Photoreverse reaction dynamics of octopus rhodopsin

Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins

The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.

Time-resolved detection of light-induced conformational changes of heliorhodopsin

Heliorhodopsins (HeRs) are a new category of rhodopsins. They exist as a dimer and exhibit a characteristic inverted topology. HeRs bind all-trans-retinal as a chromophore in the dark, and its isomerization to the 13-cis form by light illumination leads to a photocyclic reaction involving several photo-intermediates: K, L, M, and O. In this study, the kinetics of conformational changes of HeR from Thermoplasmatales archaeon SG8-52-1 (TaHeR) were studied by the transient grating (TG) and circular dichroism (CD) methods. The TG method reveals that the diffusion coefficient (D) does not change until the O formation suggesting no significant conformation change at the surface of the protein during the early steps of the reaction. Subsequently, D decreases upon the O formation. Although two time constants (202 μs and 2.6 ms) are observed for the conversion from the M to O by the absorption detection, D decreases only at the first step (202 μs). Light-induced unfolding of helical structure is detected by the CD method. To examine the contribution of a characteristic helix in the intracellular loop 1 (ICL1 helix), Tyr93 on the ICL1 helix was replaced by Gly (Y93G), and the reaction of this mutant was also investigated. It was found that this replacement partially suppresses the D-change, although the CD-change is almost the same as that of the wild type. These results are interpreted in terms of different sensitivities of TG and CD methods, that is, D is sensitive to the structure of the solvent-exposed surface and selectively observes the conformational change in the ICL1 region. It is suggested that the structure of hydrophilic residues in the ICL1 helix is changed during this process.

Applications of Time-Resolved Thermodynamics for Studies on Protein Reactions

Thermodynamics and kinetics are two important scientific fields when studying chemical reactions. Thermodynamics characterize the nature of the material. Kinetics, mostly based on spectroscopy, have been used to determine reaction schemes and identify intermediate species. They are certainly important fields, but they are almost independent. In this review, our attempts to elucidate protein reaction kinetics and mechanisms by monitoring thermodynamic properties, including diffusion in the time domain, are described. The time resolved measurements are performed mostly using the time resolved transient grating (TG) method. The results demonstrate the usefulness and powerfulness of time resolved studies on protein reactions. The advantages and limitations of this TG method are also discussed.

Spectrally Silent Protein Reaction Dynamics Revealed by Time-Resolved Thermodynamics and Diffusion Techniques

Biological functions essentially consist of a series of chemical reactions, including intermolecular interactions, and also involve the cooperation of a number of biological molecules performing these reactions. To understand this function at the molecular level, all steps of the reactions must be elucidated. However, since the biosystems including the surrounding environment are notably large, the reactions have to be elucidated from several different approaches. A variety of techniques have been developed to obtain structural information, and the knowledge of the three-dimensional structure of biomolecules has increased dramatically. Contrarily, the current information on reaction dynamics, which is essential for understanding reactions, is still not enough. Although frequently used techniques, such as spectroscopy, have revealed several important processes of reactions, there are various hidden dynamics that are not detected by these methods (silent dynamics). For example, although water molecules are essential for bioreactions, dynamics of the protein-water interaction are very difficult to trace and spectrally silent. Transient association/dissociations of proteins with partner proteins are difficult to observe. Another important property to understand the reaction of proteins is fluctuations, which are random movements that do not change the average structure and energy. The importance of fluctuations has been pointed out in order to explain enzymatic activity; however, it is extremely difficult to detect changes in fluctuation during a reaction. In this Account, unique time-resolved methods, time-resolved thermodynamics, and time-resolved diffusion methods, both of which are able to detect silent dynamics in solution at physiological temperature, are described.Thermodynamic properties are important for characterizing materials, in particular, macromolecules such as biomolecules. Therefore, the data available regarding these properties, for several stable proteins, is abundant. However, it is almost impossible to characterize short-lived intermediate species in irreversible reactions using traditional thermodynamic techniques. Similarly, although the translational diffusion coefficient is a useful property to determine the protein size and intermolecular interactions, there have been no reports revealing reaction dynamics. The transient grating (TG) method enables us to measure these quantities in a time-resolved manner for a variety of irreversible reactions. With this method, it is now possible to study biomolecule reactions from the viewpoint of thermodynamic properties and diffusion, and to elucidate reaction dynamics that cannot be detected by other spectroscopic methods.Here, the principles of the methodologies used, their characteristic advantages, and their applications to protein reactions are described. The TG measurements of octopus rhodopsin revealed a spectrally hidden intermediate and determined an energetic profile along the reaction coordinate. This emphasizes that the measurement in solution, not for trapped intermediates, is important to characterize the reaction intermediates. The application of these methods to a blue light sensor PixD revealed many spectrally silent dynamics as well as the importance of fluctuation for the reaction. As an example of the time-resolved heat capacity change and transient thermal expansion measurements, the reaction of PYP was briefly described. The reaction scheme of another blue light sensor protein, phototropins, and a spectrally silent DNA binding process of EL222 were fully elucidated by the time-resolved diffusion method.

The Two-Photon Reversible Reaction of the Bistable Jumping Spider Rhodopsin-1

Bistable opsins are photopigments expressed in both invertebrates and vertebrates. These light-sensitive G-protein-coupled receptors undergo a reversible reaction upon illumination. A first photon initiates the cis to trans isomerization of the retinal chromophore—attached to the protein through a protonated Schiff base—and a series of transition states that eventually results in the formation of the thermally stable and active Meta state. Excitation by a second photon reverts this process to recover the original ground state. On the other hand, monostable opsins (e.g., bovine rhodopsin) lose their chromophore during the decay of the Meta II state (i.e., they bleach). Spectroscopic studies on the molecular details of the two-photon cycle in bistable opsins are limited. Here, we describe the successful expression and purification of recombinant rhodopsin-1 from the jumping spider Hasarius adansoni (JSR1). In its natural configuration, spectroscopic characterization of JSR1 is hampered by the similar absorption spectra in the visible spectrum of the inactive and active states. We solved this issue by separating their absorption spectra by replacing the endogenous 11-cis retinal chromophore with the blue-shifted 9-cis JSiR1. With this system, we used time-resolved ultraviolet-visible spectroscopy after pulsed laser excitation to obtain kinetic details of the rise and decay of the photocycle intermediates. We also used resonance Raman spectroscopy to elucidate structural changes of the retinal chromophore upon illumination. Our data clearly indicate that the protonated Schiff base is stable throughout the entire photoreaction. We additionally show that the accompanying conformational changes in the protein are different from those of monostable rhodopsin, as recorded by light-induced FTIR difference spectroscopy. Thus, we envisage JSR1 as becoming a model system for future studies on the reaction mechanisms of bistable opsins, e.g., by time-resolved x-ray crystallography.

Novel physical chemistry approaches in biophysical researches with advanced application of lasers: Detection and manipulation

Novel methodologies utilizing pulsed or intense CW irradiation obtained from lasers have a major impact on biological sciences. In this article, recent development in biophysical researches fully utilizing the laser irradiation is described for three topics, time-resolved fluorescence spectroscopy, time-resolved thermodynamics, and manipulation of the biological assemblies by intense laser irradiation. First, experimental techniques for time-resolved fluorescence spectroscopy are concisely explained in Section 2. As an example of the recent application of time-resolved fluorescence spectroscopy to biological systems, evaluation of the viscosity of lipid bilayer membranes is described. The results of the spectroscopic experiments strongly suggest the presence of heterogeneous membrane structure with two different viscosity values in liposomes formed by a single phospholipid. Section 3 covers the time-resolved thermodynamics. Thermodynamical properties are important to characterize biomolecules. However, measurement of these quantities for short-lived intermediate species has been impossible by traditional thermodynamical techniques. Recently, development of a spectroscopic method based on the transient grating method enables us to measure these quantities and also to elucidate reaction kinetics which cannot be detected by other spectroscopic methods. The principle of the measurements and applications to some protein reactions are reviewed. Manipulation and fabrication of supramolecues, amino acids, proteins, and living cells by intense laser irradiation are described in Section 4. Unconventional assembly, crystallization and growth, amyloid fibril formation, and living cell manipulation are achieved by CW laser trapping and femtosecond laser-induced cavitation bubbling. Their spatio-temporal controllability is opening a new avenue in the relevant molecular and bioscience research fields. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.

Reaction dynamics of halorhodopsin studied by time-resolved diffusion

Reaction dynamics of a chloride ion pump protein, halorhodopsin (HR), from Natronomonas pharaonis (N. pharaonis) (NpHR) was studied by the pulsed-laser-induced transient grating (TG) method. A detailed investigation of the TG signal revealed that there is a spectrally silent diffusion process besides the absorption-observable reaction dynamics. We interpreted these dynamics in terms of release, diffusion, and uptake of the Cl(-) ion. From a quantitative global analysis of the signals at various grating wavenumbers, it was concluded that the release of the Cl(-) ion is associated with the L2 --> (L2 (or N) <==> O) process, and uptake of Cl(-) occurs with the (L2 (or N) <==> O) -->NpHR' process. The diffusion coefficient of NpHR solubilized in a detergent did not change during the cyclic reaction. This result contrasts the behavior of many photosensor proteins and implies that the change in the H-bond network from intra- to intermolecular is not significant for the activity of this protein pump.