Chromophore In Bacteriorhodopsin Research Articles

Born–Oppenheimer molecular dynamics study on collective protein dynamics invoked by ultrafast photoisomerization of retinal chromophore in bacteriorhodopsin

Large-scale quantum-chemistry-based Born–Oppenheimer molecular dynamics simulations of collective protein dynamics of bacteriorhodopsin initiated by photoinduced all-trans→ 13-cis isomerization of retinal Schiff base chromophore compensate for missing information from time-resolved serial femtosecond X-ray crystallography measurements in terms of electronic states, energy transfer, and details of structural dynamics.

Protein Dynamics Preceding Photoisomerization of the Retinal Chromophore in Bacteriorhodopsin Revealed by Deep-UV Femtosecond Stimulated Raman Spectroscopy.

Bacteriorhodopsin is a prototypical photoreceptor protein that functions as a light-driven proton pump. The retinal chromophore of bacteriorhodopsin undergoes C13═C14 trans-to-cis isomerization upon photoexcitation, and it has been believed to be the first event that triggers the cascaded structural changes in bacteriorhodopsin. We investigated the protein dynamics of bacteriorhodopsin using deep-ultraviolet resonance femtosecond stimulated Raman spectroscopy. It was found that the stimulated Raman signals of tryptophan and tyrosine residues exhibit significant changes within 0.2 ps after photoexcitation while they do not noticeably change during the isomerization process. This result implies that the protein environment changes first, and its change is small during isomerization. The obtained femtosecond stimulated Raman data indicate that ultrafast change is induced in the protein part by the sudden creation of the large dipole of the excited-state chromophore, providing an environment that realizes efficient and selective isomerization.

Tip-Enhanced Infrared Difference-Nanospectroscopy of the Proton Pump Activity of Bacteriorhodopsin in Single Purple Membrane Patches.

Photosensitive proteins embedded in the cell membrane (about 5 nm thickness) act as photoactivated proton pumps, ion gates, enzymes, or more generally, as initiators of stimuli for the cell activity. They are composed of a protein backbone and a covalently bound cofactor (e.g. the retinal chromophore in bacteriorhodopsin (BR), channelrhodopsin, and other opsins). The light-induced conformational changes of both the cofactor and the protein are at the basis of the physiological functions of photosensitive proteins. Despite the dramatic development of microscopy techniques, investigating conformational changes of proteins at the membrane monolayer level is still a big challenge. Techniques based on atomic force microscopy (AFM) can detect electric currents through protein monolayers and even molecular binding forces in single-protein molecules but not the conformational changes. For the latter, Fourier-transform infrared spectroscopy (FTIR) using difference-spectroscopy mode is typically employed, but it is performed on macroscopic liquid suspensions or thick films containing large amounts of purified photosensitive proteins. In this work, we develop AFM-assisted, tip-enhanced infrared difference-nanospectroscopy to investigate light-induced conformational changes of the bacteriorhodopsin mutant D96N in single submicrometric native purple membrane patches. We obtain a significant improvement compared with the signal-to-noise ratio of standard IR nanospectroscopy techniques by exploiting the field enhancement in the plasmonic nanogap that forms between a gold-coated AFM probe tip and an ultraflat gold surface, as further supported by electromagnetic and thermal simulations. IR difference-spectra in the 1450–1800 cm–1 range are recorded from individual patches as thin as 10 nm, with a diameter of less than 500 nm, well beyond the diffraction limit for FTIR microspectroscopy. We find clear spectroscopic evidence of a branching of the photocycle for BR molecules in direct contact with the gold surfaces, with equal amounts of proteins either following the standard proton-pump photocycle or being trapped in an intermediate state not directly contributing to light-induced proton transport. Our results are particularly relevant for BR-based optoelectronic and energy-harvesting devices, where BR molecular monolayers are put in contact with metal surfaces, and, more generally, for AFM-based IR spectroscopy studies of conformational changes of proteins embedded in intrinsically heterogeneous native cell membranes.

Probing Biophysicochemical Interactions at Nano-Bio Interface of Perovskite Tandem Biosolar Cells

A first-principles study of the dielectric spectrum from Spectroscopic Ellipsometry associated with the photoactive chromophore in bacteriorhodopsin (bR) and its various mutant (Cys-35, D96N, triple glutamic mutationsE9Q/E194Q/E204Q) forms allowed the explanation of the effective coupling existing between the π electrons of the chromophore and the local environment of the Schiff base when adsorbed to the metal substrate. The role of the counter-ion on the electronic structure of the chromophore bulk is investigated by means of Gradient Projector Augmented density functional theory (GPAW-DFT) calculations. Experimental Spectroscopic Ellipsometry data have been interpreted in the light of these theoretical findings with an interesting accumulation of points along the optical band-gap. XANES and Photoemission measurements are further performed to study the bio-physicochemical interactions at the nano-biointerface for bR adsorbed on Au and Mesoporous TiO2 Substrates. The HOMO-LUMO interaction with the bR environment can stabilize the chromophore. Based on the spectroscopy results and DFT Calculation, a new FTO/TiO2/perovskite/Spiro//bR/Au Solar cell architecture could be proposed. The role of the traditional Semiconducting quantum dots (SQDs) in terms of their spintronic functionality and photosensitization will now be performed by the organohalide Perovskite in the proposed tandem solar cell architecture.

Ultrafast photoisomerisation of an isolated retinoid.

The photoinduced excited state dynamics of gas-phase trans-retinoate (deprotonated trans-retinoic acid, trans-RA-) are studied using tandem ion mobility spectrometry coupled with laser spectroscopy, and frequency-, angle- and time-resolved photoelectron imaging. Photoexcitation of the bright S3(ππ*) ← S0 transition leads to internal conversion to the S1(ππ*) state on a ≈80 fs timescale followed by recovery of S0 and concomitant isomerisation to give the 13-cis (major) and 9-cis (minor) photoisomers on a ≈180 fs timescale. The sub-200 fs stereoselective photoisomerisation parallels that for the retinal protonated Schiff base chromophore in bacteriorhodopsin. Measurements on trans-RA- in methanol using the solution photoisomerisation action spectroscopy technique show that 13-cis-RA- is also the principal photoisomer, although the 13-cis and 9-cis photoisomers are formed with an inverted branching ratio with photon energy in methanol when compared with the gas phase, presumably due to solvent-induced modification of potential energy surfaces and inhibition of electron detachment processes. Comparison of the gas-phase time-resolved data with transient absorption spectroscopy measurements on retinoic acid in methanol suggest that photoisomerisation is roughly six times slower in solution. This work provides clear evidence that solvation significantly affects the photoisomerisation dynamics of retinoid molecules.

Driving electrocatalytic activity by interface electronic structure control in a metalloprotein hybrid catalyst for efficient hydrogen evolution

The rational design of metalloprotein hybrid structures and precise calculations for understanding the role of the interfacial electronic structure in regulating the HER activity of water splitting sites and their microscopic effect for obtaining robust hydrogen evolution possess great promise for developing highly efficient nano-bio hybrid HER catalysts. Here, we employ high-accuracy linear-scaling density functional theory calculations using a near-complete basis set and a minimal parameter implicit solvent model within the self-consistent calculations, on silver (Ag) ions assimilated on bacteriorhodopsin (bR) at specific binding sites. Geometry optimization indicates the formation of active sites at the interface of the metalloprotein complex and the density of states reflects the metallic nature of the active sites. The reduced value of the canonical orbital gap indicates the state of dynamic nature after Ag ion assimilation on active sites and smooth electron transfer. These incorporated active protein sites are more efficient in electrolytic splitting of water than pristine sites due to their low value of Gibbs free energy for the HER in terms of hydrogen coverages. Volcano plot analysis and the free energy diagram are compared for understanding the hydrogen evolution efficiency. Moreover, the essential role of the interfacial electronic properties in regulating the HER catalytic activity of water splitting sites and enhancing the efficiency is elucidated.

Fragment-based configuration interaction wave function to calculate environmental effect on excited states in proteins and solutions

• Coarse-grained analysis to figure out excited-state w.f. including environments. • A fragment-based truncated CIS for the excited-state w.f. including environments. • CTs between environmental fragments give negligible contributions. Solvatochromic effect in proteins and solutions was described by a configuration interaction singles (CIS) wave function with fragment-localized molecular orbitals. Coarse-grained analysis indicated that the CI wave function can be described by local excitations and charge-transfer (CT) excitations between the chromophore and the environment. We developed an atomic-orbital direct runcated CIS code and applied the excited states of retinal chromophore in bacteriorhodopsin and MeOH environments, and those of s -trans-acrolein in water. Number of excitation operators was significantly reduced by eliminating the CT excitations between the environmental fragments. The truncated CIS wave functions reproduced the original excitation energies very well.

Ground‐ and Excited‐State Vibrational Coherence Dynamics in Bacteriorhodopsin Probed With Degenerate Four‐Wave‐Mixing Experiments

Vibrational coherence dynamics in the all-trans retinal chromophore in Bacteriorhodopsin (BR) are investigated by means of temporally and spectrally resolved degenerate four-wave-mixing experiments. The coherence dynamics depend on the excitation wavelength when BR samples are excited at different wavelengths in a spectral range between 520 nm to above 620 nm. The trends in the dynamics observed by tuning of the excitation wavelength allow an assignment of the wave packet dynamics to ground- and excited-state potential energy surfaces. Specifically, the intensity of so-called "out-of-plane" modes of polyene-chain substituents increases for excitation wavelengths near 500 nm. It is shown that this is consistent with the assignment of out-of-plane modes to excited-state coherence dynamics. Moreover, intense low-frequency coherence dynamics around 200 cm(-1) are observed for signal detection in two different spectral regions of excited-state absorption. These modulations are assigned to excited-state dynamics due to the observed dependence on the excitation wavelength. In addition, we show that generally high-frequency modes (>1010 cm(-1)) originate from wave packet motion in the electronic ground state of all-trans retinal.

Retinal in bacteriorhodopsin and related molecular models investigated with Raman spectroscopy and density functional theory calculations

AbstractA first‐principles assisted study of the Raman spectrum associated with the photoactive chromophore in bacteriorhodopsin (bR) allowed the elucidation of the effective coupling existing between the π electrons of the retinylidene chromophore and the local environment of the Schiff base. The role of the counter‐ion on the electronic and vibrational structure of the chromophore is investigated by means of density functional theory (DFT) calculations. Several molecular models of the retinylidene chromophore interacting with different counter‐ions facing the Schiff base have been considered. The counter‐ion induces a strong modulation of the position of both the UV–vis absorption maximum and the strong Raman active collective CC stretching mode, related to the effective conjugation coordinate (ECC). Experimental Raman and UV–vis absorption data are interpreted in the light of these theoretical findings. The data collected in this paper provide an interesting accumulation of points along the optical gap versus ECC wavenumber relationship. Copyright © 2011 John Wiley & Sons, Ltd.

Model Systems for the Investigation of the Opsin Shift in Bacteriorhodopsin

Donor-acceptor substituted styrenes and phenylbutadienes with substituents varying in donor and acceptor strength and as reconstituted chromophore-protein complexes were investigated as model compounds for the protonated Schiff base chromophore in bacteriorhodopsin (bR) both experimentally and theoretically. Charge distribution, donor-acceptor strength, and the shift of the absorption energy are correlated. The effect of the external electrostatic field was tested with a compound carrying an additional nonconjugated charge. The concept of overpolarization by the external charge, that is, the reversal of the relative importance of the two main resonance structures in S(0) and S(1), has been emphasized and related to a simple qualitative 2 x 2 interaction model. The variable donor approach is a new way for a better understanding of the Opsin shift in Bacteriorhodopsin.

The Infrared Spectra of the Retinal Chromophore in Bacteriorhodopsin Calculated by a DFT/MM Approach

In the preceding paper (DOI 10.1021/jp902428x), we have derived the polarized force field "PBR" for bacteriorhodopsin (BR) using hybrid methods which combine density functional theory (DFT) with molecular mechanics (MM) models. This polarized force field has enabled extended molecular dynamics (MD) simulations of BR's chromophore binding pocket which closely preserve the experimentally well-known structure. Here, we employ the PBR-MD trajectories obtained for the conformational substates prevalent at physiological temperatures as material for the DFT/MM computation of the chromophore's vibrational spectra. By comparison with DFT results on the structure and vibrational spectra of an isolated chromophore, we identify the structural and spectral changes induced by the protein environment. Comparisons with the wealth of experimental data available in the literature on the chromophore's vibrational spectra yield estimates on the accuracy of the DFT/MM descriptions. We discuss why highly accurate DFT/MM descriptions are expected to become a decisive tool for solving the long-standing enigma of how the light-driven proton pump BR actually works.

Bacteriorhodopsins containing modified chromophores: A study on the wild type and D96N mutant of Halobacterium salinarum

Modification of the chromophore in bacteriorhodopsin (BR) from ET1001 and D96N strains of Halobacterium salinarum (halobium) was carried out. Purple membranes were decolored by means of light-dependent hydroxylaminolysis. The all-trans -isomers of retinal and its 3,4-didehydro-, 4-keto-, and phenyl analogs were reconstituted into apomembranes. Absorption maxima of the homonymic pigments in both strains were similar. The kinetics of the M-intermediates in the mode of a single turnover of the photocycle induced by a short light flash (532 nm, 15 ns) was compared. For the investigated bacteriorhodopsin analogs the efficiency of the M-intermediate formation did not exhibit any reliable dependence on the point mutation. Both for ET1001 and for D96N strains the M-relaxation of the 4-ketoBR was distinctly biphasic, with the slow phase comprising about 10–15% of the signal amplitude. Replacement of the ionone ring by phenyl caused a weak deceleration of the M relaxation (∼1.5-fold decrease in t 1/2). Independence of the photocycle deceleration of the point mutation and chromophore modification was shown for all BR analogs studied.

Site-Specific Difference 2D-IR Spectroscopy of Bacteriorhodopsin

We demonstrate the extension of the principle of difference Fourier transform infrared (FTIR) spectroscopy to difference 2D-IR spectroscopy. To this end, we measure difference 2D-IR spectra of the protein bacteriorhodopsin in its early J- and K-intermediates. By comparing with the static 2D-IR spectrum of the protonated Schiff base of all-trans retinal, we demonstrate that the 2D-IR spectrum of the all-trans retinal chromophore in bacteriorhodopsin can be measured with the background from the remainder of the protein completely suppressed. We discuss several models to interpret the detailed line shape of the difference 2D-IR spectrum.

Rapid Thermal Tuning of Chromophore Structure in Membrane Protein

We show that the configuration and the optical property of the retinal chromophore in bacteriorhodopsin (bR) can be tuned dynamically from the all-trans configuration to the 13-cis by using a nanosecond laser-induced temperature-jump. The rapid bleach in the visible absorption optical density of retinal has an apparent formation time of ca. 170 ns, whereas the relaxation process finishes within tens of ms. The dynamical transition of retinal from the all-trans to 13-cis species is believed to occur as a result of rapid protein conformational change especially in the vicinity of retinal binding site. Our study reveals the intrinsic dynamical aspect of the retinal chromophore with respect to the protein structure.

Photochemical dynamics of all-trans retinal protonated Schiff-base in solution: Excitation wavelength dependence

Photochemistry of protonated all-trans retinal Schiff-base (RPSB), the active chromophore in bacteriorhodopsin (BR) and sensory rhodopsins has been investigated with femtosecond multichannel pump probe spectroscopy at two excitation wavelengths. In a recent study of an RPSB analogue which mimics the opsin shift in BR, significant excitation wavelength dependence of the transient spectra was observed and assigned to structural inhomogeneity in the ground state. Our aim is to determine if similar inhomogeneity is manifest also in the native RPSB in solution which is the archtypical model for appreciating the apoproteins effect on retinal protein photochemistry. Significant differences in transient spectra collected after 390 and 480 nm excitation are observed and are likewise assigned to ground state structural inhomogeneity. For both excitation wavelengths the stimulated emission band extends well beyond 900 nm, much deeper than previously reported in the near IR. The shallowness of this feature and a newly revealed dip in its intensity near 760 nm are attributed to an overlapping excited state absorption, as reported for BR. This assignment identifies the documented RPSB excited state absorption band which peaks at 500 nm as the counterpart of the 460 nm absorption feature reported for the reactive excited state of BR coined I 460. Implications of this assignment, and possible mechanisms for inhomogeneous broadening of the electronic absorption spectrum of RPSB in solution are discussed.

Sub-5-fs Real-time Spectroscopy of Transition States in Bacteriorhodopsin During Retinal Isomerization†

By using a sub-5-fs visible laser pulse, we have made the first observation of the vibrational spectra of the transition state during trans-cis isomerization in the retinal chromophore of bacteriorhodopsin (bR(S68). No instant isomerization of the retinal occurs in spite of electron promotion from the bonding pi-orbital to the anti-bonding pi*-orbital. The difference between the in-plane and out-of-plane vibrational frequencies (about 1150-1250 and 900-1000 cm(-1), respectively) is reduced during the first time period. The vibrational spectra after this period became very broad and weak and are ascribed to a "silent state." The silent state lasts for 700-900 fs until the chromophore isomerizes to the cis-C13 = C14 conformation. The frequency of the C = C stretching mode was modulated by the torsion mode of the C13 = C14 double bond with a period of 200 fs. The modulation was clearly observed for four to five periods. Using the empirical equation for the relation between bond length and stretching frequency, we determined the transitional C = C bond length with about 0.01 angstroms accuracy during the torsion motion around the double bond with 1-fs time resolution.

High-resolution powder diffraction study of purple membrane with a large Guinier-type camera

X-ray diffraction patterns from a film of oriented purple membranes, which comprise two-dimensional crystals of bacteriorhodopsin (BR) trimers, were recorded with a 1 m-pathlength Guinier-type camera at SPring-8 BL40B2. A well focused X-ray beam and a camera with a high angular resolution of 0.024 degrees enabled a powder diffraction profile with very sharp and well separated peaks to be obtained up to a resolution of 2.3 A. Using integrated diffraction intensities up to a Bragg spacing of 4.2 A, a cluster of bulky amino acid residues and the head group of the BR chromophore are apparent in the electron density map projected along the membrane normal. Thus, a combination of synchrotron X-rays and large Guinier camera can be used for analyzing the conformational changes of BR in the intact state. In addition, the method might be extended to the structural analysis of film materials composed of two-dimensional arrays of nanoparticles.

The retinal chromophore/chloride ion pair: Structure of the photoisomerization path and interplay of charge transfer and covalent states

Ab initio multi-reference second-order perturbation theory computations are used to explore the photochemical behavior of two ion pairs constituted by a chloride counterion interacting with either a rhodopsin or bacteriorhodopsin chromophore model (i.e., the 4-cis-gamma-methylnona-2,4,6,8-tetraeniminium and all-trans-nona-2,4,6,8-tetraeniminium cations, respectively). Significant counterion effects on the structure of the photoisomerization paths are unveiled by comparison with the paths of the same chromophores in vacuo. Indeed, we demonstrate that the counterion (i) modulates the relative stability of the S0, S1, and S2 energy surfaces leading to an S1 isomerization energy profile where the S1 and S2 states are substantially degenerate; (ii) leads to the emergence of significant S1 energy barriers along all of the isomerization paths except the one mimicking the 11-cis --> all-trans isomerization of the rhodopsin chromophore model; and (iii) changes the nature of the S1 --> S0 decay funnel that becomes a stable excited state minimum when the isomerizing double bond is located at the center of the chromophore moiety. We show that these (apparently very different) counterion effects can be rationalized on the basis of a simple qualitative electrostatic model, which also provides a crude basis for understanding the behavior of retinal protonated Schiff bases in solution.

Dynamics of Primary Events in the Photocycle of Excited Bacteriorhodopsin

Transient dynamic behavior of the excited bacteriorhodopsin (BR), which was isolated from the strain H. salinarum, was studied at excitation wavelength from 585 to 639 nm. With the one-color femtosecond (fs) pump-probe technique, we revealed the primary events in BR's photocycle that took place in an ultrafast time scale. From the analysis of the decay components of the dynamical traces, it was evident that the isomerization of the retinal chromophore in BR and the intermediate J's formation occurred within 500 fs. BR exhibited pH-dependent dynamical behaviors. When the medium pH was between 5 and 9, the BR ultrafast dynamics has no obvious change. In contrast, the dynamical curves were obviously affected when the pH was out of that region.

Effect of β-particles on the retinal chromophore in bacteriorhodopsin of Halobacterium salinarium

Bacteriorhodopsin (bR) is an attractive intelligent material. Understanding the mechanism of its light-driven proton pumping outward the cell implicates it in many technical applications, particularly, in what is called optical computers, and the biotechnology is waiting for this promised biological molecule. An ionizing radiation source handling could be computerized in radiation fields. The computer containing such biological material will not be out of reach of the fields of ionizing radiation. So it is interesting to report on the working of such biological computer if it is subjected to ionizing radiation. The functional unit in this molecule is retinal chromophore. In the present work, it is interested to assess the functionality of bR through determining the electronic transition dipole moment of its chromophore. Significant changes in the values of the absorption transition dipole moment were noticed at different doses of β-particles in the range of 0.1– 0.3 kGy . Ionizing radiation-induced changes in bR were followed by intrinsic fluorescence spectroscopy. An analysis of the fluorescence data bears on the tertiary structure of bR. The emission spectrum is, however, red shifted with an increase in intensity with the different doses; in the meanwhile, gradual decrease in the visible absorbance has occurred till almost complete loss is attained. This bleaching due to ionizing radiation may offer an alternative way of data processing in such optical devices based on bR. Nevertheless, bR has proofed to be used as a biological indicator of ionizing radiation. However, the potential of bR for use as a biosensor to detect ionizing radiation should be considered.