Dynamics of the protein structure of T169S pyranose 2-oxidase in solution: Molecular dynamics simulation.

Pyranose 2-oxidase (P2O) from Trametes multicolor contains FAD as cofactor, and forms a tetramer. The protein structure of a mutated P2O, T169S (Thr169 is replaced by Ser), in solution was studied by means of molecular dynamics simulation and analyses of photoinduced electron transfer (ET) from Trp168 to excited isoalloxazine (Iso*), and was compared with wild type (WT) P2O. Hydrogen bonding between Iso and nearby amino acids was very similar as between T169S and WT protein. Distances between Iso and Tyr456 were extremely heterogeneous among the subunits, 1.7 (1.5 in WT) in subunit A (Sub A), 0.97 (2.2 in WT) in Sub B, 1.3 (2.1 in WT) in Sub C, 1.3 nm (2.0 in WT) in Sub D. Mean values of root of mean square fluctuation over all residues were greater by four times than those in WT. This suggests that the protein structure of T169S is much more flexible than that of WT. Electrostatic (ES) energies between Iso anion in one subunit and ionic groups in the entire protein were evaluated. It was found that more than 50% of the total ES energy in each subunit is contributed from other subunits. Reported fluorescence decays were analyzed by a method as WT, previously reported. Electron affinities of Iso* in T169S were appreciably higher than those in WT. Static dielectric constants near Iso and Trp168 were also quite higher in T169S than those in WT.

Boiling effect in liquid nitrogen directly cooled Yb³âº:YAG laser.

Liquid nitrogen (LN2) behavior on the surface of excited Yb(3+):YAG is investigated using fluorometry. From the time-resolved temperature variations and integrated fluorescence spectra intensity on this directly cooled Yb(3+):YAG surface, we observe a phase transition of LN2 from nucleate boiling to film boiling. As a result of this pool boiling, good beam quality should occur when the temperature and heat flux at an excited surface of Yb(3+):YAG are below 95 K and 15.8 W/cm2, respectively. That is, the LN2 should remain in a steady state of nucleate boiling to produce good beam quality using pool boiling.

Classification of the mechanisms of photoinduced electron transfer from aromatic amino acids to the excited flavins in flavoproteins.

In many flavoproteins photoinduced electron transfer (ET) efficiently takes place from aromatic amino acids such as tryptophan or tyrosine to the excited isoalloxazine, so that the fluorescence lifetimes of isoalloxazine in some flavoproteins become ultrashort. The mechanism of ET in the flavoproteins was classified into four classes from the relationship between logarithmic ET rates (ln Rate) and the donor-acceptor distances (Rc), using reported data. The physical quantity, GT, is defined as the sum of solvent reorganization energy, electrostatic energy between a donor cation and an Iso anion, the standard free energy gap between the photoproducts and reactants, and net electrostatic energy between the photoproducts and other ionic groups in the flavoproteins (NetES). When GT fluctuates around zero with Rc, the ET rate becomes fastest (faster than 1 ps(-1)) in Kakitani and Mataga rates. In the ultrafast ET processes, the ln Rate becomes a parabolic function (category 1) of Rc as in FMN binding proteins and pyranose 2-oxidase at the shorter emission wavelengths, when NetES is negligible compared to the other quantities in the GT function. In the ultrafast ET processes, the ln Rate does not display any clear function of Rc (category 2) when NetES is dominant in the GT function, because of no direct relation between NetES and Rc. ET in flavodoxin from Helicobacter pylori may be classified into category 2. When GT linearly varies with Rc around a certain positive value, the ET rates become much slower (<1 ps(-1)). In this case the ln Rate linearly decreases with Rc (category 3), as Tyr224 in d-amino acid oxidase dimers. It is also conceivable that the ln Rate decreases with much scattered function of Rc (category 4), when NetES is dominant in the GT function, as Tyr314 in d-amino acid oxidase dimers. In ET processes of category 1, ET rates decrease as Rc becomes shorter than the distance at the maximum values of ln Rates, where GT is negative. Conditions and physical meanings were discussed for the GT-negative region.

Amplification characteristics of a cryogenic Yb³âº:YAG total-reflection active-mirror laser.

We have studied the amplification characteristics of a cryogenically cooled Yb³âº:YAG total-reflection active-mirror (TRAM) ceramic laser including wavefront distortion, birefringence loss, small signal gain (SSG), and temperature rise for developing high-performance master oscillator power amplifier (MOPA) systems. A 0.6 mm thick Yb³âº:YAG ceramic sample was used, and maximum pump intensity ~10 kW/cm² was reached. The transmitted wavefront was measured by using a Shack-Hartmann wavefront sensor, and we evaluated the thermal lens focal length and Strehl ratio for different pump conditions. We have also observed a butterfly-like leakage profile of thermally induced birefringence loss at the maximum pump intensity. From SSG measurements, we obtained moderate laser gain of G=3 for one bounce with a near aberration-free wavefront. Gain calculations, which included also temperature dependence of the emission cross section and reabsorption of Yb³âº:YAG, were in good agreement with the experiments. These experimental results will be useful as benchmark data for numerical simulations of temperature distribution in TRAM and for designing multikilowatt-class high-performance MOPA systems.

Ultrafast carbonyl motion of the photoactive yellow protein chromophore probed by femtosecond circular dichroism.

Motions of the trans-p-coumaric acid carbonyl group following the photoexcitation of the R52Q mutant of photoactive yellow protein (PYP) are investigated, for the first time, by ultrafast time-resolved circular dichroism (TRCD) spectroscopy. TRCD is monitored in the near-ultraviolet, over a time scale of 10 ps. Immediately after excitation, TRCD is found to exhibit a large negative peak, which decays within a few picoseconds. A quantitative analysis of the signals shows that, upon excitation, the carbonyl group undergoes a fast (≪0.8 ps) and unidirectional flipping motion in the excited state with an angle of ca. 17-53°. For the subset of proteins that do not enter the signaling photocycle, TRCD provides strong evidence that the carbonyl group moves back to its initial position, leading to the formation of a nonreactive ground-state intermediate of trans conformation. The initial ground state is then restored within ca. 3 ps. Comparative study of R52Q and wild-type PYP provides direct evidence that the absence of Arg52 has no effect on the conformational changes of the chromophore during those steps.

ASE and parasitic lasing in thin disk laser with anti-ASE cap.

The amplified spontaneous emission (ASE) and parasitic lasing (PL) effects in thin disk laser with an anti-ASE cap have been investigated in detail by measuring both time-resolved radiated intensity at longer axis of elliptical pump profile (dominant ASE direction) and small signal gain (SSG) in laser amplifier. A cryogenically-cooled total-reflection active-mirror laser consisting of 9.8 at.% doped, 0.6-mm thick Yb:YAG and un-doped YAG trapezoidal ceramics cap was used as a sample. The phased transitions from spontaneous emission (SE) to ASE and from ASE to PL have been unambiguously observed. For several pump beam diameters, the ASE gain parameter g(0)l(ASE) at ASE threshold was about 3, and the SSG coefficient was down to about 65% until PL started. To the best of our knowledge, this is the first quantitative characterization of the ASE/PL effects in the thin disk laser with an anti-ASE cap.

Interferometric phase shift compensation technique for high-power, tiled-aperture coherent beam combination.

We propose a simple coherent beam combining technique for applications in high-power multichannel laser amplifier systems with tiled aperture design. Using a photodiode pair coupled with piezo-actuator mirrors, we demonstrated robust beam combining bandwidth (~1 KHz) and root mean-square deviation (~λ/25) for two beam channels. We estimate that the performance of this technique can be further enhanced in terms of operational bandwidth and phase locking accuracy. It is not limited by single beam power or channel number restrictions, does not require optical phase retrieval algorithms, or calibrations, and can be integrated into various master oscillator power amplifier architectures.

Terahertz generation by optical rectification in lithium niobate crystal using a shadow mask.

A simple approach to generate high energy, frequency and bandwidth tunable multicycle THz pulses by optical rectification (OR) of spatially shaped femtosecond laser pulses in the lithium niobate (LN) crystal is proposed and demonstrated. A one dimensional binary shadow mask is used as a laser beam shaper. By building the mask's image in the bulk LN crystal with various demagnifications, the frequency of THz generation was tuned in the range of 0.3 - 1.2 THz. There exist also an opportunity to tune the bandwidth of THz generation from 20 GHz to approximately 1 THz by changing the optical beam size on the crystal. The energy spectral density of narrowband THz generation is almost independent of the bandwidth and is typically 0.18 µJ/THz for ~1 W pump power at 1 kHz repetition rate.

Output characteristics of high power cryogenic Yb:YAG TRAM laser oscillator.

We analyzed the output power characteristics of a cryogenically cooled Yb:YAG total-reflection active-mirror (TRAM) laser oscillator including the temperature dependence of the emission cross section and the reabsorption loss of the Yb:YAG TRAM. A CW multi-transverse mode oscillation of a 9.8 at.% doped 0.6 mm thick Yb:YAG ceramic TRAM was investigated for various pump spot sizes and compared with theoretical results. The Yb:YAG temperatures were inferred from the ratio between fluorescence intensities at 1022 nm and 1027 nm which varied significantly with temperature below 200 K. Output power calculations using evaluated temperatures were in good agreement with the experimental data measured between 77 and 200 K, and the output power suppression due to the temperature rise observed above ~140 K. To the best of our knowledge, this is the first evaluation of output power for a cryogenically cooled Yb:YAG TRAM laser.

Photochemistry of fac-[Re(bpy)(CO)3Cl].

The photochemistry of fac-[Re(bpy)(CO)(3)Cl] (1 a; bpy=2,2'-bipyridine) initiated by irradiation using <330 nm light has been investigated. Isomerization proceeded in THF to give the corresponding mer-isomer 1 b. However, in the presence of a small amount of MeCN, the main product was the CO-ligand-substituted complex (OC-6-24)-[Re(bpy)(CO)(2) Cl(MeCN)] (2 c; bpy=2,2'-bipyridine). In MeCN, two isomers, 2 c and its (OC-6-34) form (2 a), were produced. Only 2 c thermally isomerized to produce the (OC-6-44) form 2 b. A detailed investigation led to the conclusion that both 1 b and 2 c are produced by a dissociative mechanism, whereas 2 a forms by an associative mechanism. A comparison of the ultrafast transient UV-visible absorption, emission, and IR spectra of 1 a acquired by excitation using higher-energy light (e.g., 270 nm) and lower-energy light (e.g., 400 nm) gave detailed information about the excited states, intermediates, and kinetics of the photochemical reactions and photophysical processes of 1 a. Irradiation of 1 a using the higher-energy light resulted in the generation of the higher singlet excited state with τ≤25 fs, from which intersystem crossing proceeded to give the higher triplet state ((3)HES(1)). In THF, (3)HES(1) was competitively converted to both the triplet ligand field ((3)LF) and metal-to-ligand charge transfer ((3)MLCT) with lifetimes of 200 fs, in which the former is a reactive state that converts to [Re(bpy)(CO)(2)Cl(thf)](+) (1 c) within 10 ps by means of a dissociative mechanism. Re-coordination of CO to 1 c gives both 1 a and 1 b. In MeCN, irradiation of 1 a by using high-energy light gives the coordinatively unsaturated complex, which rapidly converted to 2 c. A seven-coordinate complex is also produced within several hundred femtoseconds, which is converted to 2 a within several hundred picoseconds.

Equivalence between inverted regions of the energy gap law and inverted regions of donor-acceptor distances in photoinduced electron transfer processes in flavoproteins.

In the present work, we discuss about the relationship between the energy gap law and extended Dutton law in flavoproteins. The extend Dutton law is defined herein as the dependence of logarithmic rates (ln Rate) of photoinduced electron transfer (ET) from aromatic amino acids to excited isoalloxazine (Iso*) on donor-acceptor distances (Rcs). Both functions of ln Rate vs. negative values of the standard free energy gap and ln Rate vs. Rc display a parabolic behavior, when the ET rates are ultrafast. The negative values of the standard free energy gap at peaks of ln Rate [X m(ES)] were obtained for FMN-binding protein, wild-type pyranose 2-oxidase, T169S (Thr169 is replaced by Ser) pyranose 2-oxidase, and medium-chain acyl-CoA dehydrogenase. The values of Rc at peaks of ln Rate [X m(Rc)] were also obtained for these flavoproteins. The negative values of the standard free energy gap decreased with approximate linear functions of Rc. The negative values of standard free energy gap [X m(ESRc)] at Rc = X m(Rc) were evaluated using the linear functions of the negative standard free energy gap with Rc. The values of X m(ESRc) were mostly in very good agreement with the values of X m(ES). This implies that the energy gap law and the extend Dutton law are equivalent. X m(ES) values in ET donors displaying the linear extend Dutton law with Rc were obtained by energy gap law, and then X m(Rc) values were evaluated with the negative standard free energy gap. Thus, the obtained X m(Rc) values were much smaller than the Rc range obtained by the method of molecular dynamics simulation. This suggests that ET processes with linear profiles of the extend Dutton law could be parabolic when Rc becomes much shorter than the Rc range obtained by the method of molecular dynamics simulation.

Ultrafast photodissociation dynamics of a hexaarylbiimidazole derivative with pyrenyl groups: dispersive reaction from femtosecond to 10 ns time regions.

The photodissociation dynamics of a hexaarylbiimidazole (HABI) derivative with two pyrenyl groups was investigated by time-resolved transient absorption spectroscopy and fluorescence measurements. Transient absorption spectroscopy revealed that photodissociation took place in the wide time region of <100 fs to 10 ns. On the other hand, fluorescence time profiles showed the dynamic red shift in the time region <100 ps. The apparent dispersive photodissociation process was attributed to the increase in the interaction between the pyrenyl moiety in the excited state and the other moiety in the ground state, resulting in the gradual increase of the activation energy for the crossing between the attractive potential surface of an excited pyrenyl unit and the repulsive potential surface.

Ultrafast solvation dynamics of flavin mononucleotide in the reductase component of p-hydroxyphenylacetate hydroxylase.

The reductase unit of p-hydroxyphenylacetate hydroxylase contains flavin mononucleotide (FMN) as a cofactor. Fluorescence decay curves measured by fluorescence up-conversion method were remarkably dependent on monitored emission wavelength. The fluorescence lifetime was shorter at the shorter emission wavelengths and longer at the longer wavelengths. Spectral shift correlation function of p-coumaric acid in water and FMN in C1 protein in buffer solution were expressed by two-exponential functions. Correlation times, phi1 and phi2, of p-coumaric acid were 0.053 and 0.650 ps, respectively, which was similar to previous works. phi1 and phi2 of C1 were 0.455 and 250 ps, respectively. The Stokes shift from t=0 to t=infinity was 2200 cm(-1), while it is 500 cm(-1) in the static Stokes shift obtained by the solvent effect of the fluorescence spectrum under static excitation. This suggests that the isoalloxazine ring of FMN in C1 is exposed in hydrophilic environment. Such large Stokes shift was unusual among flavoproteins. The biphasic decay of the spectral correlation function in C1 was discussed and compared to the biphasic decay of tryptophan in proteins.

Comparative studies on picosecond-resolved fluorescence of d-amino acid oxidases from human with one from porcine kidney. Photoinduced electron transfer from aromatic amino acids to the excited flavin.

Fluorescence dynamics of human d-amino acid oxidase (hDAAO) and its five inhibitors have been studied in the picoseconds time domain, and compared with one in d-amino acid oxidase from porcine kidney (pkDAAO) reported. The fluorescence lifetimes were identified as 47 ps in the dimer, 235 ps in the monomer, which are compared with those of pkDAAO (45 ps-185 ps). The fluorescence lifetimes of the hDAAO did not change upon the inhibitor bindings despite of modifications in the absorption spectra. This indicates that the lifetimes of the complexes are too short to detect with the picosecond lifetime instrument. Numbers of the aromatic amino acids are similar between the both DAAOs. The fluorescence lifetimes of hDAAO were analysed with an ET theory using the crystal structure. The difference in the lifetimes of the dimer and monomer was well described in terms of difference in the electron affinity of the excited isoalloxazine (Iso*) between the two forms of the protein, though it is not known whether the structure of the monomer is different from the dimer. Three fastest ET donors were Tyr314, Trp52 and Tyr224 in the dimer, while Tyr314, Tyr224 and Tyr55 in the monomer, which are compared to those in pkDAAO, Tyr314, Tyr224 and Tyr228 in the dimer, and Tyr224, Tyr314 and Tyr228 in the monomer. The ET rate from Trp55 in hDAAO dimer was much faster compared to the rate in pkDAAO dimer. A rise component with negative pre-exponential factor was not observed in hDAAO, which are found in pkDAAO.

Quantum mechanical study of photoinduced charge transfer in FMN binding protein.

CT interactions between Iso* and nearby aromatic amino acids in FBP were investigated by a semiempirical MO method. Atomic coordinates of lumiflavin as Iso, 3-methylindole as Trp, and 4-methylphenol as Tyr, used for MO calculations, were obtained from crystal, 20 NMR structures and 40 MD structures (20 ps time intervals). Geometries of Iso-Trp32, Iso-Trp106 and Iso-Tyr35 systems were optimized by the PM3 method. The interaction energies (kcal/mol) of crystal structure were -16.9 in the Iso-Trp32 system, -7.4 in the Iso-Trp106 system and 1.4 in the Iso-Tyr35 system. The interaction energies (kcal/mol) of NMR structures were -16.5 +/- 0.28 in the Iso-Trp32 system, -10.6 +/- 0.14 in the Iso-Trp106 system, and 0.97 +/- 0.09 in the Iso-Tyr35 system. The interaction energies (kcal/mol) of MD structures were -24.3 +/- 0.19 in the Iso-Trp32 system, -10.2 +/- 0.49 in the Iso-Trp106 system, and 0.285 +/- 0.037 in the Iso-Tyr35 system. CT interaction from the aromatic amino acids to Iso* was judged from negative charge at Iso*. The charge in the Iso-Trp32 system was -0.490 in crystals, -0.439 +/- -0.099 in NMR structures, -0.454 +/- 0.048 in MD structures. The charge in the Iso and Trp106 system was -0.011 +/- 0.004 in MD structures, but negligible in other structures. CT interactions in Iso-Tyr35 system were also negligible. The ET rate obtained with Kakitani and Mataga theory and MD decreased as the magnitude of the interaction energy decreased. Correlation between the ET rate and CT interaction in FBP was examined. The interaction energy (Y) was approximated with ln(ET rate) (X) by a function, Y = 0.0036X(3) + 0.0306X(2) - 1.7822X - 21.177.

Simultaneous analysis of ultrafast fluorescence decays of FMN binding protein and its mutated proteins by molecular dynamic simulation and electron transfer theory.

Ultrafast fluorescence decays of FMN binding proteins (FBP) from Desulfovibrio vulgaris (Miyazaki F) were analyzed with an electron transfer (ET) theory by Kakitani and Mataga (KM theory). Time-dependent distances among isoalloxazine (Iso) and Trp-32, Tyr-35, and Trp-106 in wild-type FBP (WT), among Iso and Tyr-32, Tyr-35, and Trp-106 in W32Y (Trp-32 was replaced by Tyr-32), and among Iso and Tyr-35 and Trp-106 in W32A (Trp-32 was replaced by Ala-32) were determined by molecular dynamic simulation (MD). Electrostatic energies between Iso anion and all other ionic groups, between Trp-32 cation and all other ionic groups, and between Tyr-32 cation and all other ionic groups were calculated in WT, W32Y, and W32A, from the MD coordinates. ET parameters contained in KM theory, such as frequency (nu 0), a coefficient of the ET process (beta), a critical distance of the ET process ( R 0), standard free energy related to the electron affinity of the excited Iso ( G Iso (0)), and the static dielectric constant in FBP species (epsilon 0), were determined with and without inclusion of the electrostatic energy, so as to fit the calculated fluorescence decays with the observed decays of all FBP species, by a nonlinear least-squares method according to the Marquardt algorithm. In the analyses the parameters, nu 0, beta, and R 0 were determined separately between Trp residues and Tyr residues among all FBP species. Calculated fluorescence intensities with the inclusion of the electrostatic energy fit quite well with the observed ones of all WT, W32Y, and W32A.

Comparison between ultrafast fluorescence dynamics of FMN binding protein from Desulfovibrio vulgaris, strain Miyazaki, in solution vs crystal phases.

Ultrafast fluorescence dynamics of FMN binding protein (FBP) from Desulfobivrio vulgaris, strain Miyaxaki F, were compared in solution and crystal phases. Fluorescence lifetimes of FBP were 167 fs (96%) and 1.5 ps (4%) in solution (tau(av) = 220 fs), and 730 fs (60%) and longer than 10 ps (40%) in crystals (tau(av) = 4.44 ps). The quenching of the fluorescence of flavin in the protein was considered to be due to photoinduced electron transfer (ET) from Trp or Tyr to the excited isoalloxazine (Iso) nearby. The average lifetime was 20 times longer in crystal vs in solution. Averaged distances between Iso and nearby Trp-32, Tyr-35, and Trp-106 were 8.42, 7.36, and 8.15 A in solution, respectively (obtained by NMR spectroscopy), and 7.05, 7.72, and 8.49 A in crystal, respectively (obtained by X-ray crystallography). The prolonged lifetime in crystal cannot be elucidated by the change in the distances between the states. It was suggested that the longer lifetime in crystal was ascribed to the absence of water molecules around FBP with rapid motional freedom, which may be the driving force for the ET in flavoproteins.

Donor-acceptor distance-dependence of photoinduced electron-transfer rate in flavoproteins.

Ultrafast fluorescence quenching of flavin in flavodoxin from Megasphaera elsdenii was investigated by means of a fluorescence up-conversion method. Fluorescence lifetimes of flavodoxin from M. elsdenii were estimated to be tau(1) approximately 165 fs (0.97%) and tau(2) approximately 10 ps (0.03%). Correlation of photoinduced electron-transfer rates (k(ET)) with averaged distances (D(av)) between isoalloxazine and nearby tryptophan or tyrosine was examined and obtained an empirical equation of ln k(ET) vs D(av) by means of a nonlinear least-squares method using reported data together with flavodoxin from M. elsdenii. The values of D(av) were calculated from X-ray structures of the flavoproteins. The ln k(ET) was approximately linear at D(av) shorter than 7 A. The model free empirical equation was expressed as ln k(ET) = 29.7 + (-0.327 D(av) + 2.84 x 10(-5))/(0.698 - D(av)(2)). We also analyzed the observed values of ln k(ET) with Marcus theory, but could not obtain reasonable results. Our analysis suggests that the average distance, rather than the shortest (edge to edge) distance or interplanar angles between the aromatics rings, is the key factor in the process of the photoinduced electron transfer in these flavoproteins.

Ultrafast fluorescence upconversion technique and its applications to proteins.

The basic principles and main characteristics of the ultrafast time-resolved fluorescence upconversion technique (conventional and space-resolved), including requirements for nonlinear crystals, mixing spectral bandwidth, acceptance angle, etc., are presented. Applications to flavoproteins [wild-type (WT) FMN-binding protein and its W32Y, W32A, E13R, E13K, E13Q and E13T mutants] and photoresponsive proteins [WT photoactive yellow protein and its R52Q mutant in solution and as single crystals] are demonstrated. For flavoproteins, investigations elucidating the effects of ionic charges on ultrafast electron transfer (ET) dynamics are summarized. It is shown that replacement of the ionic amino acid Glu13 and the resulting modification of the electrostatic charge distribution in the protein chromphore-binding pocket substantially alters the ultrafast fluorescence quenching dynamics and ET rate in FMN-binding protein. It is concluded that, together with donor-acceptor distances, electrostatic interactions between ionic photoproducts and other ionic groups in the proteins are important factors influencing the ET rates. In WT photoactive yellow protein and the R52Q mutant, ultrafast photoisomerization dynamics of the chromophore (deprotonated trans-p-coumaric acid) in liquid and crystal phases are investigated. It is shown that the primary dynamics in solution and single-crystal phases are quite similar; hence, the photocycle dynamics and structural differences observed at longer time scales arise mostly from the structural restraints imposed by the crystal lattice rigidity versus the flexibility in solution.