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The aggregation of amyloid β(Aβ) peptides is at the heart of Alzheimer's disease development and progression. As a result, amyloid aggregates have been studied extensively in vitro, and detailed structural information on fibrillar amyloid aggregates is available. However, forwarding these structural models to amyloid plaques in the human brain is still a major challenge. The chemistry of amyloid plaques, particularly in terms of the protein secondary structure and associated chemical moieties, remains poorly understood. In this report, we use Raman microspectroscopy to identify the presence of carotenoids in amyloid plaques and demonstrate that the abundance of carotenoids is correlated with the overall protein secondary structure of plaques, specifically to the population of β-sheets. While the association of carotenoids with plaques has been previously identified, their correlation with the β structure has never been identified. To further validate these findings, we have used optical photothermal infrared (O-PTIR) spectroscopy, which is a spatially resolved technique that yields complementary infrared contrast to Raman. O-PTIR unequivocally demonstrates the presence of elevated β-sheets in carotenoid-containing plaques and the lack of β structure in noncarotenoid plaques. Our findings underscore the potential link between anti-inflammatory species as carotenoids to specific secondary structural motifs within Aβ plaques and highlight the possible role of chemically distinct plaques in neuroinflammation, which can uncover new mechanistic insights and lead to new therapeutic strategies for AD.

Raman multivariate curve resolution (Raman-MCR) spectra obtained from pure and isotopically dilute water are used to probe the influence of intermolecular resonance couplings on water OH and OD stretch band shapes and intensities, in the absence of intramolecular coupling. Intermolecular resonant coupling is found to broaden and red-shift the OH stretch band of water, in qualitative agreement with the predictions of Yang and Skinner. The influence of intermolecular coupling is found to increase with decreasing temperature, and to increase the Raman scattering cross section of the OH stretch, but decrease the OD stretch cross section. Moreover, we find that intermolecular coupling slightly perturbs the vibrational spectra of water molecules surrounding HOD. [ABSTRACT FROM AUTHOR]

Aqueous proton transport involves the ultrafast interconversion of hydrated proton species that are closely linked to the hydrogen bond dynamics of water, which has been a long-standing challenge to experiments. In this study, we use ultrafast IR spectroscopy to investigate the distinct vibrational transition centered at 1750 cm-1 in strong acid solutions, which arises from bending vibrations of the hydrated proton complex. Broadband ultrafast two-dimensional IR spectroscopy and transient absorption are used to measure vibrational relaxation, spectral diffusion, and orientational relaxation dynamics. The hydrated proton bend displays fast vibrational relaxation and spectral diffusion timescales of 200-300 fs; however, the transient absorption anisotropy decays on a remarkably long 2.5 ps timescale, which matches the timescale for hydrogen bond reorganization in liquid water. These observations are indications that the bending vibration of the aqueous proton complex is relatively localized, with an orientation that is insensitive to fast hydrogen bonding fluctuations and dependent on collective structural relaxation of the liquid to reorient. We conclude that the orientational relaxation is a result of proton transfer between configurations that are well described by a Zundel-like proton shared between two flanking water molecules. [ABSTRACT FROM AUTHOR]

A synergic approach combining molecular dynamics (MD) simulations and X-ray absorption spectroscopy (XAS) has been used to investigate diluted (0.1 M) aqueous solutions of two lanthanide ions (Ln3+), namely, La3+ and Dy3+, with triflate, nitrate, and bis(trifluoromethylsulfonyl)imide (Tf2N-) as counterions. The different complexing ability of the three anions has been highlighted by the analysis of the MD simulations: Tf2N- does not form inner-sphere complexes, while a small amount of triflate coordinates both the La3+ and Dy3+ cations in their first solvation shell. On the other hand, the nitrate ion is almost absent in the La3+ first coordination sphere, while forming contact ion pairs with Dy3+. Both lanthanide ions are found to preferentially interact with the water molecules, and the total number of oxygen atoms coordinating the Ln3+ cations in their first solvation sphere is the same in all of the solutions, regardless of whether they belong to water molecules or to the counterion. The presence of counterions in the cation first or second shell changes neither the first shell distance nor the symmetry of the hydration complex formed in solution. The MD results have been confirmed by comparison with the Ln K-edge XAS experimental data, and the quantitative analysis of the extended X-ray absorption fine structure (EXAFS) spectra of the three salt solutions has provided a definite proof of the accuracy of the force field employed in the simulations and of the MD structural result. The anion-water and water-water hydrogen bond lifetimes have been analyzed highlighting the slow down effect of the triflate, nitrate, and Tf2N- anions on the hydrogen bond dynamics in the Ln3+ first solvation shell, with the effect being stronger in the Dy3+ solutions, due to the higher charge density of the Dy3+ ion as compared to La3+ [ABSTRACT FROM AUTHOR]

A simple exciton theory for the description of anisotropic circular dichroism (ACD) spectra of multichromophoric systems is presented that is expected to be of general use for the analysis of structure-function relationships of molecular aggregates such as photosynthetic light-harvesting antennae. The theory is applied to the baseplate of green sulfur bacteria. It is demonstrated that only the combined analysis of ACD and circular dichroism (CD) spectra for the present baseplate bacteriochlorophyll (BChl) a dimer allows for an unambiguous determination of the parameters of the exciton Hamiltonian from experimental data. The analysis of experimental absorption and linear dichroism spectra suggests that either the NMR structure has to be refined or in addition to the dimers seen in the NMR structure and in the CD and ACD spectra, BChl a monomers are present in the baseplate carotenosome sample. A refined dimer structure is presented, explaining all four optical spectra. [ABSTRACT FROM AUTHOR]

Poly-l-alanine (PLA) sequences are a key element in the structure of the crystalline domains of spider dragline silks, wild silkworm silks, antifreeze proteins, and amyloids. To date, no atomic-level structures of antiparallel (AP)-PLA longer than Ala4 have been reported using the single-crystal X-ray diffraction analysis. In this work, dipolar-assisted rotational resonance solid-state NMR spectra were observed to determine the effective internuclear distances of 13C uniformly labeled alanine tetramer with antiparallel (AP) β-sheet structure whose atomic coordinates are determined from the X-ray crystallographic analysis. Initial build-up rates, Rj,k, were obtained from the build-up curves of the cross peaks by considering the internuclear distances arising in the master equation. Subsequently, experimentally obtained effective internuclear distances, reffj,k(obs), were compared with the calculated reffj,k(calc) values obtained from the X-ray crystallographic data. Fairly good correlation between reffj,k(obs) and reffj,k(calc) was obtained in the range of 1.0-6.0 Å, with the standard deviation of 0.244 Å, without considering the zero-quantum line-shape functions. It was further noted that the internuclear distances of intermolecular contributions provide details relating to the molecular packing in solid-state samples. Thus, the present data agree well with AP-β-sheet packing but do not agree with P-β-sheet packing. [ABSTRACT FROM AUTHOR]

Consolidated knowledge of conformation and stability of amino acids and their clusters is required to understand their biochemical recognition. Often, alkali ions interact with amino acids and proteins. Herein, infrared photodissociation (IRPD) spectra of cryogenic metalated glutamic acid ions (GluM+, M = Li-Cs) are systematically analyzed in the isomer-specific fingerprint and XH stretch ranges (1100-1900, 2600-3600 cm-1) to provide a direct measure for cation-size-dependent conformational locking. GluM+ ions are generated by electrospray ionization and cooled down to 15 K in a cryogenic quadrupole ion trap. The assignment of the IRPD spectra is supported by density functional theory calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level. In the global minimum of GluM+, the flexibility of Glu is strongly reduced by the formation of rigid ionic CO···M+···OC metal bridges, corresponding to charge solvation. The M+ binding energy decreases monotonically with increasing cation size from D0 = 314 to 119 kJ/mol for Li-Cs. Whereas for Li and Na only the global minimum of GluM+ is observed, for K-Cs at least three isomers exist at cryogenic temperature. The IRPD spectra of cold GluM+ ions are compared to IR multiple-photon dissociation spectra measured at room temperature. Furthermore, we elucidate the differences of the impact of protonation and metalation on the structure and conformational locking of Glu. [ABSTRACT FROM AUTHOR]

The desorption kinetics for benzene and cyclohexane from a graphene covered Pt(111) surface were investigated using temperature-programmed desorption (TPD). The benzene desorption spectra show well-resolved monolayer and multilayer desorption peaks. The benzene monolayer and submonolayer TPD spectra for coverages greater than ~0.1 ML have nearly the same desorption peak temperature and have line shapes which are consistent with first-order desorption kinetics. For benzene coverages greater than 1 ML, the TPD spectra align on a common leading edge which is consistent with zero-order desorption. An "inversion" procedure in which the prefactor is varied to find the value that best reproduces the entire set of experimental desorption spectra was used to analyze the benzene data. The inversion analysis of the benzene TPD spectra yielded a desorption activation energy of 54 ± 3 kJ/mol with a prefactor of 1017±1 s-1. The TPD spectra for cyclohexane also have well-resolved monolayer and multilayer desorption features. The desorption leading edges for the monolayer and the multilayer TPD spectra are aligned indicating zero-order desorption kinetics in both cases. An Arrhenius analysis of the monolayer cyclohexane TPD spectra yielded a desorption activation energy of 53.5 ± 2 kJ/mol with a prefactor of 1016±1 ML s-1. [ABSTRACT FROM AUTHOR]

Polyamidoamine (PAMAM) dendrimers at different generations (from G2 to G6) were functionalized with pyridine (Py) groups at the external surface, and their complexation behavior with Cu(II) at increasing molar ratios between the ions and the Py groups was analyzed in the absence and presence of reducing agents and a spin trap. These Cu(II)–dendrimer complexes may be used as antitumor and antiamyloidogenesis drugs, similarly to other Cu(II) –dendrimer complexes, and as biocatalysts. Indeed, they have revealed to selectively catalyze molecular oxygen reduction to generate reactive oxygen species (ROS). A computer-aided electron paramagnetic resonance (EPR) study of these complexes allowed us to identify different complexes by increasing the Cu(II)/Py molar ratio for the different generations. Binuclear EPR-silent complexes were formed at the highest generations. The differently complexed Cu(II) ions showed a different capability to be reduced, starting from the most exposed at the dendrimer surface bearing a stable Cu(II) –Py2 coordination. Cu(II) –G5 showed peculiar structural properties which probably favored its activity as biocatalyst. The spin trap was able to capture hydroxyl radicals, which became clearly EPR visible after all Cu(II) ions were reduced to Cu(I). This method may be used as a platform to study interactions of Cu(II) in nanosized macromolecules for biomedical purposes, mainly in biocatalysis involving redox reactions and formation of ROS. [ABSTRACT FROM AUTHOR]

The computationally predicted presence of two structurally distinct minima in the first triplet excited (T1) state of 2-thiouracil (2TU) is substantiated by sub-picosecond transient vibrational absorption spectroscopy (TVAS) in deuterated acetonitrile solution. Following 300 nm ultraviolet excitation to the second singlet excited state of 2TU, a transient infrared absorption band centered at 1643 cm-1 is observed within our minimum time resolution of 0.3 ps. It is assigned either to 2TU molecules in the S1 state or to vibrationally hot T1-state molecules, with the latter assignment more consistent with recent computational and experimental studies. The 1643 cm-1 band decays with a time constant of 7.2 ± 0.8 ps, and there is corresponding growth of several further bands centered at 1234, 1410, 1424, 1443, 1511, 1626, and 1660 cm-1 which show no decline in intensity over the 1 ns time limit of our measurements. These spectral features are assigned to two different conformations of 2TU, corresponding to separate energy minima on the T1-state potential energy surface, on the basis of their extended lifetimes, computed infrared frequencies, and the observed quenching of the bands by addition of styrene. Corresponding measurements for the 4-thiouracil (4TU) isomer show sub-picosecond population of the T1 state, which vibrationally cools with a time constant of 5.2 ± 0.6 ps. However, TVAS measurements in the carbonyl stretching region do not distinguish the two computed T1-state conformers of 4TU because of the similarity of their vibrational frequencies. [ABSTRACT FROM AUTHOR]

The bioluminescent reaction of the "sea firefly" Cypridina hilgendorfii is a prototypical system for marine bioluminescence, as its substrate possesses an imidazopyrazinone core that is a common link among organisms of eight phyla. The elucidation of the mechanism behind Cypridina bioluminescence is essential for future applications in bioimaging, biomedicine, and bioanalysis. In this study we have investigated the key step of chemiexcitation with a combined experimental and theoretical approach. The obtained results indicate that neutral dioxetanone is responsible for efficient chemiexcitation, as the thermolysis of this species gives access to a long region of the potential energy surface (PES), where the ground and excited singlet states are degenerated. Contrary to expected, neither chemically induced electron-exchange luminescence (CIEEL) nor charge transfer-initiated luminescence (CTIL) can be used to explain imidazopyrazinone-based bioluminescence, as there is no clear relationship between electron (ET)/charge (CT) transfer (occurring between the electron-rich moiety and dioxetanone) and chemiexcitation. Attractive electrostatic interactions between the CO2 and oxyluciferin moieties allow neutral dioxetanone to spend time in the PES region of degeneracy, while repulsive interactions for anionic dioxetanone lead to a quicker CO2 detachment. [ABSTRACT FROM AUTHOR]

The light harvesting-reaction center (LH1-RC) complex from a new thermophilic purple sulfur bacterium Allochromatium (Alc.) tepidum was isolated and characterized by spectroscopic and thermodynamic analyses. The purified Alc. tepidum LH1-RC complex showed a high thermostability comparable to that of another thermophilic purple sulfur bacterium Thermochromatium tepidum, and spectroscopic characteristics similar to those of a mesophilic bacterium Alc. vinosum. Approximately 4-5 Ca2+ per LH1-RC were detected by inductively coupled plasma atomic emission spectroscopy and isothermal titration calorimetry. Upon removal of Ca2+, the denaturing temperature of the Alc. tepidum LH1-RC complex dropped accompanied by a blue-shift of the LH1 Q y absorption band. The effect of Ca2+ was also observed in the resonance Raman shift of the C3-acetyl νC=O band of bacteriochlorophyll-a, indicating changes in the hydrogen-bonding interactions between the pigment and LH1 polypeptides. Thermodynamic parameters for the Ca2+-binding to the Alc. tepidum LH1-RC complex indicated that this reaction is predominantly driven by the largely favorable electrostatic interactions that counteract the unfavorable negative entropy change. Our data support a hypothesis that Alc. tepidum may be a transitional organism between mesophilic and thermophilic purple bacteria and that Ca2+ is one of the major keys to the thermostability of LH1-RC complexes in purple bacteria. [ABSTRACT FROM AUTHOR]

Broadband dielectric spectroscopy measurements were performed on partially crystallized gelatin-water mixtures with gelatin concentrations of 1-5 wt % for temperatures between 123 and 298 K to study the dynamics of ice. These systems contain only hexagonal ice. Nevertheless, four dielectric relaxation processes of ice were observed. At temperatures below the crystallization temperature, a loss peak was observed, and it separated into four loss peaks at around 225 K. Using the temperature and concentration dependencies of these relaxation processes, we confirmed that these four processes originated from ice. For the relaxation time of ice, τice, the deviation of the temperature dependence of τice from the Arrhenius type is larger for the relaxation process at the higher-frequency side. For the temperature dependence of τice for the dominant process, three temperature ranges with different activation energies, Ea, were investigated. The intermediate-temperature range of τice with the smallest Ea decreased as the gelatin concentration increased; therefore, τice of the dominant process changed from the relaxation process with the smaller τice to that with the larger τice as the gelatin concentration increased. In addition, the relaxation process of ice with larger τice values was found to have larger values of Ea. These results suggest that a higher gel network density affects the temperature dependence of τice. [ABSTRACT FROM AUTHOR]

The magnetic properties of the Rieske protein purified from Chlorobaculum tepidum were investigated using electron paramagnetic resonance and hyperfine sublevel correlation spectroscopy (HYSCORE). The g -values of the Fe2S2 center were g x = 1.81, g y = 1.90, and g z = 2.03. Four classes of nitrogen signals were obtained by HYSCORE. Nitrogens 1 and 2 had relatively strong magnetic hyperfine couplings and were assigned as the nitrogen directly ligated to Fe. Nitrogens 3 and 4 had relatively weak magnetic hyperfine couplings and were assigned as the other nitrogen of the His ligands and peptide nitrogen connected to the sulfur atom via hydrogen bonding, respectively. The anisotropy of nitrogen 3 reflects the different spin density distributions on the His ligands, which influences the electron transfer to quinone. [ABSTRACT FROM AUTHOR]

Fluorescence correlation spectroscopy (FCS) is a primary tool in the time-resolved analysis of nonreacting or reacting molecules in solution, based on fluorescence intensity fluctuations. However, conventional FCS alone is insufficient for a complete determination of reaction or mixture parameters. In an accompanying article, a technique for the computation of artifact-free higher-order correlations with microsecond time resolution was described. Here, we demonstrate the applications of the technique to analyze the systems of fast and slow reactions. As an example of non- or slow-reacting systems, the technique is applied to resolve two-component mixtures of labeled oligonucleotides. Next, the protonation reaction of fluorescein isothiocyanate in phosphate buffer is analyzed as an example of fast reactions (relaxation time <1 μs). By reference to an (apparent) nonreacting system, the simple factorized form of cumulant-based higher-order correlations is exploited to remove the dependence on the molecular detection function (MDF). Therefore, there is no need to model and characterize the experimental MDF, and the precision and the accuracy of the technique are enhanced. It is verified that the higher-order correlation analysis enables a complete and simultaneous determination of the number and brightness parameters of mixing or reacting molecules, the reaction relaxation time, and forward and reverse reaction rates. [ABSTRACT FROM AUTHOR]

Fluorescence correlation spectroscopy (FCS) is a powerful tool in the time-resolved analysis of nonreacting or reacting molecules in solution, based on fluorescence intensity fluctuations. However, conventional (second-order) FCS alone is insufficient to measure all parameters needed to describe a reaction or mixture, including concentrations, fluorescence brightnesses, and forward and reverse rate constants. For this purpose, correlations of higher powers of fluorescence intensity fluctuations can be calculated to yield additional information from the single-photon data stream collected in an FCS experiment. To describe systems of diffusing and reacting molecules, considering cumulants of fluorescence intensity results in simple expressions in which the reaction and diffusion parts factorize. The computation of higher-order correlations in experiments is hindered by shot-noise and common detector artifacts, the effects of which become worse with increasing order. In this article, we introduce a technique to calculate artifact-free higher-order correlation functions with improved time resolution, and without any need for modeling and calibration of detector artifacts. The technique is formulated for general multidetector experiments and verified in both two-detector and single-detector configurations. Good signal-to-noise ratio is achieved down to 1 μs in correlation curves up to order (2, 2). This capability makes possible a variety of new measurements including multicomponent analysis and fast reaction kinetics, as demonstrated in a companion article (10.1021/acs.jpcb.7b00408). [ABSTRACT FROM AUTHOR]

Ultrafast photochemistry of pharaonis halorhodopsin (p-HR) in the intact membrane of Natronomonas pharaonis has been studied by photoselective femtosecond pump-hyperspectral probe spectroscopy with high time resolution. Two variants of this sample were studied, one with wild-type retinal prosthetic groups and another after shifting the retinal absorption deep into the blue range by reducing the Schiff base linkage, and the results were compared to a previous study on detergent-solubilized p-HR. This comparison shows that retinal photoisomerization dynamics is identical in the membrane and in the solubilized sample. Selective photoexcitation of bacterioruberin, which is associated with the protein in the native membrane, in wild-type and reduced samples, demonstrates conclusively that unlike the carotenoids associated with some bacterial retinal proteins the carrotenoid in p-HR does not act as a light-harvesting antenna. [ABSTRACT FROM AUTHOR]

By applying a controlled mechanical load using optical tweezers, we measured the diffusive barrier crossing in a 49 nt long P5ab RNA hairpin. We find that in the free-energy landscape the barrier height (G‡) and transition distance (x‡) are dependent on the loading rate (r) along the pulling direction, x, as predicted by Bell. The barrier shifted toward the initial state, whereas ΔG‡ reduced significantly from 50 to 5 kT, as r increased from 0 to 32 pN/s. However, the equilibrium work (ΔG) during strand separation, as estimated by Crook's fluctuation theorem, remained unchanged at different rates. Previously, helix formation and denaturation have been described as two-state (F ↔ U) transitions for P5ab. Herein, we report three intermediate states I1, I, and I2 located at 4, 11, and 16 nm respectively, from the folded conformation. The intermediates were observed only when the hairpin was subjected to an optimal r, 7.6 pN/s. The results indicate that the complementary strands in P5ab can zip and unzip through complex routes, whereby mismatches act as checkpoints and often impose barriers. The study highlights the significance of loading rates in force-spectroscopy experiments that are increasingly being used to measure the folding properties of biomolecules. [ABSTRACT FROM AUTHOR]

For biomembranes, which are composed of neutral as well as charged lipids, the local pH at lipid/water interfaces is extremely important in their structural formation and functional activity. In our previous study of the charged lipid/water interfaces, we found that the local pH at the interface is governed by the positive or negative sign of the charge of the lipid: i.e., the local pH is dictated by the repulsive or attractive electrostatic interaction between the charged lipid headgroup and the proton. Because of the lack of net charge in the headgroup of the neutral lipid, the factor determining the local pH at neutral lipid/water interfaces is less straightforward, and therefore it is more challenging to predict the local pH. Here we apply heterodyne-detected electronic sum frequency generation (HD-ESFG) spectroscopy to nonionic and zwitterionic lipids to investigate the local pH at the neutral lipid/water interfaces. The obtained results indicate that the local pH at the nonionic lipid/water interface is higher than in bulk water by 0.8 whereas the local pH at the zwitterionic lipid/water interface is lower by 0.6, although the latter is subject to significant uncertainty. The present HD-ESFG study on neutral lipids, combined with the previous study on charged lipids, presents a unified view to consider the local pH at biomembranes based on the balance between the electrostatic interaction and the hydrophobicity provided by the lipid.

Elucidating the origin of large Stokes shift (LSS) in certain fluorescent proteins absorbing in blue/blue-green and emitting in red/far-red has been quite illusive. Using a combination of spectroscopic measurements, corroborated by theoretical calculations, the presence of four distinct forms of the chromophore of the red fluorescent protein mKeima is confirmed, two of which are found to be emissive: a feeble bluish-green fluorescence (∼520 nm), which is enhanced appreciably in a low pH or deuterated medium but significantly at cryogenic temperatures, and a strong emission in red (∼615 nm). Using femtosecond transient absorption spectroscopy, the trans-protonated form is found to isomerize within hundreds of femtoseconds to the cis-protonated form, which further yields the cis-deprotonated form within picoseconds followed by structural reorganization of the local environment of the chromophore. Thus, the mechanism of LSS is substantiated to proceed via stepwise excited-state isomerization followed by proton transfer involving three isomers, leaving the fourth one (trans-deprotonated) as a bystander. The exquisite pH sensitivity of the dual emission is further exploited in fluorescence microscopy.

Lead is a toxic metal harmful to human beings because of its long history and wide use in human society. The interaction of lead with proteins is one of the most common ways it exerts toxicity. Due to its thiophilic property, lead targets thiol-rich proteins with high affinity and forms stable Pb-S bonds, which may replace the originally bound metal ion and incapacitate the protein/enzyme. Thus, the knowledge of the Pb-S bonds in proteins is important. To study Pb-S bonds, we chose a de novo designed protein α 3 DIV, able to bind Pb(II) via its three cysteines, as the model protein. Using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), we proved the formation of a triangular pyramidal PbS 3 site in α 3 DIV by detecting specific Pb-S bond rupture signals, including the previously undetected Pb-S(Cys67) bond. Moreover, the pH-dependent weakening of Pb-S bond strength was revealed and quantified, leading to the dissociation of the PbS 3 site at pH 4.5.

The polymer α relaxation process for net-PEA gels swollen with nonpolar p-xylene is studied by employing dielectric relaxation spectroscopy. The results present the in situ monitoring of the dielectric behavior of α relaxation process under p-xylene cold crystallization, isothermal crystallization as well as crystallization from quenching. For the partially crystallized systems, the results exhibit that the amount of p-xylene crystal phase has no remarkable effects on the time scale, being controlled mainly by the amount of the noncrystallized p-xylene (cpx= 0.11-0.15) gel phase. Surprisingly, the stretching exponent βKWW obtains higher values in the isothermal crystallization process as the p-xylene crystallization is in progress and the reorganization of p-xylene through diffusion to crystallites approaches thermodynamic equilibrium. This directly indicates that any α process broadening is originated not solely from the amount of p-xylene crystallites and the induced heterogeneities, but from the presence of remarkable concentration fluctuations close to respective effective glass transition temperature, enhanced for higher solvent contents as well. Finally, the results suggest that the existence of p-xylene crystallites decrease significantly the dielectric strength of α process. The effective medium theory is applied to check whether this recorded reduction originates from the induced spatial heterogeneities (p-xylene crystallites) or from the immobilization in parts of polymer configurations. [ABSTRACT FROM AUTHOR]

Most cyanobacteria utilize a water-soluble Orange Carotenoid Protein (OCP) to protect their light-harvesting complexes from photodamage. The Fluorescence Recovery Protein (FRP) is used to restore photosynthetic activity by inactivating OCP via dynamic OCP-FRP interactions, a multistage process that remains underexplored. In this work, applying time-resolved spectroscopy, we demonstrate that the interaction of FRP with the photoactivated OCP begins early in the photocycle. Interacting with the compact OCP state, FRP completely prevents the possibility of OCP domain separation and formation of the signaling state capable of interacting with the antenna. The structural element that prevents FRP binding and formation of the complex is the short α-helix at the beginning of the N-terminal domain of OCP, which masks the primary site in the C-terminal domain of OCP. We determined the rate of opening of this site and show that it remains exposed long after the relaxation of the red OCP states. Observations of the OCP transitions on the ms time scale revealed that the relaxation of the orange photocycle intermediates is accompanied by an increase in the interaction of the carotenoid keto group with the hydrogen bond donor tyrosine-201. Our data refine the current model of photoinduced OCP transitions and the interaction of its intermediates with FRP.

Much of the thermodynamic parameter values that support life are set by the properties of proteins. While the denaturing effects of pressure and temperature on proteins are well documented, their precise structural nature is rarely revealed. This work investigates the destabilization of multiple Ca 2+ binding sites in the cyclic LH1 light-harvesting membrane chromoprotein complexes from two Ca-containing sulfur purple bacteria by hydrostatic high-pressure perturbation spectroscopy. The native (Ca-saturated) and denatured (Ca-depleted) phases of these complexes are well distinguishable by much-shifted bacteriochlorophyll a exciton absorption bands serving as innate optical probes in this study. The pressure-induced denaturation of the complexes related to the failure of the protein Ca-binding pockets and the concomitant breakage of hydrogen bonds between the pigment chromophores and protein environment were found cooperative, involving all or most of the Ca 2+ binding sites, but irreversible. The strong hysteresis observed in the spectral and kinetic characteristics of phase transitions along the compression and decompression pathways implies asymmetry in the relevant free energy landscapes and activation free energy distributions. A phase transition pressure equal to about 1.9 kbar was evaluated for the complexes from Thiorhodovibri o strain 970 from the pressure dependence of biphasic kinetics observed in the minutes to 100 h time range.

Purple phototrophic bacteria are ancient anoxygenic phototrophs and attractive research tools because they capture light energy in the near-infrared (NIR) region of the spectrum and transform it into chemical energy by way of uphill energy transfers. The heart of this reaction occurs in light-harvesting 1-reaction center (LH1-RC) complexes, which are the simplest model systems for understanding basic photosynthetic reactions within type-II (quinone-utilizing) reaction centers. In this Perspective, we highlight structure-function relationships concerning unresolved fundamental processes in purple bacterial photosynthesis, including the diversified light-harvesting capacity of LH1-associated BChl molecules, energies necessary for photoelectric conversion in the RC special pairs, and quinone transport mechanisms. Based on recent progress in the spectroscopic and structural analysis of LH1-RC complexes from a variety of purple phototrophs, we discuss several key factors for understanding how purple bacteria resource light energy in the inherently energy-poor NIR region of the electromagnetic spectrum.

While the static structure of aqueous electrolytes has been studied for decades, their dynamic microscopic structure remains unresolved yet critical in many areas. We report a comparative study of dc and ac (1 Hz to 20 GHz) conductivity data of weak and strong electrolytes, highlighting previously missing differences and similarities. Based on these results, we introduce into consideration the intrinsic short-lived ions of water, namely, excess protons (H 3 O + ) and proton holes (OH - ). We show that the model accounting for the neutralization of these ions by the species of electrolyte explains the conductivity of aqueous solutions in the concentration range 10 -7 -10 M. Based on independent experimental data, we hypothesize that the aggregation of the species in weak electrolytes may determine the main difference between the conductivity of weak and strong electrolytes. Our results push forward the understanding of the dynamic structure of aqueous electrolyte solutions and are important to nanofluidic, biological, and electrochemical systems.

The effect of spermidine on the kinetics, conformation, and dynamics of native trypsin was studied by steady-state thermal stability, intrinsic fluorescence, circular dichroism (CD), ultraviolet-visible (UV-vis) spectroscopy, and kinetic techniques, as well as molecular docking, at the temperatures of 298 and 308 K. The Stern-Volmer quenching constants (Ksv) for the trypsin-spermidine complex were obtained at two temperatures, revealing that spermidine quenched the intensity of trypsin through the static mode of the quenching mechanism. The corresponding thermodynamic parameters, Gibbs free-energy, enthalpy, and entropy changes, showed that the binding process was spontaneous. These values and the molecular docking technique revealed that the hydrogen bonding and van der Waals forces played a major role in stabilizing the complex. CD, absorption, and fluorescence results also indicated that spermidine binding had a partial effect on trypsin structure. Spermidine could also influence the activity of trypsin. Upon spermidine binding, the Vmax value of the enzyme was increased and the kcat/Km values were enhanced slightly. The Tm of the trypsin-spermidine complex was enhanced probably due to the higher H-bond formation and lower surface hydrophobicity after spermidine modification, as confirmed by UV-vis spectroscopy and fluorescence spectra. UV absorption and CD studies also indicated that the binding of spermidine to trypsin had induced microenvironmental changes around the enzyme, leading to changes in its secondary structure. [ABSTRACT FROM AUTHOR]

Bacterial spores are rich in calcium dipicolinate (CaDPA). The role of this compound in the high UV resistance of spore DNA and their unique DNA photochemistry is not yet clarified. Here, the photophysical properties of CaDPA dissolved in water are studied by means of steady-state and time-resolved spectroscopy as well as quantum chemistry. Upon 255 nm excitation, a fluorescence emission with a yield of 1.7 × 10-5 is detected. This low yield is in line with a measured fluorescence lifetime of 110 fs. Transient absorption experiments point to further transitions with time constants of 92 ps and 6.8 μs. The microsecond time constant is assigned to the decay of a triplet state. The yield of this state is close to unity. With the aid of quantum chemistry (TD-DFT, DFT-MRCI), the following transitions are identified. The primarily excited 1ππ* state depletes within 110 fs. The depletion results in the population of an energetically close lying 1nπ* state. An El-Sayed allowed intersystem crossing process with a time constant of 92 ps ensues. Implications of these findings on the interaction between photoexcited CaDPA and spore DNA are discussed. [ABSTRACT FROM AUTHOR]

When a finite system is at equilibrium with a heat bath, the equilibrium temperature is dictated by the heat bath and not by the intrinsic thermostatistics of the finite system. If not sufficiently large, it may be necessary for the finite system to change its thermostatistics in order to be at equilibrium with the heat bath. We account for this process by invoking Landsberg's notion of temperature-dependent energy levels. We establish that the mismatch between the intrinsic temperature of the excited finite system and that of the heat bath drives a spectrum perturbation which enables thermal equilibrium. We show that the temperature-induced spectrum perturbation is equivalent to Hill's purely thermodynamic subdivision potential. The difference between intrinsic and equilibrium temperature provides us with a measure for how large a system can be before it no longer needs to be regarded as small. The theoretical framework proposed in this paper identifies the role of temperature in a bottom-up thermostatistical description of finite systems. [ABSTRACT FROM AUTHOR]

Fireflies generate flashes of visible light via luciferase-catalyzed chemiexcitation of the substrate (luciferin) to the first excited state of the emitter (oxyluciferin). Microenvironment effects are often invoked to explain the effects of the luciferase active pocket on the emission; however, the exceedingly complex spectrochemistry and synthetic burdens have precluded elucidation of the nature of these interactions. To decipher the effects of microenvironment on the light emission, here the hydrophobic interior of cucurbit[7]uril (CB7) is used to mimic the nonpolar active pocket of luciferase. The hydrophobic interior of CB7 induces shifts of the ground-state pKas by 1.9-2.5 units to higher values. Upon sequestration, the emission maxima of neutral firefly oxyluciferin and its conjugate monodeprotonated base are blue-shifted by 40 and 39 nm, respectively, resulting in visual color changes of the emitted light. [ABSTRACT FROM AUTHOR]

NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 ¹H and 123 13C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the ¹H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites. [ABSTRACT FROM AUTHOR]

The unique structure of cholesterol and its role in modulating lipid translocation (flip-flop) were examined using sum-frequency vibrational spectroscopy (SFVS). Two structural analogues of cholesterol?cholestanol and cholestene--were examined to explore the influence of ring rigidity and amphiphilicity on controlling distearoylphosphocholine (DSPC) flip-flop. Kinetic rates for DSPC flip-flop were determined as a function of sterol concentration and temperature. All three sterols increased the rate of DSPC flip-flop in a concentration-dependent manner following the order cholestene > cholestanol > cholesterol. Rates of DSPC flip-flop were used to calculate the thermodynamic activation free energy barrier (ΔG‡) in the presence of cholesterol, cholestanol, and cholestene. The acyl chain gauche content of DSPC, mean lipid area, and membrane compressibility were correlated to observed trends in ΔG‡. ΔG‡ for DSPC flip-flop showed a strong positive correlation with the molar compression modulus (K*) of the membrane, influenced by the type and concentration of the sterol added. Interestingly, cholesterol is distinctive in maintaining invariant membrane compressibility over the range of 2-10 mol %. The results in this study demonstrate that the compression modulus of a membrane plays a significant role in moderating ΔG‡ and the kinetics of native, protein-free, lipid translocation in membranes. [ABSTRACT FROM AUTHOR]

THz absorption spectra of two polymorphs of diflunisal, form I and form III, exhibit distinct features due to the influence of packing conformations on the frequency distributions and IR activities of gamma point phonon modes within the 100 cm-1 region. In order to understand the origins of these THz modes, we perform a detailed mode analysis. The result shows that although the spectral features are different, these low-frequency phonon modes of the two molecular polymorphs have similar vibrational characteristics in terms of harmonic couplings of intermolecular and intramolecular vibrations. [ABSTRACT FROM AUTHOR]

Reliable determination of the spectral features and their phases in sum-frequency generation vibrational spectroscopy (SFG-VS) for surfaces with closely overlapping peaks has been a standing issue. Here we present two approaches toward resolving such issue. The first utilizes the high-resolution and accurate line shape from the recently developed subwavenumber high-resolution broadband SFG-VS (HR-BB-SFG-VS), from which the detail spectral parameters, including relative spectral phases, of overlapping peaks can be determined through reliable spectral fitting. These results are further validated by using the second method that utilizes the azimuthal angle phase dependence of the z-cut α-quartz crystal, a common phase standard, through the spectral interference between the SFG fields of the quartz surface, as the internal phase reference, and the adsorbed molecular layer. Even though this approach is limited to molecular layers that can be transferred or deposited onto the quartz surface, it is simple and straightforward, as it requires only an internal phase standard with a single measurement that is free of phase drifts. More importantly, it provides unambiguous SFG spectral phase information on such surfaces. Using this method, the absolute phase of the molecular susceptibility tensors of the CH3, CH2, and chiral C-H groups in different Langmuir-Blodgett (LB) molecular monolayers and drop-cast peptide films are determined. These two approaches are fully consistent with and complement to each other, making both easily applicable tools in SFG-VS studies. More importantly, because the HR-BB-SFG-VS technique can be easily applied to various surfaces and interfaces, such validation of the spectral and phase information from HR-BB-SFG-VS measurement demonstrates it as one of the most promising tools for interrogating the detailed structure and interactions of complex molecular interfaces. [ABSTRACT FROM AUTHOR]

Spores are uniquely stable cell types that are produced when bacteria encounter nutrient limitations. Spores are encased in a complex multilayered coat, which provides protection against environmental insults. The spore coat of Bacillus subtilis is composed of around 70 individual proteins that are organized into four distinct layers. Here we explored how morphogenetic protein CotE guides formation of the outermost layer of the coat, the crust, around the forespore by focusing on three proteins: CotE, CotY, and CotX. Single molecule force spectroscopy (SMFS) was used to investigate the interactions among CotE, CotY, and CotX at the single-molecule level. Direct interactions among these three proteins were observed. Additionally, the dissociation kinetics was also studied by measuring the unbinding forces of the complexes at different loading rates. A series of kinetic data of these complexes were acquired. It was found that the interaction of CotE and CotY was stronger than that of CotE and CotX. [ABSTRACT FROM AUTHOR]

Alkylacetamide-based model peptides display an intense Debye-type dielectric relaxation. In order to explore the extent to which this feature has to be regarded analogous to that in other supramolecular liquids, notably the monohydroxy alcohols, we applied broadband dielectric, time-dependent solvation, and near-infrared spectroscopies as well as shear rheology and various nuclear magnetic resonance techniques to mixtures of N-methylacetamide (NMA) or N-ethylacetamide (NEA) with N-methylformamide. Compared in the modulus format, dielectric relaxation, solvation dynamics, and mechanical response indicate a common global and local dynamics. The present spin-relaxation measurements reflect motional processes which are significantly faster than the dominant Debye dielectric response, and a similar conclusion is drawn from measurements of the shear viscosity. The NH overtone stretching vibrations reveal a temperature-dependent hydrogen-bond equilibrium that changes its characteristics near temperatures of 325 K. Finally, dielectric low-temperature data recorded for (NEA)0.4(NMF)0.6 mixed with 2-picoline indicate the existence of a critical concentration akin to the situation in various monohydroxy alcohol mixtures. [ABSTRACT FROM AUTHOR]

Recently, it was shown that the spectralgraph theory is exceptionallyuseful for understanding not only morphological structural differencesin ion aggregates but also similarities between an ion network anda water H-bonding network in highly concentrated salt solutions. Here,we present spectral graph analysis results on osmolyte aggregatesand water H-bonding network structures in aqueous renal osmolyte solutions.The quantitative analyses of the adjacency matrices that are graph-theoreticalrepresentations of aggregates of osmolyte molecules and water H-bondstructures provide the ensemble average eigenvalue spectra and degreedistribution. We show that urea molecules form quite different morphologicalstructures compared to other protecting renal osmolyte molecules inwater, particularly sorbitol and trimethylglycine, which are well-knownprotecting osmolytes, and at high concentrations exhibit a strongpropensity to form morphological structures that are graph-theoreticallysimilar to that of the water H-bond network. Conversely, urea molecules,even at similarly high concentrations, form separated clusters insteadof extended osmolyte–osmolyte networks. This difference inmorphological structure of osmolyte–osmolyte aggregates betweenprotecting and destabilizing osmolytes is considered to be an importantobservation that led us to propose a hypothesis on the osmolyte aggregategrowth mechanism via either osmolyte network formation or segregatedosmolyte cluster formation. We anticipate that the present spectralgraph analyses of osmolyte aggregate structures and their interplaywith the water H-bond network structure in highly concentrated renalosmolyte solutions could provide important information on the osmolyteeffects of not only water structures but also protein stability inbiologically relevant osmolyte solutions. [ABSTRACT FROM AUTHOR]

Ultrafastspectroscopy on solutes, whose dynamics is very sensitiveto the friction in its local environment, has strong potential toreport on the microenvironment existing in complex fluids such asionic liquids. In this work, the torsional relaxation dynamics ofThioflavin-T (ThT), an ultrafast molecular rotor, is investigatedin two fluoroalkylphosphate ([FAP])-based ionic liquids, namely, 1-ethyl-3-methylimidazoliumtris(pentafluoroethyl)trifluorophosphate ([EMIM][FAP]) and 1-(2-hydroxyethyl)-3-methylimidazoliumtris(pentafluoroethyl)trifluorophosphate ([OHEMIM][FAP]), using ultrafastfluorescence up-conversion spectroscopy. The emission quantum yieldand the excited-state fluorescence lifetime measurement suggest thatthe torsional relaxation of Thioflavin-T, in this class of ionic liquids,is guided by the viscosity of the medium. The temporal profile ofthe dynamic Stokes’ shift of ThT, measured from time-resolvedemission spectrum (TRES), displays a multiexponential behavior inboth ionic liquids. The long time dynamics of the Stokes’ shiftis reasonably slower for the hydroxyethyl derivative as compared tothe ethyl derivative, which is in accordance with their measured shearviscosity. However, the short time dynamics of Stokes’ shiftis very similar in both the ionic liquids, and seems to be independentof the measured shear viscosity of the ionic liquid. We rationalizethese observations in terms of different locations of ThT in theseionic liquids. These results suggest that despite having a higherbulk viscosity in the ionic liquid, they can provide unique microenvironmentin their complex structure, where the reaction can be faster thanexpected from their measured shear viscosity. [ABSTRACT FROM AUTHOR]

Interaction of small molecules with collagen has far reaching consequences in biological and industrial processes. The interaction between collagen and selected polyphenols, viz., gallic acid (GA), pyrogallol (PG), catechin (CA), and epigallocatechin gallate (EGCG), has been investigated by various solution NMR measurements, viz., 1H and 13C chemical shifts (δHand δC), 1H nonselective spin–lattice relaxation times (T1NS) and selective spin–lattice relaxation times (T1SEL), as well as spin–spin relaxation times (T2). Furthermore, we have employed saturation transfer difference (STD) NMR method to monitor the site of GA, CA, PG, and EGCG which are in close proximity to collagen. It is found that −COOH group of GA provides an important contribution for the interaction of GA with collagen, as evidenced from 13C analysis, while PG, which is devoid of −COOH group in comparison to GA, does not show any significant interaction with collagen. STDNMR data indicates that the resonances of A-ring (H2′, H5′and H6′) and C-ring (H6 and H8) protons of CA, and A-ring (H2′and H6′), C-ring (H6 and H8), and D-ring (H2″and H6″) protons of EGCG persist in the spectra, demonstrating that these protons are in spatial proximity to collagen, which is further validated by independent proton spin-relaxation measurement and analysis. The selective 1H T1measurements of polyphenols in the presence of protein at various concentrations have enabled us to determine their binding affinities with collagen. EGCG exhibits high binding affinity with collagen followed by CA, GA, and PG. Further, NMR results propose that presence of gallic acid moiety in a small molecule increases its affinity with collagen. Our experimental findings provide molecular insights on the binding of collagen and plant polyphenols. [ABSTRACT FROM AUTHOR]

Single-molecule spectroscopy at lowtemperature was used to studythe spectral properties, heterogeneities, and spectral dynamics ofthe chlorophyll a(Chl a) moleculesresponsible for the fluorescence emission of photosystem I monomers(PS I-M) from the cyanobacterium Thermosynechococcuselongatus. The fluorescence spectra of single PS I-Mare dominated by several red-shifted chlorophyll amolecules named C708 and C719. The emission spectra show broad spectraldistributions and several zero-phonon lines (ZPLs). Compared withthe spectra of the single PS I trimers, some contributions aremissing due to the lower number of C719 Chl’s in monomers.Polarization-dependent measurements show an almost perpendicular orientationbetween the emitters corresponding to C708 and C719. These contributionscan be assigned to chlorophyll dimers B18B19, B31B32, and B32B33. [ABSTRACT FROM AUTHOR]

Thecatalytic site of [FeFe]-hydrogenase, the “H-cluster”,composed of a [4Fe–4S] unit connected by a cysteinyl residueto a [2Fe] center coordinated by three CO, two CN–, and a bridging dithiolate, is assembled in a complex maturationpathway, at present not fully characterized, involving three conservedproteins, HydG, HydE, and HydF. HydF is a complex enzyme, which isthought to act as a scaffold and carrier for the [2Fe] subunit ofthe H-cluster. This maturase protein contains itself a [4Fe–4S]cluster binding site, with three conserved cysteine residues and anoncysteinyl fourth ligand. In this work, we have exploited 3p-ESEEMand HYSCORE spectroscopies to get insight into the structure and thechemical environment of the [4Fe–4S] cluster of HydF from thehyperthermophilic organism Thermotoga neapolitana. The nature of the fourth ligand and the solvent accessibility ofthe active site comprising the [4Fe–4S] cluster are discussedon the basis of the spectroscopic results obtained upon H/D exchange.We propose that the noncysteinyl ligated Fe atom of the [4Fe–4S]cluster is the site where the [2Fe] subcluster precursor is anchoredand finally processed to be delivered to the hydrogenase (HydA). [ABSTRACT FROM AUTHOR]

A new experimental result from dielectric spectroscopy of poly(N-isopropylacrylamide)/poly(acrylic acid) semi-interpenetrating polymer network (PNIPAM/PAA SIPN) microgel, which undergoes significant volume phase transition, is reported. Two significant dielectric relaxations were observed around 0.1–0.5 MHz and 1–5 MHz, respectively. The high-frequency relaxation is attributed to the migration of counterions tangentially and radially along the domain formed by linear PAA chains (counterion polarization). The temperature dependence of the domain size obtained from this relaxation shows that the SIPN microgel with higher content of PAA has better thermal response and swelling property. The low-frequency relaxation shows two separate mechanisms below and above the volume phase transition temperature (VPTT), which are dominated by different relaxation processes, respectively: micro-Brownian movement of solvated side groups of PNIPAM dominates when T < VPTT, while the interfacial polarization does when T > VPTT. A dielectric model was proposed to describe the collapsed microspheres suspension, from which the electrical parameters of microgel were calculated. The permittivity of microgel shows that a special ordered arrangement of water molecules is formed in microgel with less PAA. Thermodynamic parameters obtained from Eyring equation reveal that the difference in PAA content has a great influence on the thermodynamics of the phase transition process. Besides, it was found that the VPTT of the SIPN microgel was significantly increased compared with pure PNIPAM hydrogel microspheres. The essence of anomalous VPTT revealed by relaxation mechanism is the difference in composition content leading to different hydrophilic/hydrophobic and electrostatic interaction. Determining the reason for anomalous VPTT is of instructive significance to understand the volume phase transition of complex polymer materials. [ABSTRACT FROM AUTHOR]

Four isomeric sugar methylglycosides (α- and β-d-gluco- and galactopyranosides) were evaluated as rubidium cation coordination adducts in the gas phase using variable-wavelength multiple-photon dissociation in the range from 2750 to 3750 cm–1. The adducts dissociated following photon absorption to yield neutral sugars and the rubidium cation, resulting in infrared “action” spectra. Well-resolved hydroxyl stretching bands clearly differentiate stereoisomers that vary solely in their asymmetry at single carbons. Density functional theory calculations of the lowest-energy gas-phase complexes indicate that rubidium coordinates with lone pairs of oxygen atoms as either bi- or tridentate complexes and that more than one positional coordination isomer could adequately account for most of the O–H stretch frequencies observed for each methylglycoside. [ABSTRACT FROM AUTHOR]

Immobilization of Cytochrome c oxidase(CcO) on electrodes makesvoltage-driven reduction of oxygen to water possible. Efficient catalyticturnover in CcO/electrode systems is, however, often observed at largeoverpotentials that cannot be rationalized by the redox propertiesof the enzyme itself. To understand the structural basis for thisobservation, CcO was electrostatically adsorbed on amino-functionalizedAg electrodes, and the redox transitions of heme aand a3were monitored via surface enhancedresonance Raman spectroscopy (SERRS) as a function of applied potential.Under completely anaerobic conditions, the reduction of heme a3could be seen at potentials close to thosemeasured in solution indicating an intact catalytic center. However,in the immobilized state, a new non-native heme species was observedthat exhibited a redox potential much more negative than measuredfor the native hemes. Analysis of the high and low frequency SERRspectra indicated that this new species is formed from heme aupon axial loss of one histidine ligand. It is concludedthat the formation of the non-native heme aspeciesalters the potential-dependent electron supply to the catalytic reactionand, thus, can have a impact on the applicability of this enzyme inbiofuel cells. [ABSTRACT FROM AUTHOR]

The main barrier to permeabilityin human skin resides in the stratumcorneum (SC), a layered structure consisting of anucleated, flattenedcells (corneocytes) embedded in a heterogeneous lamellar lipid matrix.While lipid structures and packing propensities in the SC and in SCmodels have been extensively investigated, only limited data are availableconcerning the kinetics and mechanism of formation of lamellar phasesand particular lipid packing motifs. In our prior investigation, kineticIR spectroscopy measurements probed the temporal sequence of phaseseparation leading to ordered structures in a three component SC modelof equimolar structurally heterogeneous ceramide[NS], chain perdeuteratedstearic acid, and cholesterol. In the current work, the phase separationkinetic effects of specific fatty acid chain lengths with a syntheticstructurally homogeneous ceramide[NS] in similar ternary mixturesare examined. These are compared with a mixture containing ceramide[NS]with an unsaturated acid chain. The kinetic events are sensitive tothe difference in chain lengths between the ceramide acid chain andthe fatty acid as well as to the presence of unsaturation in the former.The observed kinetic behaviors span a wide range of phase separationtimes, ranging from the formation of a solid solution stable for atleast 200 h, to a system in which an orthorhombic fatty acid structureis essentially completely formed within the time resolution of theexperiment (15 min). The data seem to offer some features of a spinodalphase separation at relatively short times. Overall the approach offersa possible means for addressing several unanswered questions pertinentto skin pharmacology, such as the roles of a wide variety of ceramideand fatty acid species and the design of therapeutic interventionsfor repair of pathological conditions of the SC. [ABSTRACT FROM AUTHOR]

Saline aqueous solutions at elevatedpressures and temperaturesplay an important role in processes such as supercritical water oxidation(SCWO) and supercritical water gasification (SCWG), as well as innatural geochemical processes in Earth and planetary interiors. Somesolutions exhibit a negative temperature coefficient of solubilityat high temperatures, thereby leading to salt precipitation with increasingtemperature. Using modulated FT-IR Raman spectroscopy and classicalmolecular dynamics simulations (MD), we studied the solute speciationin solutions of 10 wt % Na2SO4, at conditionsclose to the saturation limit. Our experiments reveal that ion pairingand cluster formation are favored as solid saturation is approached,and ionic clusters form prior to the precipitation of solid sulfate.The proportion of such clusters increases as the phase boundary isapproached either by decreasing pressure or by increasing temperaturein the vicinity of the three-phase (vapor–liquid–solid)curve. [ABSTRACT FROM AUTHOR]

The human enzyme dihydroorotate dehydrogenase(HsDHODH) has been studied for being a target fordevelopment of newantineoplasic and antiproliferative drugs. The synthetic peptide N-t(DH)represents the N-terminal microdomain of this enzyme, responsiblefor anchoring it to the inner mitochondrial membrane. Also, it isknown to harbor quinones that are essential for enzyme catalysis.Here we report structural features of the peptide/membrane interactionsobtained by using CD and DEER spectroscopic techniques, both in micellesand in lipid vesicles. The data revealed different peptide conformationalstates in micelles and liposomes, which could suggest that this microdomainacts in specific regions or areas of the mitochondria, which can berelated with the control of the quinone access to the HsDHODH active site. This is the first study to report on conformationalchanges of the HsDHODH N-terminal microdomain througha combination of CD and DEER spectroscopic techniques. [ABSTRACT FROM AUTHOR]

In large light harvesting systems,not all pigments are coupledstrongly. This is evidenced by the formation of delocalized statesin certain domains of strongly coupled pigments. The threshold valuefor assigning pigments to domains is usually defined, and the pigmentpairs in which the electronic coupling is greater than this valueare included in the same domain to describe the dynamic localizationeffect implicitly. However, domain assignment by a single thresholdvalue may make it difficult to include the possible localization ofexciton states by temperature and the difference in the electronicexcitation energy between pigments. In this study, we use the variationalpolaron approach for domain assignment to include such possible localization.To demonstrate the validity of domain assignment by the variationalapproach, we applied it to pigments in photosystem II (PSII) and comparedthe domain model constructed by the single threshold value. We showedthat domain assignment by the variational approach could be used todetermine the valid domain model in PSII without using the empiricalthreshold value at least at 77 K. [ABSTRACT FROM AUTHOR]

Weare reporting development and initial applications of the light-inducedand thermally induced spectral diffusion modeling software, coveringnonphotochemical spectral hole burning (NPHB), hole recovery, andsingle-molecule spectroscopy and involving random generation of themultiwell protein energy landscapes. The model includes tunnelingand activated barrier-hopping in both ground and excited states ofa protein–chromophore system. Evolution of such a system ispredicted by solving the system of rate equations. Using the barrierparameters from the range typical for the energy landscapes of thepigment–protein complexes involved in photosynthesis, we (a)show that realistic cooling of the sample must result in proteinsquite far from thermodynamic equilibrium, (b) demonstrate hole evolutionin the cases of burning, fixed-temperature recovery and thermocyclingthat mostly agrees with the experiment and modeling based on the NPHBmaster equation, and (c) explore the effects of different proteinenergy landscapes on the antihole shape. Introducing the multiwellenergy landscapes and starting the hole burning experiments in realisticnonequilibrium conditions are not sufficient to explain all experimentalobservations even qualitatively. Therefore, for instance, one is requiredto invoke the modified NPHB mechanism where a complex interplay ofseveral small conformational changes is poising the energy landscapeof the pigment–protein system for downhill tunneling. [ABSTRACT FROM AUTHOR]

Wereport mid-infrared spectra and potential energy surfaces offour anionic, 2′-deoxynucleotide-5′-monophosphates (dNMPs)and the ionic DNA pairs [dGMP-dCMP–H]1–,[dAMP-dTMP–H]1–with a total charge of thecomplex equal to −1. We recorded IR action spectra by resonantIR multiple-photon dissociation (IRMPD) using the FELIX free electronlaser. The potential energy surface study employed an on-the-fly moleculardynamics quenching method (MD/Q), using a semiempirical AM1 method,followed by an optimization of the most stable structures using densityfunctional theory. By employing infrared multiple-photon dissociation(IRMPD) spectroscopy in combination with high-level computationalmethods, we aim at a better understanding of the hydrogen bondingcompetition between the phosphate moieties and the nucleobases. Wefind that, unlike in multimer double stranded DNA structures, thehydrogen bonds in these isolated nucleotide pairs are predominantlyformed between the phosphate groups. This intermolecular interactionappears to exceed the stabilization energy resulting from base pairingand directs the overall cluster structure and alignment. [ABSTRACT FROM AUTHOR]