Time-Resolved Thermodynamics: Heat Capacity Change of Transient Species during Photoreaction of PYP

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.

Regulation of Photocycle Kinetics of Photoactive Yellow Protein by Modulating Flexibility of the β-Turn

The role of the significant flexibility of the β-turn in photoactive yellow protein (PYP) due to Gly115 was studied. G115A and G115P mutations were observed to accelerate the photocycle and shift the equilibrium between the late photocycle intermediate (pB) and its precursor (pR) toward pR. Thermodynamic analysis of dark-state recovery from pB demonstrated that the transition state (pB^⧧) has a negative change in transition heat capacity, suggesting that an exposed hydrophobic surface of pB is buried in pB^⧧. Fourier transform infrared spectroscopy showed that the structural ensemble of pB is populated by the compact structure in G115P. Taken together, the rigid structure induced by mutation of Gly115 facilitates its transition to pB^⧧, which adopts a substantially more compact structure as opposed to the ensemble-averaged structure of pB. The photocycle kinetics of PYP may be fine-tuned by modulating the flexibility of the 115 loop to activate an appropriate number of transducer proteins.

Copper-catalyzed arene amination in pure aqueous ammonia

A simple protocol for copper-catalyzed arene amination using aqueous ammonia without any additional ligands and organic coordinating solvents has been developed. The reaction pathway via a Cu(i)/Cu(iii) mechanism is proposed based on the results of control experiments as well as DFT calculations.

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.

Transient conformational fluctuation of TePixD during a reaction

Knowledge of the dynamical behavior of proteins, and in particular their conformational fluctuations, is essential to understanding the mechanisms underlying their reactions. Here, transient enhancement of the isothermal partial molar compressibility, which is directly related to the conformational fluctuation, during a chemical reaction of a blue light sensor protein from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixD, Tll0078) was investigated in a time-resolved manner. The UV-Vis absorption spectrum of TePixD did not change with the application of high pressure. Conversely, the transient grating signal intensities representing the volume change depended significantly on the pressure. This result implies that the compressibility changes during the reaction. From the pressure dependence of the amplitude, the compressibility change of two short-lived intermediate (I1 and I2) states were determined to be +(5.6 ± 0.6) × 10(-2) cm(3) ⋅ mol(-1) ⋅ MPa(-1) for I1 and +(6.6 ± 0.7) × 10(-2) cm(3) ⋅ mol(-1) ⋅ MPa(-1) for I2. This result showed that the structural fluctuation of intermediates was enhanced during the reaction. To clarify the relationship between the fluctuation and the reaction, the compressibility of multiply excited TePixD was investigated. The isothermal compressibility of I1 and I2 intermediates of TePixD showed a monotonic decrease with increasing excitation laser power, and this tendency correlated with the reactivity of the protein. This result indicates that the TePixD decamer cannot react when its structural fluctuation is small. We concluded that the enhanced compressibility is an important factor for triggering the reaction of TePixD. To our knowledge, this is the first report showing enhanced fluctuations of intermediate species during a protein reaction, supporting the importance of fluctuations.

On the binding of BODIPY-GTP by the photosensory protein YtvA from the common soil bacterium Bacillus subtilis

The YtvA protein, which is one of the proteins that comprises the network carrying out the signal transfer inducing the general stress response in Bacillus subtilis, is composed of an N-terminal LOV domain (that binds a flavin [FMN]) and a C-terminal STAS domain. This latter domain shows sequence features typical for a nucleotide (NTP) binding protein. It has been proposed (FEBS Lett., 580 [2006], 3818) that BODIPY-GTP can be used as a reporter for nucleotide binding to this site and that activation of the LOV domain by blue light is reflected in an alteration of the BODIPY-GTP fluorescence. Here we confirm that BODIPY-GTP indeed binds to YtvA, but rather nonspecifically, and not limited to the STAS domain. Blue-light modulation of fluorescence emission of YtvA-bound BODIPY-GTP is observed both in the full-length YtvA protein and in a truncated protein composed of the LOV-domain plus the LOV-STAS linker region (YtvA(1-147)) as a light-induced decrease in fluorescence emission. The isolated LOV domain (i.e. without the linker region) does not show such BODIPY-GTP fluorescence changes. Dialysis experiments have confirmed the blue-light-induced release of BODIPY-GTP from YtvA.

Studies of photo-induced protein reactions by spectrally silent reaction dynamics detection methods: applications to the photoreaction of the LOV2 domain of phototropin from Arabidopsis thaliana

Biological function involves a series of chemical reactions of biological molecules, and during these reactions, there are numerous spectrally silent dynamic events that cannot be monitored by absorption or emission spectroscopic techniques. Such spectrally silent dynamics include changes in conformation, intermolecular interactions (hydrogen bonding, hydrophobic interactions), inter-protein interactions (oligomer formation, dissociation reactions) and conformational fluctuations. These events might be associated with biological function. To understand the molecular mechanisms of reactions, time-resolved detection of such dynamics is essential. Recently, it has been shown that time-resolved detection of the refractive index is a powerful tool for measuring dynamic events. This technique is complementary to optical absorption detection methods and the signal contains many unique properties, which are difficult to obtain by other methods. The advantages and methods for signal analyses are described in detail in this review. A typical example of an application of time-resolved refractive index change detection is given in the second part: The photoreaction of the LOV2 domain of a blue light photoreceptor from Arabidopsis Thaliana (phototropin). This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.

Modulating native-like residual structure in the fully denatured state of photoactive yellow protein affects its refolding

Residual structure in the fully unfolded state is a key element for understanding protein folding. We show that the residual structure in fully denatured photoactive yellow protein (PYP) is affected by isomerization of its p-coumaric acid (pCA) chromophore. The exposure of total surface area and hydrophobic surface area upon unfolding was quantified by denaturant m values and heat capacity changes (DeltaC(p)), respectively. The exposure of the buried surface area upon the unfolding of the acid-denatured state of PYP containing trans-pCA is approximately 20% smaller than that of the native state. In contrast, for the partially unfolded pB photocycle intermediate containing cis-pCA, unfolding-induced exposure of the surface area is not decreased. These results show that pCA photoisomerization reduces residual structure in the fully unfolded state. Thus, residual structure in the fully unfolded state of PYP is under direct experimental control by photoexcitation. The sensitivity of the unfolded state to pCA isomerization provides a novel criterion that residual structure in the unfolded state of PYP is native-like, involving native-like protein-chromophore interactions. A largely untested prediction is that native-like residual structure facilitates the conformational search during folding. In the case of PYP, refolding from the less disordered fully unfolded state containing trans-pCA indeed is substantially accelerated. The burial of hydrophobic surface area in the fully unfolded state suggests that a significant part of the hydrophobic collapse process already has occurred in the denatured state.

Energy landscape of a hydrogen-bonded non-degenerate molecular shuttle

In rotaxane 1, two co-conformations are populated in CDCl(3) at temperatures between 250 and 330 K. The thermodynamic parameters show strong enthalpy-entropy compensation, and a non-negligible heat capacity difference between the two forms.

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.

Spectrally silent light induced conformation change in photosynthetic reaction centers

Spectrally silent conformation change after photoexcitation of photosynthetic reaction centers isolated from Rhodobacter sphaeroides R-26 was observed by the optical heterodyne transient grating technique. The signal showed spectrally silent structural change in photosynthetic reaction centers followed by the primary P+BPh- charge separation and this change remains even after the charge recombination. Without bound quinone to the RC, the conformation change relaxes with about 28micros lifetime. The presence of quinone at the primary quinone (QA) site may suppress this conformation change. However, a weak relaxation with 30-40micros lifetime is still observed under the presence of QA, which increases up to 40micros as a function of the occupancy of the secondary quinone (QB) site.

An optical high-pressure cell for transient grating measurements of biological substance with a high reproducibility

We describe a high-pressure optical cell that can be used for time-resolved transient grating measurements to determine the thermodynamic properties of transient species under high pressure. This high-pressure cell enables us to compare the grating signal intensities of different samples quantitatively. Using this high-pressure cell with an inner sample cell, one can measure various thermodynamic properties of a biological substance in time domain. The stability and reproducibility of this apparatus are described.

Energetics and role of the hydrophobic interaction during photoreaction of the BLUF domain of AppA

A recently developed method for time-resolved thermodynamic measurements was used to study the photochemical reaction(s) of the BLUF domain of AppA (AppA-BLUF), which has a dimeric form in the ground state, in terms of the energetics and heat capacity changes (DeltaC(p)) in different time domains. The enthalpy change (DeltaH) of the first intermediate that forms within 1 ns after photoexcitation was 38 (+/-8) kJ mol(-1) at 298 K. The heat capacity change (DeltaC(p)) upon formation of this intermediate was positive [1.4 (+/-0.3) kJ mol(-1) K(-1)]. This positive DeltaC(p) suggests that the hydrophobic surface area of AppA-BLUF exposed to the bulk solvent increased. After this initial transition, a dimerization reaction with another ground-state dimer (i.e., tetramer formation) takes place. Upon this reaction, the energy was stabilized to 26 (+/-6) kJ mol(-1) at 298 K. Interestingly, the dimer formation was accompanied by a larger but negative DeltaC(p) [-6.0 (+/-1) kJ mol(-1) K(-1)]. This negative DeltaC(p) might indicate buried hydrophobic residues at the interface of the dimer and/or the existence of trapped water at the interface. We suggest that hydrophobic interactions are the main driving force for the formation of the dimer upon photoactivation of AppA-BLUF.

Photochemical Intermediates of Arabidopsis Phototropin 2 LOV Domains Associated with Conformational Changes

The photochemical reactions of Arabidopsis phototropin 2 light- oxygen-voltage domain 2 (LOV2) with the linker region (LOV2-linker), without the linker (LOV2), and LOV1 were studied using the time-resolved transient grating (TG) and transient lens (TrL) methods. Although the absorption spectra did not change after the formation of the adduct species, a small volume expansion process with a time constant of 9 ms was observed for LOV2. For the LOV2-linker, at 293 K, a volume contraction process with a time constant of 140 mus was observed in addition to a volume expansion process with 9 ms and the diffusion coefficient change with 2 ms. The reaction intermediate species were characterized on the basis of their thermodynamic properties, such as changes in enthalpy, thermal expansion, and heat capacity. For the first intermediate (S(390)), the values of these properties were similar to those of the ground state for both LOV2 and LOV2-linker. A relatively large thermal expansion volume (0.09 cm(3)mol(-1)K(-1)) and a positive heat capacity change (4.7 kJ mol(-1)K(-1)) were detected for the intermediates of LOV2-linker. These characteristic features were interpreted in terms of structural fluctuation and exposure of hydrophobic residues in the linker domain, respectively. The enthalpy change of S(390) of the LOV1 domain was significantly greater than changes for the LOV2 or LOV2-linker samples. Data from this study support a major conformational change of the linker region in the photochemical reaction of phototropin.

Conformational changes of PYP monitored by diffusion coefficient: effect of N-terminal alpha-helices

Conformational changes in the light illuminated intermediate (pB) of photoactive yellow protein (PYP) were studied from a viewpoint of the diffusion coefficient (D) change of several N-truncated PYPs, which lacked the N-terminal 6, 15, or 23 amino acid residues (T6, T15, and T23, respectively). For intact PYP (i-PYP), D of pB (D(pB)) was approximately 11% lower than that (D(pG)) of the ground state (pG) species. The difference in D (D(pG) - D(pB)) decreased upon cleavage of the N-terminal region in the order of i-PYP>T6>T15>T23. This trend clearly showed that conformational change in the N-terminal group is the main reason for the slower diffusion of pB. This slower diffusion was interpreted in terms of the unfolding of the two alpha-helices in the N-terminal region, increasing the intermolecular interactions due to hydrogen bonding with water molecules. The increase in friction per one residue by the unfolding of the alpha-helix was estimated to be 0.3 x 10(-12) kg/s. The conformational change in the N-terminal group upon photoillumination is discussed.