vibrations, but not the C = N stretching mode. These changes are consistent with a reorientation of the chromophore which leaves the angle of the C = N bond unchanged relative to the membrane plane. In the case of the K intermediate, two different forms can be isolated at 135 K on the basis of wavelength-dependent photoalteration. One form is identical to the low temperature K630 species, whereas a second blue-shifted form is present only above 135 K. This new form exhibits a 985 cm-1 peak in the hydrogen-out-of-plane bending region, which is similar to a reported room-temperature resonance Raman spectrum of K. Temperature-dependent changes in the conformation of the protein involving possible alterations in peptide hydrogen bonding are also detected.

Picosecond events in the photochemical cycle of the light-driven chloride-pump halorhodopsin

The early events in halorhodopsin after light excitation are studied with picosecond time resolution. Absorption and fluorescence measurements show that the electronically excited state of the incorporated retinal has a lifetime of 5 ps. Within that time a red-shifted photoproduct is formed that remains stable for at least 2 ns.

Excited-state dynamics of bacteriorhodopsin

Near infrared emission of bacteriorhodopsin at neutral pH and at room temperature was characterized by a large Stokes shift. This characteristic was lost in an acidic pH (approximately pH 2) where a remarkable enchancement (more than 10 times) in the fluorescence quantum yield accompanied the red shift in the main absorption band. It is suggested from fluorescence polarization measurements that the emission occurs from the first allowed excited state of the retinylidene chromophore, irrespective of pH. We suggest that the large Stokes shift observed at neutral pH is a result of a charge displacement (e.g., proton translocation) that occurs immediately after excitation, and is prevented by protonation (in the ground state) of an amino-acid residue in the protein.

Photoselection and circular dichroism in the purple membrane

The transient dichroic ratio D = delta A parallel/delta A perpendicular has been measured in the visible absorption region of bacteriorhodopsin in purple membrane by a flash photolysis method. D is found to be wavelength independent throughout the visible absorption band, and reaches a maximum value of 2.75 +/- 0.15 on reduction of the excitation intensity. This value is close to that expected for a single nondegenerate transition dipole moment and is incompatible with the strong exciton coupling model used to explain circular dichroism (CD) spectrum of purple membrane. A time-dependent analysis of the exciton interaction and consideration of the coupling strength suggests an explanation of these observations. It is concluded that excitation interaction between retinals in purple membrane is of the weak or very weak type defined by Förster.