Is the translational diffusion of organic radicals different from that of closed-shell molecules?

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.

A Time-Resolved Diffusion Technique for Detection of the Conformational Changes and Molecular Assembly/Disassembly Processes of Biomolecules

Biological liquid-liquid phase separation (LLPS) is driven by dynamic and multivalent interactions, which involves conformational changes and intermolecular assembly/disassembly processes of various biomolecules. To understand the molecular mechanisms of LLPS, kinetic measurements of the intra- and intermolecular reactions are essential. In this review, a time-resolved diffusion technique which has a potential to detect molecular events associated with LLPS is presented. This technique can detect changes in protein conformation and intermolecular interaction (oligomer formation, protein-DNA interaction, and protein-lipid interaction) in time domain, which are difficult to obtain by other methods. After the principle and methods for signal analyses are described in detail, studies on photoreactive molecules (intermolecular interaction between light sensor proteins and its target DNA) and a non-photoreactive molecule (binding and folding reaction of α-synuclein upon mixing with SDS micelle) are presented as typical examples of applications of this unique technique.

Spin-Correlated Radical Ion Pairs Generated in Liquid Haloalkanes Using High-Energy Radiation

The probability of formation of spin-correlated secondary radical ion pairs (RIPs) in diluted solutions of charge acceptors in irradiated haloalkanes is believed to be extremely low due to the dissociative attachment of excess electrons to solvent molecules. Contrary to this, it has been found that spin-correlated RIPs can be formed upon irradiation in some liquid chloroalkanes with yield sufficient to observe the recombination fluorescence of the RIP's partners. This allowed the study of primary radical cations (RCs) as well as radical ionic states of molecules dissolved in haloalkanes using the method of time-resolved magnetic field effect (TR MFE) in radiation-induced fluorescence. With this method, the magnetic resonance characteristics of the solvent RCs in a series of liquid haloalkanes were examined for the first time. For the 1,2-dichloroethane RC, the rate of scavenging by solute molecules and the dominant mechanisms of paramagnetic relaxation were determined. Polysulfone and poly(ethyl methacrylate) were used to demonstrate that due to their high dissolving ability, chloroalkanes can be exploited as solvents to study the magnetic resonance characteristics of radical ionic states of polymeric molecules in solutions with the TR MFE method.

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.

Radical Cage Effects: The Prediction of Radical Cage Pair Recombination Efficiencies Using Microviscosity Across a Range of Solvent Types

This study reports a method for correlating the radical recombination efficiencies (F_cP) of geminate radical cage pairs to the properties of the solvent. Although bulk viscosity (macroviscosity) is typically used to predict or interpret radical recombination efficiencies, the work reported here shows that microviscosity is a much better parameter. The use of microviscosity is valid over a range of different solvent system types, including nonpolar, aromatic, polar, and hydrogen bonding solvents. In addition, the relationship of F_cP to microviscosity holds for solvent systems containing mixtures of these solvent types. The microviscosities of the solvent systems were straightforwardly determined by measuring the diffusion coefficient of an appropriate probe by NMR DOSY spectroscopy. By using solvent mixtures, selective solvation was shown to not affect the correlation between F_cP and microviscosity. In addition, neither solvent polarity nor radical rotation affects the correlation between F_cP and the microviscosity.

Multiple scale investigation of molecular diffusion inside functionalized porous hosts using a combination of magnetic resonance methods

Diffusion in organo-functionalized porous hosts could be tracked by evaluation of spin exchange processes using EPR spectroscopy.

Photoreactions of aureochrome-1

Aureochrome is a recently discovered blue light photosensor that controls a light-dependent morphology change. As a photosensor, it has a unique DNA binding domain (bZIP). Although the biological functions of aureochrome have been revealed, the fundamental photochemistry of this protein has not been elucidated. The photochemical reaction dynamics of the LOV (light, oxygen, or voltage) domain of aureochrome-1 (AUREO1-LOV) and the LOV domain with the bZIP domain (AUREO1-ZL) were studied by employing the transient-grating (TG) technique, using size-exclusion chromatography to verify results. For both samples, adduct formation takes place with a time constant of 2.8 μs. Although significant diffusion changes were observed for both AUREO1-LOV and AUREO1-ZL after adduct formation, the origins of these changes were significantly different. The TG signal of AUREO1-LOV was strongly concentration-dependent. From analysis of the signal, it was concluded that AUREO1-LOV exists in equilibrium between the monomer and dimer, and dimerization of the monomer is the main reaction, i.e., irradiation with blue light enhances the strength of the interdomain interaction. On the other hand, the reaction of AUREO1-ZL is independent of concentration, suggesting that an intraprotein conformational change occurs in the bZIP domain with a time constant of 160 ms. These results revealed the different reactions and roles of the two domains; the LOV domain acts as a photosensor, leading to a subsequent conformational change in the bZIP domain, which should change its ability to bind to DNA. A model is proposed that demonstrates how aureochrome uses blue light to control its affinity for DNA.

Light-induced conformational changes in full-length Arabidopsis thaliana cryptochrome

Cryptochromes (CRYs) are widespread flavoproteins with homology to photolyases (PHRs), a class of blue-light-activated DNA repair enzymes. Unlike PHRs, both plant and animal CRYs have a C-terminal domain. This cryptochrome C-terminal (CCT) domain mediates interactions with other proteins, while the PHR-like domain converts light energy into a signal via reduction and radical formation of the flavin adenine dinucleotide cofactor. However, the mechanism by which the PHR-like domain regulates the CCT domain is not known. Here, we applied the pulsed-laser-induced transient grating method to detect conformational changes induced by blue-light excitation of full-length Arabidopsis thaliana cryptochrome 1 (AtCRY1). A significant reduction in the diffusion coefficient of AtCRY1 was observed upon photoexcitation, indicating that a large conformational change occurs in this monomeric protein. AtCRY1 containing a single mutation (W324F) that abolishes an intra-protein electron transfer cascade did not exhibit this conformational change. Moreover, the conformational change was much reduced in protein lacking the CCT domain. Thus, we conclude that the observed large conformational changes triggered by light excitation of the PHR-like domain result from C-terminal domain rearrangement. This inter-domain modulation would be critical for CRYs' ability to transduce a blue-light signal into altered protein-protein interactions for biological activity. Lastly, we demonstrate that the transient grating technique provides a powerful method for the direct observation and understanding of photoreceptor dynamics.

Transient dissociation of the transducer protein from anabaena sensory rhodopsin concomitant with formation of the M state produced upon photoactivation

Anabaena sensory rhodopsin (ASR), a microbial rhodopsin in the cyanobacterium sp. PCC7120, has been suggested to regulate cell processes in a light-quality-dependent manner (color-discrimination) through interaction with a water-soluble transducer protein (Tr). However, light-dependent ASR-Tr interaction changes have yet to be demonstrated. We applied the transient grating (TG) method to investigate protein-protein interaction between ASR with Tr. The molecular diffusion component of the TG signal upon photostimulation of ASR(AT) (ASR with an all-trans retinylidene chromophore) revealed that Tr dissociates from ASR upon formation of the M-intermediate and rebinds to ASR during the decay of M; that is, light induces transient dissociation of ASR and Tr during the photocycle. Further correlating the dissociation of the ASR-Tr pair with the M-intermediate, no transient dissociation was observed after the photoexcitation of the blue-shifted ASR(13C) (ASR with 13-cis, 15-syn chromophore), which does not produce M. This distinction between ASR(AT) and ASR(13C), the two isomeric forms in a color-sensitive equilibrium in ASR, provides a potential mechanism for color-sensitive signaling by ASR.

Light-induced conformational change and product release in DNA repair by (6-4) photolyase

Proteins of the cryptochrome/photolyase family share high sequence similarities, common folds, and the flavin adenine dinucleotide (FAD) cofactor, but exhibit diverse physiological functions. Mammalian cryptochromes are essential regulatory components of the 24 h circadian clock, whereas (6-4) photolyases recognize and repair UV-induced DNA damage by using light energy absorbed by FAD. Despite increasing knowledge about physiological functions from genetic analyses, the molecular mechanisms and conformational dynamics involved in clock signaling and DNA repair remain poorly understood. The (6-4) photolyase, which has strikingly high similarity to human clock cryptochromes, is a prototypic biological system to study conformational dynamics of cryptochrome/photolyase family proteins. The entire light-dependent DNA repair process for (6-4) photolyase can be reproduced in a simple in vitro system. To decipher pivotal reactions of the common FAD cofactor, we accomplished time-resolved measurements of radical formation, diffusion, and protein conformational changes during light-dependent repair by full-length (6-4) photolyase on DNA carrying a single UV-induced damage. The (6-4) photolyase by itself showed significant volume changes after blue-light activation, indicating protein conformational changes distant from the flavin cofactor. A drastic diffusion change was observed only in the presence of both (6-4) photolyase and damaged DNA, and not for (6-4) photolyase alone or with undamaged DNA. Thus, we propose that this diffusion change reflects the rapid (50 μs time constant) dissociation of the protein from the repaired DNA product. Conformational changes with such fast turnover would likely enable DNA repair photolyases to access the entire genome in cells.

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.

Temperature-sensitive reaction of a photosensor protein YcgF: possibility of a role of temperature sensor

The spectrally silent photoreaction of a blue light sensor protein YcgF, composed of the N-terminal BLUF domain and the C-terminal EAL domain, was investigated by the time-resolved transient grating method. Comparing photoinduced reactions of full-length YcgF with that of the BLUF-linker construct, it was found that a major conformation change after photoinduced dimerization is predominantly localized on the EAL domain. Furthermore, the photoinduced conformational change displayed significant temperature dependence. This result is explained by an equilibrium of reactive and nonreactive YcgF species, with the population of photoreactive species decreasing as the temperature is lowered in the dark state. We consider that the dimer form is the nonreactive species and it is the dominant species at lower temperatures. The temperature sensitivity of the photoreaction of YcgF suggests that this protein could have a biological function as a temperature sensor as well as behaving as a light sensor.

Protein diffusion probed by the transient grating method with a new type of photochromic molecule

A new type of photochromic molecule that can be used for diffusion coefficient (D) measurements of various proteins in solution is described. The absorption spectrum of this molecule is changed upon photoexcitation by the trans-cis isomerization reaction. Target proteins were labeled by this photochromic molecule in the dark and the translational motion of the proteins was detected by the transient grating (TG) method. The TG signal was simple enough to determine D accurately and was stable even for long-time irradiation by the laser light. The TG method using this probe molecule improves many drawbacks of the other techniques.

Signal transmission through the HtrII transducer alters the interaction of two alpha-helices in the HAMP domain

A conformational change of the transducer HtrII upon photoexcitation of the associated photoreceptor sensory rhodopsin II (SRII) was investigated by monitoring the kinetics of volume changes and the diffusion coefficient (D) of the complex during the photochemical reaction cycle. To localize the region of the transducer responsible, we truncated it at various positions in the cytoplasmic HAMP (histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) domain. The truncations do not alter receptor binding, which is dependent primarily on membrane-embedded domain interactions. We found that the light-induced reduction in D occurs in transducers of lengths 120 and 157 residues (Tr120 and Tr157), which are both predicted to contain a HAMP domain consisting of two amphipathic alpha-helices (AS-1 and AS-2). In contrast, the change in D was abolished in a transducer of 114 amino acid residues (Tr114), which lacks a distal portion of the second alpha-helix AS-2. The volume changes in SRII-Tr114 are comparable in amplitude and kinetics with those in SRII-Tr120 and SRII-Tr157, confirming the integrity of the complex, which was previously concluded from the similar SRII binding affinity and similar blocking of SRII proton transport by full-length HtrII and Tr114. Our results indicate that a substantial conformational change occurs in the HAMP domain during SRII-HtrII signaling. The data presented here are the first demonstration of stimulus-induced conformational changes of a HAMP domain and provide evidence that the presence of AS-2 is crucial for the conformational alterations. The reduction in diffusion coefficient is likely to due to structural changes in the AS-1 and AS-2 helices such that hydrogen bonding with the surrounding water molecules is increased, thereby increasing friction with the solvent. Similar structural changes may be a general feature in HAMP domain switching, which occurs in diverse signaling proteins, including sensor kinases, taxis receptors/transducers, adenylyl cyclases, and phosphatases.

Diffusion coefficient and the secondary structure of poly-L-glutamic acid in aqueous solution

The diffusion coefficients (D) of poly-L-glutamic acid (PLG) at various pHs are investigated by the laser-induced transient-grating method with a new photoreactive probe molecule. The pH dependence of D is compared with that of the helical content of PLG measured by circular dichroism. It is found that the pH dependences of both quantities are very similar. Since the frictions of the translational diffusion of charged and protonated carboxyl groups are found to be similar each other, it is concluded that the conformation of the main polymer chain is the main factor in determining the diffusion process; in other words, the alpha-helix conformation makes the molecular diffusion faster. This result indicates that the conformational change of a protein can be detected by monitoring the diffusion coefficient.

Transient dimerization and conformational change of a BLUF protein: YcgF

The photochemical reaction dynamics of YcgF, a BLUF protein, were investigated by the pulsed laser-induced transient grating (TG) technique. The TG signal showed three reaction time constants: 2.7 micros, 13 micros, and 2 ms. The fastest was tentatively attributed to relaxation of the excited triplet state of the chromophore, flavin adenine dinucleotide (FAD), and the others represented conformational changes of the protein. The TG signal provided clear evidence that the diffusion coefficient (D) of the photoproduct (3.8x10(-11) m2 s-1) was significantly less than that of the reactant (8.3x10(-11) m2 s-1), with a time constant of 2 ms at a protein concentration of 700 microM. Interestingly, the rate constant increased in proportion to the concentration of the protein, indicating that protein dimerization was one of the main reactions occurring after photoexcitation. The significant reduction in D indicates that a conformational change leading to an increase in interactions with water molecules occurs upon formation of the signaling state. The 13 mus dynamics was attributed to the conformational change that induced transient dimerization. This conformational change might be an essential process for the creation of the signaling state. A detailed scheme for the photochemical reaction of YcgF is proposed.

Photoreverse reaction dynamics of octopus rhodopsin

Photoreverse reactions of octopus rhodopsin (Rh) from acid-metarhodopsin (Acid-Meta), which is the final product of the photoreaction of Rh, to Rh were studied by the time-resolved transient absorption and transient grating methods. The time course of the absorption signal showed a rapid change within 500 ns followed by one phase with a time constant of approximately 470 micros, whereas the transient grating signal indicates three phases with time constants of <500 ns, approximately 490 micros, and 2.6 ms. The faster two phases indicate the conformational change in the vicinity of the chromophore, and the slowest one represents conformational change far from the chromophore. The absorption spectrum of the first intermediate created just after the laser excitation (<500 ns) is already very similar to the final product, Rh. This behavior is quite different from that of the forward reaction from Rh to Acid-Meta, in which several intermediates with different absorption spectra are involved within 50 ns-500 micros. This result indicates that the conformation around the chromophore is easily adjusted from all-trans to 11-cis forms compared with that from 11-cis to all-trans forms. Furthermore, it was found that the protein energy is quickly relaxed after the excitation. One of the significantly different properties between Rh and Acid-Meta is the diffusion coefficient (D). D is reduced by about half the transformation from Rh to Acid-Meta. This large reduction was interpreted in terms of the helix opening of the Rh structure.

Dynamics of conformational changes of Arabidopsis phototropin 1 LOV2 with the linker domain

Conformational changes of Arabidopsis phot1-LOV2 with the linker (phot1-LOV2-linker) were investigated from the viewpoint of the changes in molecular volume and molecular diffusion coefficient (D) by time-resolved transient grating (TG) and transient lens (TrL) methods. Although the absorption spectrum change completes within a few microseconds, the D-value detected by the TG method decreased drastically with a time constant of 1.0 ms from 9.2(+/-0.4)x10(-11) m(2)/s to 5.0(+/-0.3)x10(-11) m(2)/s. This time-dependent D was interpreted in terms of the unfolding of alpha-helices in the linker region. The change of the alpha-helices was confirmed by observing the recovery of the circular dichroism intensity. The TrL signal showed that the molecular volume decreases with two time constants; 300 micros and 1.0 ms. The former time constant is close to the previously observed photo-dissociation reaction rate of the phot1-LOV2 (without the linker) dimer, and the latter one agrees well with the rate of the D-change. Considering a similar time constant of the dissociation reaction of the LOV2 dimer, we interpreted these kinetics in terms of the dissociation step of the linker region from the LOV2 domain (T(390)(pre) state). After this step, the protein volume and D are decreased significantly with the lifetime of 1.0 ms. The D decrease indicates the increase of the intermolecular interaction between the protein and water molecules. On the basis of these observations, a two-step mechanism of the linker unfolding is proposed.

Laser-induced transient grating analysis of dynamics of interaction between sensory rhodopsin II D75N and the HtrII transducer

The interaction between sensory rhodopsin II (SRII) and its transducer HtrII was studied by the time-resolved laser-induced transient grating method using the D75N mutant of SRII, which exhibits minimal visible light absorption changes during its photocycle, but mediates normal phototaxis responses. Flash-induced transient absorption spectra of transducer-free D75N and D75N joined to 120 amino-acid residues of the N-terminal part of the SRII transducer protein HtrII (DeltaHtrII) showed only one spectrally distinct K-like intermediate in their photocycles, but the transient grating method resolved four intermediates (K(1)-K(4)) distinct in their volumes. D75N bound to HtrII exhibited one additional slower kinetic species, which persists after complete recovery of the initial state as assessed by absorption changes in the UV-visible region. The kinetics indicate a conformationally changed form of the transducer portion (designated Tr*), which persists after the photoreceptor returns to the unphotolyzed state. The largest conformational change in the DeltaHtrII portion was found to cause a DeltaHtrII-dependent increase in volume rising in 8 micros in the K(4) state and a drastic decrease in the diffusion coefficient (D) of K(4) relatively to those of the unphotolyzed state and Tr*. The magnitude of the decrease in D indicates a large structural change, presumably in the solvent-exposed HAMP domain of DeltaHtrII, where rearrangement of interacting molecules in the solvent would substantially change friction between the protein and the solvent.

Intermolecular Electron Transfer from Excited Benzophenone Ketyl Radical

The electron transfer from the benzophenone ketyl radical in the excited state (BPH(.-)(D(1))) to several quenchers (Qs) was investigated using nanosecond/picosecond two-color two-laser flash photolysis and nanosecond/nanosecond two-color two-laser flash photolysis. The electron transfer from BPH(.-)(D(1)) to Qs was confirmed by the transient absorption and fluorescence quenching measurements. The intermolecular electron-transfer rate constants were determined using the Stern-Volmer analysis. The driving force dependence of the electron-transfer rate was revealed.

Semiempirical Formula for the Estimation of Organic Radical Ion Mobility in Liquid n-Alkanes

The mobilities of radical ions of a series of organic compounds in n-alkanes with viscosities within the range of 0.2-4 cP were determined by applying the method of time-resolved electric field effect. The obtained data were used to express the correlation between the mobilities and solvent viscosity in the form of the modified Stokes-Einstein relation. The relation was parametrized in such a way that the specific molecular properties of both solvent and solute appear in the expression only as the ratio of the volumes of their molecules. A significant difference between aromatic and aliphatic compounds was found with respect to the dependence of radical ion mobility on this volume ratio, and two different parametrizations were suggested for mobility estimation in these cases.

Diffusion of platinum ions and platinum nanoparticles during photoreduction processes using the transient grating method

The photoreduction process of PtCl(6)2- to Pt nanoparticles in poly(N-vinyl-2-pyrrolidone) solutions upon UV light irradiation was investigated by monitoring the change in the diffusion coefficient (D). The D values of chemical species during UV irradiation was measured by the laser-induced transient grating (TG) method. The TG signal of the PtCl(6)2- solution before UV irradiation was composed of three kinds of contributions, the thermal grating, the species grating due to the creation of PtCl4(2-), and the species grating due to the depletions of PtCl6(2-). Upon UV irradiation of the solution, the species grating signal due to PtCl6(2-) diminished and then the TG signal of Pt nanoparticles gradually appeared. This result indicates that the gradual clustering of Pt0 atoms into Pt nanoparticles occurs after all PtCl(6)2- ions are photochemically reduced to PtCl(4)2- and subsequently transformed to Pt0 atoms with a short delay. With increasing time of the UV irradiation, the TG signal intensity increased, while D of the Pt nanoparticles did not change. This suggests that the number of Pt nanoparticles increases, but the size of the Pt nanoparticles with the polymer layer is unchanged, in the course of the UV irradiation.

Time-resolved detection of conformational changes in oat phytochrome A: time-dependent diffusion

Conformational changes in oat phytochrome A (phy) in solution after photoexcitation of the red-absorbing form (Pr) were studied in time-domain by the pulsed laser-induced transient grating technique. It was found that the diffusion coefficient (D) of far-red-absorbing form (Pfr) of large phy (1.3 x 10(-11) m(2) s(-1)) is markedly reduced compared with that of Pr (5.8 x 10(-11) m(2) s(-1)). This large reduction indicates that the conformation of Pfr is significantly changed from that of Pr, so that the intermolecular interaction with water molecules increases. This change completes within 1 ms after the photoexcitation. On the other hand, D of Pr of intact phy (4.1 x 10(-11) m(2) s(-1)) first decreases upon photoexcitation to 0.89 x 10(-11) m(2) s(-1) within 1 ms and then gradually increases with a time constant of 100 ms to the value of Pfr, 1.7 x 10(-11) m(2) s(-1). This slower phase suggests that the conformation of the N-terminal region changes with 100 ms to decrease the intermolecular interaction with water after a global change in the large phy region. The increase of D was interpreted in terms of alpha-helix formation in the Pfr form from the random coil structure in the Pr form.

Experimental verification of the Smoluchowski theory for a bimolecular diffusion-controlled reaction in liquid phase

We report experimental verification of the Smoluchowski theory for diffusion-controlled reactions in solution at the steady-state limit. We have determined both the diffusion coefficients and the self-termination reaction rates of the diphenylmethyl radical simultaneously. Smoluchowski theory is insufficient to discuss the reaction rate for the self-termination reaction of the diphenylmethyl radical, so the reaction rate of an encounter complex based on the Collins-Kimball treatment is estimated.

Intermolecular Interaction of Myoglobin with Water Molecules along the pH Denaturation Curve

A method of diffusion coefficient (D) measurement for proteins based on the pulsed laser-induced transient grating method using a photosensitive cross-linker was applied to the characterization of the pH denaturation process of holo- and apo-myoglobin (Mb) from the viewpoint of protein-water interaction. It was found that the pH denaturation curve monitored by D agrees quite well with that determined by the circular dichroism intensity for holo-Mb. This fact indicates that the changes in intermolecular interaction and the alpha-helix content occur simultaneously during the unfolding process. However, the pH dependence of D for apo-Mb was different from that of alpha-helix content. This different behavior can be explained in terms of the different denaturation steps for the secondary structure and the hydrogen bonding network of the intermediate species around pH 4; i.e., this intermediate is partially unfolded, but the hydrogen bonding network is dominantly an intramolecular one. Taking previously reported properties of this species into account, we conclude that water molecules are trapped in the hydrophobic core of the apo-Mb pH 4 intermediate. This fact suggests that the kinetic intermediate state of the protein folding process is a swollen state without water molecular exchange with the bulk phase.

Kinetic measurement of transient dimerization and dissociation reactions of Arabidopsis phototropin 1 LOV2 domain

Photochemical reaction of a plant blue-light photoreceptor, Arabidopsis phototropin 1-LOV (light-oxygen-voltage sensing) domain 2, was studied with a view to the diffusion coefficients (D) using the pulsed-laser-induced transient grating method. Although the reaction dynamics completes at a rate of several microseconds as long as it is monitored by the absorption change, the diffusion coefficient was found to be time-dependent in a time range of submilliseconds to seconds. The observed signal can be analyzed by the two-state model, which includes the D-value decrease from D of the reactant (9.8 +/- 0.4) x 10(-11) m2/s to D of the product (8.0 +/- 0.4) x 10(-11) m2/s. The D-value of the reactant implies that the dominant form in the ground state of phototropin 1 LOV2 is the monomeric form in a concentration range of 50-200 microM. According to the Stokes-Einstein relationship, the D-change can be explained by a volume increase of 1.8 times. Furthermore, the rate of the D-change was roughly proportional to the concentration of the sample. These two observations indicate that the LOV2 domain transiently forms a dimer upon photoexcitation. When the sample concentration is increased (>180 microM), a new signal component appears within a few milliseconds. This signal represents a D increase from 8.0 x 10(-11) m2/s to 9.8 x 10(-11) m2/s with a time constant of 300 micros. The completely opposite D-change from that observed in a lower concentration, as well as the concentration dependence, implies that a dimer is formed in the ground state in a higher concentration range, even though the fraction of the dimer is still minor in this range. This dimer is photodissociated, with a time constant of 300 micros. This research clearly shows that the time-resolved diffusion measurement is a very powerful tool for detecting spectrally silent association/dissociation processes during chemical reactions. The photoreaction of the LOV2 domain is discussed.

Photo-Fries rearrangements of 1-naphthyl (R)-2-phenylpropanoate in poly(vinyl acetate) and ethyl acetate: influence of medium polarity and polymer relaxation on motions of singlet radical pairs

Both the regio- and stereo-chemistries of the photoreactions of 1-naphthyl (R)-2-phenylpropanoate have been investigated in poly(vinyl acetate) films in their glassy (at 5ºC) and melted (at 50ºC) states and in ethyl acetate. These results are compared with those from irradiations in polyethylene films and in n-hexane. The regioselectivity of the intermediate 1-naphthoxy/(R)-2-phenylpropanoyl radical pair combinations is much higher in both the melt and glassy states of poly(vinyl acetate) films than that in the melt state of completely amorphous polyethylene films, but the stereoselectivity of intermediate prochiral 1-naphthoxy/1-phenylethyl radical pair combinations is much lower in poly(vinyl acetate). The results emphasize the need to control the ratio between the rates of radical tumbling and translation, as well as the ratio between the rates of in-cage motions and cage-escape, if high stereo- and regio-selectivities of combination products are to be achieved. A mechanistic picture of how the radicals of the intermediate pairs are affected by and interact with the various media is advanced.

Conformational dynamics of phototropin 2 LOV2 domain with the linker upon photoexcitation

Conformational dynamics of LOV2 domain of phototropin, a plant blue light photoreceptor, is studied by the pulsed laser induced transient grating (TG) technique. The TG signal of LOV2 without the linker part to the kinase domain exhibits the thermal grating signal due to the heat releasing from the excited state and a weak population grating by the adduct formation. The diffusion coefficients of the adduct product after forming the chemical bond between the chromophore and Cys residue are found to be slightly smaller than that of the reactant, which implies that the core shrinks slightly on the adduct formation. After that change, no significant conformational change was observed. On the other hand, the signal of LOV2 with the linker part to the kinase domain clearly shows very different diffusion coefficients between the original and the adduct species. The large difference indicates significant global conformational change of the protein moiety upon the adduct formation. More interestingly, the diffusion coefficient is found to be time-dependent in the observation time range. The dynamics representing the global conformational change is a clear indication of a spectral silent intermediate between the excited triplet state and the signaling product. From the temporal profile analysis of the signal, the rate of the conformational change is determined to be 2 ms.

Diffusion coefficients as a monitor of reaction kinetics of biological molecules

For revealing spectrally silent dynamics in chemical reactions, a new method, the time-dependent diffusion coefficient, is presented. Principles and typical examples of this method, in particular applications to biologically related reactions, are reviewed. The pulsed laser induced transient grating signal of the photo-decomposition reaction of caged ATP showed that the diffusion coefficient increases gradually with time reflecting the molecular size decrease by the dissociation. Hence, this rate should be a direct measurement of the photo-dissociation rate of ATP from the caged state. In an application to a protein folding reaction, the time-development of the diffusion coefficient was observed during the folding reaction. This time dependence was interpreted in terms of the intermolecular interaction change; i.e., conversion from the intermolecular hydrogen bonding to intramolecular one. It was found that the change of the hydrogen bonding network occurred by the two state manner in entire refolding process of cytochrome c. The unique feature of this time-dependent diffusion coefficient method is discussed.

Hydrogen bonding dynamics during protein folding of reduced cytochrome c: temperature and denaturant concentration dependence

Folding dynamics of reduced cytochrome c triggered by the laser-induced reduction method is investigated from a viewpoint of the intermolecular interaction change. Change of the diffusion coefficient of cytochrome c during the refolding process is traced in the time domain from the unfolded value to the native value continuously at various denaturant (guanidine hydrochloride (GdnHCl)) concentrations and temperatures. In the temperature range of 288 K-308 K and GdnHCl concentration range of 2.5 M-4.25 M, the diffusion change can be analyzed well by the two-state model consistently. It was found that the m(double dagger)-value and the activation energy of the transition state from the unfolded state for the hydrogen bonding network change are surprisingly similar to that for the local structural change around the heme group monitored by the fluorescence quenching experiment. This agreement suggests the existence of common or similar fundamental dynamics including water molecular movement to control the refolding dynamics. The nature of the transition state is discussed.