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Motivation: Accurately identifying ligands plays a crucial role in the process of structure-guided drug design. Based on density maps from X-ray diffraction or cryogenic-sample electron microscopy (cryoEM), scientists verify whether small-molecule ligands bind to active sites of interest. However, the interpretation of density maps is challenging, and cognitive bias can sometimes mislead investigators into modeling fictitious compounds. Ligand identification can be aided by automatic methods, but existing approaches are available only for X-ray diffraction and are based on iterative fitting or feature-engineered machine learning rather than end-to-end deep learning., Results: Here, we propose to identify ligands using a deep learning approach that treats density maps as 3D point clouds. We show that the proposed model is on par with existing machine learning methods for X-ray crystallography while also being applicable to cryoEM density maps. Our study demonstrates that electron density map fragments can be used to train models that can be applied to cryoEM structures, but also highlights challenges associated with the standardization of electron microscopy maps and the quality assessment of cryoEM ligands., Competing Interests: Conflict of Interest: none declared.

Chemotherapy is the commonly used treatment for advanced lung cancer. However, it produces side effects such as the development of chemoresistance. A possible responsible mechanism may be therapy-induced senescence (TIS). TIS cells display increased senescence-associated β-galactosidase (SA-β-gal) activity and irreversible growth arrest. However, recent data suggest that TIS cells can reactivate their proliferative potential and lead to cancer recurrence. Our previous study indicated that reactivation of proliferation by TIS cells might be related with autophagy modulation. However, exact relationship between both processes required further studies. Therefore, the aim of our study was to investigate the role of autophagy in the senescence-related chemoresistance of lung cancer cells. For this purpose, human and murine lung cancer cells were treated with two commonly used chemotherapeutics: cisplatin (CIS), which forms DNA adducts or docetaxel (DOC), a microtubule poison. Hypoxia, often overlooked in experimental settings, has been implicated as a mechanism responsible for a significant change in the response to treatment. Thus, cells were cultured under normoxic (~19% O 2 ) or hypoxic (1% O 2 ) conditions. Herein, we show that hypoxia increases resistance to CIS. Lung cancer cells cultured under hypoxic conditions escaped from CIS-induced senescence, displayed reduced SA-β-gal activity and a decreased percentage of cells in the G2/M phase of the cell cycle. In turn, hypoxia increased the proliferation of lung cancer cells and the proportion of cells proceeding to the G0/G1 phase. Further molecular analyses demonstrated that hypoxia inhibited the prosenescent p53/p21 signaling pathway and induced epithelial to mesenchymal transition in CIS-treated cancer cells. In cells treated with DOC, such effects were not observed. Of importance, pharmacological autophagy inhibitor, hydroxychloroquine (HCQ) was capable of overcoming short-term CIS-induced resistance of lung cancer cells in hypoxic conditions. Altogether, our data demonstrated that hypoxia favors cancer cell escape from CIS-induced senescence, what could be overcome by inhibition of autophagy with HCQ. Therefore, we propose that HCQ might be used to interfere with the ability of senescent cancer cells to repopulate following exposure to DNA-damaging agents. This effect, however, needs to be tested in a long-term perspective for preclinical and clinical applications., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Olszewska, Borkowska, Granica, Karolczak, Zglinicki, Kieda and Was.)

The results of time-resolved fluorescence measurements of flavin mononucleotide (FMN) in rigid polyvinyl alcohol films (PVA) demonstrate that fluorescence intensity decays are strongly accelerated in the presence of fluorescent dimers and nonradiative energy transfer processes. The fluorescence decay originating both from H and J dimer states of FMN was experimentally observed for the first time. The mean fluorescence lifetimes for FMN dimers were obtained: τfl = 2.66 ns (at λ exc = 445 nm) and τfl = 2.02 (at λ exc = 487 nm) at λ obs = 600 nm and T = 253 K from H and J state of dimers, respectively. We show that inhomogeneous orientational broadening of energy levels (IOBEL) affects the shape of the fluorescence decay and leads to the dependence of the average monomer fluorescence lifetime on excitation wavelength. IOBEL affected the nonradiative energy transfer and indicated that different flavin positioning in the protein pocket could (1) change the spectroscopic properties of flavins due to the existence of "blue" and "red" fluorescence centers, and (2) diminish the effectiveness of energy transfer between FMN molecules.

Photosystem I core-light-harvesting antenna supercomplexes (PSI-LHCI) were isolated from the extremophilic red alga Cyanidioschyzon merolae and studied by three fluorescence techniques in order to characterize chlorophylls (Chls) energetically uncoupled from the PSI reaction center (RC). Such Chls are observed in virtually all optical experiments of any PSI core and PSI-LHCI supercomplex preparations across various species and may influence the operation of PSI-based solar cells and other biohybrid systems. However, the nature of the uncoupled Chls (uChls) has never been explored deeply before. In this work, the amount of uChls was controlled by stirring the solution of C. merolae PSI-LHCI supercomplex samples at elevated temperature (~303 K) and was found to increase from <2% in control samples up to 47% in solutions stirred for 3.5 h. The fluorescence spectrum of uChls was found to be blue-shifted by ~20 nm (to ~680 nm) relative to the fluorescence band from Chls that are well coupled to PSI RC. This effect indicates that mechanical stirring leads to disappearance of some red Chls (emitting at above ~700 nm) that are present in the intact LHCI antenna associated with the PSI core. Comparative diffusion studies of control and stirred samples by fluorescence correlation spectroscopy together with biochemical analysis by SDS-PAGE and BN-PAGE indicate that energetically uncoupled Lhcr subunits are likely to be still physically attached to the PSI core, albeit with altered three-dimensional organization due to the mechanical stress., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Photosynthetic PSI-LHCI complexes from an extremophilic red alga C. merolae grown under varying light regimes are characterized by decreasing size of LHCI antenna with increasing illumination intensity [1]. In this study we applied time-resolved fluorescence spectroscopy to characterize the kinetics of energy transfer processes in three types of PSI-LHCI supercomplexes isolated from the low (LL), medium (ML) and extreme high light (EHL) conditions. We show that the average rate of fluorescence decay is not correlated with the size of LHCI antenna and is twice faster in complexes isolated from ML-grown cells (~25-30 ps) than from both LL- and EHL-exposed cells (~50-55 ps). The difference is mainly due to a contribution of a long ~100-ps decay component detected only for the latter two PSI samples. We propose that the lack of this phase in ML complexes is caused by perfect coupling of this antenna to PSI core and lack of low-energy chlorophylls in LHCI. On the other hand, the presence of the slow, ~100-ps, fluorescence decay component in LL and EHL complexes may be due to the weak coupling between PSI core and LHCI antenna complex, and due to the presence of particularly low-energy or red chlorophylls in LHCI. Our study has revealed the remarkable functional flexibility of light harvesting strategies that have evolved in the extremophilic red algae in response to harsh or limiting light conditions involving accumulation of low energy chlorophylls that exert two distinct functions: as energy traps or as far-red absorbing light harvesting antenna, respectively., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Perovskite solar cells, composed of a mixture of methylammonium (MA) and formamidinium (FA) cations [in the benchmark proportions of (FAPbI 3 ) 0.85 (MAPbBr 3 ) 0.15 ] and titania as an electron-accepting material, are prepared under different conditions, with the objective of finding correlations between the solar cell performance and several important stationary and dynamical parameters of the material. The effects of humidity, oxygen, the use of anti-solvent, and the presence and quality of a mesoporous titania layer are investigated. It is found that an increase in the photocurrent corresponds to a higher content of the desired cubic perovskite phase and to increased long-wavelength absorption of the sample. On the contrary, for poorer-quality cells, additional short-wavelength bands in both absorption and emission spectra are present. Furthermore, a higher photocurrent of the cells is correlated with faster interfacial charge-transfer dynamics. For the highest photocurrent of >20 mA cm -2 , the characteristic times of about 1 μs are observed by electrochemical impedance spectroscopy, and emission half-lifetimes of about 6 ns by time-resolved fluorescence spectroscopy (upon excitation with 420 nm pulses of ≈0.5 mW power). Both first- and second-order rate constants, extracted from the emission measurements, are greater for the cells showing higher photocurrents, probably owing to a more rapid charge injection., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Standard ruthenium components of dye-sensitized solar cells (sensitizer N719) and dye-sensitized photoelectrochemical cells (sensitizer RuP and water oxidation catalyst RuOEC) are investigated in the same solar cell configuration to compare their photodynamics and charge separation efficiency. The samples are studied on time scales from femtoseconds to seconds by means of transient absorption, time-resolved emission and electrochemical impedance measurements. RuP shows significantly slower electron injection into a mesoporous titania electrode and enhanced fast (sub-ns) electron recombination with respect to those of N719. Moreover, RuOEC is found to be responsible for partial light absorption and electron injection with low efficiency. The obtained results reveal new insights into the reasons for the lower charge separation efficiency in water splitting systems with respect to that in solar cells. The important role of the initial processes occurring at the dye-titania interface within the first nanoseconds in this efficiency is emphasized.

Methylammonium lead iodide films and powdered crystals were studied by time-resolved absorption and emission spectroscopy on the time scales from femtoseconds to nanoseconds. Strikingly different transient absorption signals were observed, changing from strong long-wavelength band-edge bleach to weak signatures of band-shift, which depended on the absorber form (films or polycrystals) and preparation method (stoichiometric or non-stoichiometric). The observed differences were correlated with the variation in absorption and emission spectra, changes in photo-induced carrier lifetimes and solar cell efficiency. These differences also pointed out that similar perovskite absorbers can provide significantly different transient responses and emphasize that special care must be taken when interpolating the obtained findings to the processes occurring in the most efficient devices., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Si-Bridged chromophores have been proposed as sources for blue-green emission in several technological applications. The origin of this dual emission is to be found in an internal charge transfer reaction. The current work is an attempt to describe the details of these processes in these kinds of substances, and to design a molecular architecture to improve their performance. Nuclear motions essential for intramolecular charge transfer (ICT) can involve processes from twisted internal moieties to dielectric relaxation of the solvent. To address these issues, we studied ICT between adjacent chromophores in a molecular compound containing N-isopropylcarbazole (CBL) and 1,4-divinylbenzene (DVB) linked by a dimethylsilylene bridge. In nonpolar solvents emission arises from the local excited state (LE) of carbazole whereas in solvents of higher polarity dual emission was detected (LE + ICT). The CT character of the additional emission band was concluded from the linear dependence of the fluorescence maxima on solvent polarity. Electron transfer from CBL to DVB resulted in a large excited-state dipole moment (37.3 D) as determined from a solvatochromic plot and DFT calculations. Steady-state and picosecond time-resolved fluorescence experiments in butyronitrile (293-173 K) showed that the ICT excited state arises from the LE state of carbazole. These results were analyzed and found to be in accordance with an adiabatic version of Marcus theory including solvent relaxation.

A simple protocol to study the dynamics of charge transfer to selective contacts in perovskite solar cells, based on time-resolved laser spectroscopy studies, in which the effect of bimolecular electron-hole recombination has been eliminated, is proposed. Through the proposed procedure, the interfacial charge-transfer rate constants from methylammonium lead iodide perovskite to different contact materials can be determined. Hole transfer is faster for CuSCN (rate constant 0.20 ns(-1) ) than that for 2,2',7,7'-tetrakis-(N,N-di-4-methoxyphenylamino)-9,9'-spirobifluorene (spiro-OMeTAD; 0.06 ns(-1) ), and electron transfer is faster for mesoporous (0.11 ns(-1) ) than that for compact (0.02 ns(-1) ) TiO2 layers. Despite more rapid charge separation, the photovoltaic performance of CuSCN cells is worse than that of spiro-OMeTAD cells; this is explained by faster charge recombination in CuSCN cells, as revealed by impedance spectroscopy. The proposed direction of studies should be one of the key strategies to explore efficient hole-selective contacts as an alternative to spiro-OMeTAD., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

In contrast with findings on the wild-type Rhodobacter sphaeroides reaction center, biexponential P (+) H A (-)  → PH A charge recombination is shown to be weakly dependent on temperature between 78 and 298 K in three variants with single amino acids exchanged in the vicinity of primary electron acceptors. These mutated reaction centers have diverse overall kinetics of charge recombination, spanning an average lifetime from ~2 to ~20 ns. Despite these differences a protein relaxation model applied previously to wild-type reaction centers was successfully used to relate the observed kinetics to the temporal evolution of the free energy level of the state P (+) H A (-) relative to P (+) B A (-) . We conclude that the observed variety in the kinetics of charge recombination, together with their weak temperature dependence, is caused by a combination of factors that are each affected to a different extent by the point mutations in a particular mutant complex. These are as follows: (1) the initial free energy gap between the states P (+) B A (-) and P (+) H A (-) , (2) the intrinsic rate of P (+) B A (-)  → PB A charge recombination, and (3) the rate of protein relaxation in response to the appearance of the charge separated states. In the case of a mutant which displays rapid P (+) H A (-) recombination (ELL), most of this recombination occurs in an unrelaxed protein in which P (+) B A (-) and P (+) H A (-) are almost isoenergetic. In contrast, in a mutant in which P (+) H A (-) recombination is relatively slow (GML), most of the recombination occurs in a relaxed protein in which P (+) H A (-) is much lower in energy than P (+) H A (-) . The weak temperature dependence in the ELL reaction center and a YLH mutant was modeled in two ways: (1) by assuming that the initial P (+) B A (-) and P (+) H A (-) states in an unrelaxed protein are isoenergetic, whereas the final free energy gap between these states following the protein relaxation is large (~250 meV or more), independent of temperature and (2) by assuming that the initial and final free energy gaps between P (+) B A (-) and P (+) H A (-) are moderate and temperature dependent. In the case of the GML mutant, it was concluded that the free energy gap between P (+) B A (-) and P (+) H A (-) is large at all times.

BAG3 belongs to BAG family of molecular chaperone regulators interacting with HSP70 and anti-apoptotic protein Bcl-2. It is ubiquitously expressed with strong expression in skeletal and cardiac muscle, and is involved in a panoply of cellular processes. Mutations in BAG3 and aberrations in its expression cause fulminant myopathies, presenting with progressive limb and axial muscle weakness, and respiratory insufficiency and neuropathy. Herein, we report a sporadic case of a 15-years old girl with symptoms of myopathy, demyelinating polyneuropathy and asymptomatic long QT syndrome. Genetic testing demonstrated heterozygous mutation Pro209Leu (c.626C > T) in exon 3 of BAG3 gene causing severe myopathy and neuropathy, often associated with restrictive cardiomyopathy. We did not find a mutation in any known LQT syndrome genes. Analysis of muscle biopsy revealed profound disintegration of Z-discs with extensive accumulation of granular debris and large inclusions within fibers. We demonstrated profound alterations in BAG3 distribution as the protein localized to long filamentous structures present across the fibers that were positively stained not only for α-actinin but also for desmin and filamin indicating that those disintegrated Z-disc regions contained also other sarcomeric proteins. The mutation caused a decrease in the content of BAG3 and HSP70, and also of α-actinin desmin, filamin and fast myosin heavy chain, confirming its severe effect on the muscle fiber morphology and thus function. We provide further evidence that BAG3 is associated with Z-disc maintenance, and the Pro209Leu mutation may occur worldwide. We also provide a summary of cases associated with this mutation reported so far.

The photophysical properties of 5-deazaalloxazine and 1,3-dimethyl-5-deazalloxazine at different pH values were characterized using absorption spectra, fluorescence emission spectra, fluorescence excitation spectra, synchronous fluorescence spectra and total fluorescence spectra. Their ionised and/or neutral forms were discussed in comparison with those obtained for other derivatives of 5-deazaalloxazine and/or 5-deazaisoalloxazine. Steady-state and time-resolved techniques were used to study the protonation/deprotonation equilibria between cationic and neutral forms of both compounds and between neutral and monoanionic forms of 5-deazalloxazine, as well as between monoanionic forms of this compound and its dianion. We estimated pKa values for these equilibria both in the ground and excited states. Our steady-state and time-resolved measurements indicate that the cation of 5-deazaalloxazine in its isoalloxazinic form exhibits fluorescence that is quenched by protons in a dynamic process. Contrary to that, the cation of 1,3-dimethyl-5-deazaalloxazine has almost no fluorescence. Additionally, we found that the neutral forms of 5-deazalloxazine and 1,3-methyl-5-deazalloxazine are also quenched in acidic conditions by protons. In basic conditions, 5-deazaalloxazine forms two structurally different anions, namely the alloxazinic monoanion and the isoalloxazinic monoanion; both simultaneously dissociate into the isoalloxazinic dianion at even higher pH values. The synchronous fluorescence spectra and total fluorescence spectra demonstrated their suitability to characterize and differentiate different fluorescent forms of 5-deazalloxazine, namely: the cation, the neutral form, two monoanions, and the dianion, in a wide pH range.

The important role of unconventional myosin VI (MVI) in skeletal and cardiac muscle has been recently postulated (Karolczak et al. in Histochem Cell Biol 139:873-885, 2013). Here, we addressed for the first time a role for this unique myosin motor in myogenic cells as well as during their differentiation into myotubes. During myoblast differentiation, the isoform expression pattern of MVI and its subcellular localization underwent changes. In undifferentiated myoblasts, MVI-stained puncti were seen throughout the cytoplasm and were in close proximity to actin filaments, Golgi apparatus, vinculin-, and talin-rich focal adhesion as well as endoplasmic reticulum. Colocalization of MVI with endoplasmic reticulum was enhanced during myotube formation, and differentiation-dependent association was also seen in sarcoplasmic reticulum of neonatal rat cardiomyocytes (NRCs). Moreover, we observed enrichment of MVI in myotube regions containing acetylcholine receptor-rich clusters, suggesting its involvement in the organization of the muscle postsynaptic machinery. Overexpression of the H246R MVI mutant (associated with hypertrophic cardiomyopathy) in myoblasts and NRCs caused the formation of abnormally large intracellular vesicles. MVI knockdown caused changes in myoblast morphology and inhibition of their migration. On the subcellular level, MVI-depleted myoblasts exhibited aberrations in the organization of actin cytoskeleton and adhesive structures as well as in integrity of Golgi apparatus and endoplasmic reticulum. Also, MVI depletion or overexpression of H246R mutant caused the formation of significantly wider or aberrant myotubes, respectively, indicative of involvement of MVI in myoblast differentiation. The presented results suggest an important role for MVI in myogenic cells and possibly in myoblast differentiation.

Time-resolved fluorescence measurements on grana membranes with instrumental response function of 3 ps reveal faster excitation dynamics (120 ps) than those reported previously. A possible reason for the faster decay may be a relatively low amount of "extra" LHCII trimers per reaction center of Photosystem II. Monte Carlo modeling of excitation dynamics in C2S2M2 form of PSII-LHCII supercomplexes has been performed using a coarse grained model of this complex, constituting a large majority of proteins in grana membranes. The main factor responsible for the fast fluorescence decay reported in this work was the deep trap constituted by the primary charge separated state in the reaction center (950-1090 cm(-1)). This value is critical for a good fit, whereas typical hopping times between antenna polypeptides (from ~4.5 to ~10.5 ps) and reversible primary charge separation times (from ~4 to ~1.5 ps, respectively) are less critical. Consequently, respective mean migration times of excitation from anywhere in the PSII-LHCII supercomplexes to reaction center range from ~30 to ~80 ps. Thus 1/4-2/3 of the ~120-ps average excitation lifetime is necessary for the diffusion of excitation to reaction center, whereas the remaining time is due to the bottle-neck effect of the trap. Removal of 27% of the Lhcb6 apoprotein pool by mutagenesis of DEG5 gene caused the acceleration of the excitation decay from ~120 to ~100 ps. This effect may be due to the detachment of LHCII-M trimers from PSII-LHCII supercomplexes, accompanied by deepening of the reaction center trap., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Myosin VI (MVI) is a unique motor protein moving towards the minus end of actin filaments unlike other known myosins. Its important role has recently been postulated for striated muscle and myogenic cells. Since MVI functions through interactions of C-terminal globular tail (GT) domain with tissue specific partners, we performed a search for MVI partners in myoblasts and myotubes using affinity chromatography with GST-tagged MVI-GT domain as a bait. A kinase anchoring protein 9 (AKAP9), a regulator of PKA activity, was identified by means of mass spectrometry as a possible MVI interacting partner both in undifferentiated and differentiating myoblasts and in myotubes. Coimmunoprecipitation and proximity ligation assay confirmed that both proteins could interact. MVI and AKAP9 colocalized at Rab5 containing early endosomes. Similarly to MVI, the amount of AKAP9 decreased during myoblast differentiation. However, in MVI-depleted cells, both cAMP and PKA levels were increased and a change in the MVI motor-dependent AKAP9 distribution was observed. Moreover, we found that PKA phosphorylated MVI-GT domain, thus implying functional relevance of MVI-AKAP9 interaction. We postulate that this novel interaction linking MVI with the PKA pathway could be important for targeting AKAP9-PKA complex within cells and/or providing PKA to phosphorylate MVI tail domain.

Desmin is a muscle-specific intermediate filament protein which forms a network connecting the sarcomere, T tubules, sarcolemma, nuclear membrane, mitochondria and other organelles. Mutations in the gene coding for desmin (DES) cause skeletal myopathies often combined with cardiomyopathy, or isolated cardiomyopathies. The molecular pathomechanisms of the disease remain ambiguous. Here, we describe and comprehensively characterize two DES mutations found in Polish patients with a clinical diagnosis of desminopathy. The study group comprised 16 individuals representing three families. Two mutations were identified: a novel missense mutation (Q348P) and a small deletion of nine nucleotides (A357&#95;E359del), previously described by us in the Polish population. A common ancestry of all the families bearing the A357&#95;E359del mutation was confirmed. Both mutations were predicted to be pathogenic using a bioinformatics approach, including molecular dynamics simulations which helped to rationalize abnormal behavior at molecular level. To test the impact of the mutations on DES expression and the intracellular distribution of desmin muscle biopsies were investigated. Elevated desmin levels as well as its atypical localization in muscle fibers were observed. Additional staining for M-cadherin, α-actinin, and myosin heavy chains confirmed severe disruption of myofibrill organization. The abnormalities were more prominent in the Q348P muscle, where both small atrophic fibers as well large fibers with centrally localized nuclei were observed. We propose that the mutations affect desmin structure and cause its aberrant folding and subsequent aggregation, triggering disruption of myofibrils organization.

Myosin VI (MVI) is a unique unconventional myosin translocating, unlike other myosins, towards the minus end of actin filaments. It is involved in numerous cellular processes such as endocytosis, intracellular trafficking, cell migration, and transcription. In mammalian skeletal muscles it localizes mainly to sarcoplasmic reticulum and is also present within the muscle nuclei and at the neuromuscular junction (Karolczak et al. Histochem Cell Biol 2013; 23:219-228). We have also shown that in denervated rat hindlimb muscle the MVI expression level is significantly increased and its localization is changed, indicating an important role of MVI in striated muscle pathology. Here, we addressed this problem by examining the distribution and expression levels of myosin VI in biopsies of skeletal muscles from patients with different myopathies. We found that, particularly in myopathies associated with fiber atrophy, the amount of MVI was enhanced and its localization in affected fibers was changed. Also, since a mutation within the human MVI gene was shown to be associated with cardiomyopathy, we assessed MVI localization and expression level in cardiac muscle using wild type and MLP(-/-) mice, a dilated cardiomyopathy model. No significant difference in MVI expression level was observed for both types of animals. MVI was found at intercalated discs and also at the sarcoplasmic reticulum. In the knockout mice, it was also present in ring-like structures surrounding the nuclei. The data indicate that in striated muscle MVI could be engaged in sarcoplasmic reticulum maintenance and/or functioning, vesicular transport, signal transmission and possibly in gene transcription., (© 2014 Wiley Periodicals, Inc.)

Time-resolved laser spectroscopy techniques in the time range from femtoseconds to seconds were applied to investigate the charge separation processes in complete dye-sensitized solar cells (DSC) made with iodide/iodine liquid electrolyte and indoline dye D149 interacting with TiO2 or ZnO nanoparticles. The aim of the studies was to explain the differences in the photocurrents of the cells (3-4 times higher for TiO2 than for ZnO ones). Electrochemical impedance spectroscopy and nanosecond flash photolysis studies revealed that the better performance of TiO2 samples is not due to the charge collection and dye regeneration processes. Femtosecond transient absorption results indicated that after first 100 ps the number of photoinduced electrons in the semiconductor is 3 times higher for TiO2 than for ZnO solar cells. Picosecond emission studies showed that the lifetime of the D149 excited state is about 3 times longer for ZnO than for TiO2 samples. Therefore, the results indicate that lower performance of ZnO solar cells is likely due to slower electron injection. The studies show how to correlate the laser spectroscopy methodology with global parameters of the solar cells and should help in better understanding of the behavior of alternative materials for porous electrodes for DSC and related devices.

The temperature dependence of charge recombination of the pair P(+)HA(-) in isolated reaction centers from the purple bacterium Rhodobacter sphaeroides with prereduced quinone QA was studied by sub-nanosecond to microsecond time-scale transient absorption. Overall, the kinetics slowed down substantially upon cooling from room temperature to ∼200 K, and then remained virtually unchanged down to 77 K, indicating the coexistence of two competitive pathways of charge recombination, a thermally-activated pathway appearing only above ~200 K and a temperature-independent pathway. In our modelling, the thermally activated pathway includes an uphill electron transfer from HA(-) to BA(-) leading to transient formation of the state P(+)BA(-), whereas the temperature-independent pathway is due to direct downhill electron transfer from HA(-) to P(+). At all temperatures studied, the kinetics could be approximated by a four-component decay. Detailed analysis of the lifetimes and amplitudes of particular phases over the range of temperatures suggests that the kinetically resolved phases reveal the consecutive appearance of three conformational states characterized by an increasing free energy gap between the states P(+)BA(-) and P(+)HA(-). The initial gap between these states was estimated to be only ~8 meV, the intermediate gap being ~92 meV, and the final gap ~135 meV, with no dependence on temperature. It was also calculated through a very straightforward approach that the relaxation process from the initial to the intermediate state occurs within 0.6 ± 0.1 ns, whereas the second step of relaxation from the intermediate to the final state takes 11 ± 2 ns. Both phases of the protein relaxation process are essentially temperature-independent. Possible alternative models to describe the experimental data that cannot be definitely excluded are also discussed.

This paper reports on the investigations of the synthesized di-(o-hydroxyaryl ketoimine) compound by the steady state absorption and emission techniques as well as picosecond time resolved emission and femtosecond transient absorption methods in different solvents. The results of the experimental observation have been supported by the theoretical DFT and TD-DFT calculations. The theoretical data have revealed the completed influence of the environmental polarity on particular conformers of studied compound. Dependencies between the activation rate constant and polarizability function as well as Kamlet-Abbond-Taft hydrogen-bonding parameter have been obtained in different solvent. The mechanism of photodynamic changes of di-(o-hydroxyaryl ketoimine) is presented.

Myosin VI (MVI) is a unique unconventional motor moving backwards on actin filaments. In non-muscle cells, it is involved in cell migration, endocytosis and intracellular trafficking, actin cytoskeleton dynamics, and possibly in gene transcription. An important role for MVI in striated muscle functioning was suggested in a report showing that a point mutation (H236R) within the MVI gene was associated with cardiomyopathy (Mohiddin et al., J Med Genet 41:309-314, 2004). Here, we have addressed MVI function in striated muscle by examining its expression and distribution in rat hindlimb skeletal muscle. We found that MVI was present predominantly at the muscle fiber periphery, and it was also localized within muscle nuclei. Analysis of both the hindlimb and cardiac muscle longitudinal sections revealed ~3 μm striation pattern, corresponding to the sarcoplasmic reticulum. Moreover, MVI was detected in the sarcoplasmic reticulum fractions isolated from skeletal and cardiac muscle. The protein also localized to the postsynaptic region of the neuromuscular junction. In denervated muscle, the defined MVI distribution pattern was abolished and accompanied by significant increase in its amount in the muscle fibers. In addition, we have identified several novel potential MVI-binding partners, which seem to aid our observations that in striated muscle MVI could be involved in postsynaptic trafficking as well as in maintenance of and/or transport within the sarcoplasmic reticulum and non-sarcomeric cytoskeleton.

A complete, functioning dye-sensitized solar cell made of popular indoline D149 sensitizer is studied by means of transient absorption in visible light in the time scale of nanoseconds to seconds. Photocurrent and photovoltage decays are also measured under the same experimental conditions. A local electric field causing a Stark shift of the D149 absorption band is found to strongly influence the transient spectra and kinetics. The presence of electrons in titania has a major contribution to the Stark shift and the effect disappears over many time scales with an average rate of 5 × 10(3) s(-1). This is much slower than the decay of the oxidized dye (2 × 10(6) s(-1)) but, on the other hand, significantly faster than the decay of electrons in titania nanoparticles (3 × 10(2) s(-1) at standard AM1.5 irradiation and open circuit conditions). Possible explanations of this phenomenon are discussed. Electron recombination from the titania conduction band to the oxidized dyes proceeds at an average rate of 2-16 × 10(4) s(-1), depending on the excitation energy density, and does not influence the efficiency of dye regeneration.

Centronuclear myopathies constitute a group of heterogeneous congenital myopathies characterized by the presence of abnormal, centrally located nuclei within muscle fibers. Centronuclear myopathies can be caused by mutations of several different genes, including DNM2, encoding dynamin 2 (DNM2) a large GTPase involved in membrane trafficking and endocytosis. We report a 52-year-old female with slowly progressive muscle weakness, and a family history of the disease. Clinical, morphological, biochemical and genetic analyses of the proband and her family members were performed, including analyses of the proband's muscle biopsy. A novel D614N mutation, located in the C-terminal region pleckstrin-homology (PH) domain of DNM2 was identified in the proband and four family members, who exhibited similar symptoms. The mutation was associated with profound changes in the localization of DNM2 in muscle fibers without significant changes in protein expression. Mutated DNM2 and proteins involved in the membrane trafficking or membrane compartments maintenance were dislocalized within the myofiber, and concentrated at centrally located nuclei. This novel causative mutation (D614N) within the DNM2 gene in a large Polish centronuclear myopathy family with a late age of overt clinical manifestation caused profound changes in DNM2 localization and impaired proper organization of myofibers, and skeletal muscle functioning., (Copyright © 2012 Elsevier B.V. All rights reserved.)

In a recent paper (J Fluoresc (2011) 21:1547-1557) a temperature induced modulation of Coumarin 153 (C153) fluorescence lifetime and quantum yield for the probe dissolved in the polar, nonspecifically interacting 1-chloropropane was reported. This modulation was also observed in temperature dependencies of the radiative and nonradiative rates. Here, we show that the modulation is also observed in another 1-chloroalkane-1-chlorohexane, as well as in hydrogen bonding propionitrile, ethanol and trifluoroethanol. Change in the equilibrium distance between S (0) an S (1) potential energies surfaces was identified as the source of this modulation. This change is driven by temperature changes. It leads to a modulation of the fluorescence transition dipole moment and it is the primary source of the experimental effects observed. Additionally, we have found that proticity of the solvent induces a rise in the fluorescence transition dipole moment, which leads to a shortening of the fluorescence lifetime. Hydrogen bonds are formed by C153 also with hydrogen accepting solvents like propionitrile. We show that while such bonds do not affect the transition probability, they do change the S(0) an S(1) energy gap which in turn implies a change in non-radiative transition rate in a similar way as in protic solvents, as well as in the fluorescence spectrum position. Finally, the influence of temperature on the energies of hydrogen bonds formed by C153 when acting as hydrogen donor or acceptor is reported.

The protonation/deprotonation equilibrium was investigated for N-p-chlorobenzyl-substituted (E)-4'-hydroxy stilbazolium halide, namely (E)-1-(4-chlorobenzyl)-4-(4-hydroxystyryl)pyridinium chloride (EPC). Absorption, emission and synchronous scanning spectra were used to explain the observed phenomena. The excited state lifetimes of the protonated and deprotonated forms of EPC were measured and discussed. Absorption spectra were used to determine its pK(a) value in the ground state. We conclude that the protonation/deprotonation equilibrium is not attained in the first excited state of EPC, for kinetic reasons. The quinoid and benzenoid structures of EPC in the ground and excited state are discussed in acidic and basic range of pH. Aqueous solutions of EPC were yellow at pH < 7 and red at pH > 7, and addition of alcohols (methanol or 2-propanol) enhanced this change. Therefore, quaternary stilbazolium salts were investigated for application as acid-base indicators.

Lumichrome photophysical properties at different pH were characterized by UV-vis spectroscopy and steady-state and time-resolved fluorescence techniques, in four forms of protonation/deprotonation: neutral form, two monoanions, and dianion. The excited-state lifetimes of these forms of lumichrome were measured and discussed. The results were compared to those obtained for similar forms of alloxazine and/or isoalloxazine, and also to those of 1-methyl- and 3-methyllumichrome and 1,3-dimethyllumichrome. The absorption, emission, and synchronous spectra of lumichrome, 1-methyl- and 3-methyllumichrome, and 1,3-dimethyllumichrome at different pH were measured and used in discussion of fluorescence of neutral and deprotonated forms of lumichrome. The analysis of steady-state and time-resolved spectra and the DFT calculations both predict that the N(1) monoanion and the N(1,3) dianion of lumichrome have predominantly isoalloxazinic structures. Additionally, we confirmed that neutral lumichrome exists in its alloxazinic form only, in both the ground and the excited state. We also confirmed the existence and the alloxazinic structure of a second N(3) monoanion. The estimated values of pK(a) = 8.2 are for the equilibrium between neutral lumichrome and alloxazinic and isoalloxazinic monoanions, with proton dissociation from N(1)-H and N(3)-H groups proceeding at the almost the same pH, while the second value pK(a) = 11.4 refers to the formation of the isoalloxazinic dianion in the ground state.

Thermochromic emission shifts of 4-aminophthalimide (4-AP) dissolved in three 1-chloroalkanes, namely, 1-chloropropane, 1-chlorobutane, and 1-chlorohexane, together with fluorescence decays measured at different wavelengths, all solvents containing different small amounts of water (10(-4)-10(-2) M), are reported in a broad temperature range covering the bulk water melting point. Our studies have shown that 4-AP is an effective indicator of water presence even at concentrations given by solvent suppliers for so-called "dry" solvents. Additionally, indications of water ice-clusters formation in 1-chloroalkanes, starting at different temperatures depending on water concentration, have been found. Finally, 4-AP in 1-chloroalkane + water mixture is shown to present at different temperatures three basic types of sources of time-resolved emission spectra (TRES) time/spectral evolution: emission of two kinetically coupled species, solvent relaxation, and simultaneous emission of two independent species.

The aim of the study was to test whether the considerable differences in the hindlimb muscles mass, the number and diameter of muscles fibers were connected with differences in the myosin heavy chain isoform content (expressed as the percentage of the given isoform in respect to total myosin heavy chains). Therefore, the content of myosin heavy chain (MHC) isoforms was studied in four hindlimb muscles: flexor digitorum brevis, soleus, tibialis anterior and gastrocnemius medialis of female and male rats by means of polyacrylamide gel electrophoresis supplemented with densitometric analyses. Muscles were isolated and homogenized prior to electrophoretic analysis. The most interesting result concerned considerably different composition of myosin isoforms for male and female subjects in the slow soleus muscles, which contained predominantly slow MHC isoform (MHC I). However, in the male muscle about 13% of IIa isoform (MHC IIa) was also detected; this isoform was not found in the majority of the studied female muscles (81% of muscle samples). This dimorphic difference was further confirmed by immunofluorescence stainining for slow and fast skeletal myosin isoforms and by assessment of the fiber ATPase activity. For the three remaining fast muscles (flexor digitorum brevis, tibialis anterior and gastrocnemius medialis) all four MHC isoforms were detected with the fast isoforms being dominant ones. However, there were not statistically significant differences observed between males and females, with the exception of IIx isoform, which was more frequent in male tibialis anterior muscle.

Absorption, steady-state and timed-resolved fluorescence spectra of nine N-p-bromobenzyl substituted (E)-4'-hydroxy-4-stilbazolium bromides and N-p-bromo- (or nitro-) benzyl substituted (E)-4'-hydroxy-3'methoxy-4-stilbazolium bromides, belonging to the hemicyanine class of compounds, were studied in dry and water-containing polar solvents and in water. All of the studied compounds displayed negative solvatochromism. In solvents with small amounts of water the solutions of each of the compounds change color to red, blue-green or blue, while in extra dry solvents they are all yellow. The new band causing the change in color is interpreted as belonging to the deprotonated form of the respective compound. The absorption and emission spectra of protonated and deprotonated forms of hemicyanines in solvents are presented in comparison with those of selected, isolated deprotonated forms (merocyanines) of the same compounds. The discrimination between the quinoid and zwitterionic deprotonated forms was achieved based on the absorption band location. Time-resolved fluorescence measurements in selected dry and water-containing solvents were also performed., (This journal is © The Royal Society of Chemistry and Owner Societies 2011)

In previous studies we have demonstrated that prion protein (PrP) binds directly to tubulin and this interaction leads to the inhibition of microtubule formation by inducement of tubulin oligomerization. This report is aimed at mapping the regions of PrP and tubulin involved in the interaction and identification of PrP domains responsible for tubulin oligomerization. Preliminary studies focused our attention to the N-terminal flexible part of PrP encompassing residues 23-110. Using a panel of deletion mutants of PrP, we identified two microtubule-binding motifs at both ends of this part of the molecule. We found that residues 23-32 constitute a major site of interaction, whereas residues 101-110 represent a weak binding site. The crucial role of the 23-32 sequence in the interaction with tubulin was confirmed employing chymotryptic fragments of PrP. Surprisingly, the octarepeat region linking the above motifs plays only a supporting role in the interaction. The binding of Cu(2+) to PrP did not affect the interaction. We also demonstrate that PrP deletion mutants lacking residues 23-32 exhibit very low efficiency in the inducement of tubulin oligomerization. Moreover, a synthetic peptide corresponding to this sequence, but not that identical with fragment 101-110, mimics the effects of the full-length protein on tubulin oligomerization and microtubule assembly. At the cellular level, peptide composed of the PrP motive 23-30 and signal sequence (1-22) disrupted the microtubular cytoskeleton. Using tryptic and chymotryptic fragments of alpha- and beta-tubulin, we mapped the docking sites for PrP within the C-terminal domains constituting the outer surface of microtubule.

The effect of temperature on spectroscopic properties (stationary and time-resolved) of selected compounds belonging to the salicylideneaniline and hydroquinone families of photochromic Schiff bases is studied. The nonradiative decay of the excited keto tautomer consists of two components: the temperature-independent one (internal conversion, dominant below 200 K) and the temperature-dependent one (assigned to structural changes). The parameters of these components are remarkably different in the two families of the photochromic compounds. The influence of the hydrogen bonding ability of the solvent on the tautomeric equilibrium between the enol and keto forms indicates changes in the order of the ground state energy levels when going from methanol to trifluoroethanol.

A photochromic symmetric Schiff base, N,N'-bis(salicylidene)-p-phenylenediamine, has been studied by means of stationary and time-resolved spectroscopic absorption and emission techniques in the UV-vis spectral range with particular attention to the role of intermolecular hydrogen bonds. They are found to be responsible for the solvent-assisted excited-state proton transfer (the time constant of about 400 fs) in very strongly protic solvents and the photochrome deactivation (the time constant from 0.5 micros to 3 ms) in both protic and nonprotic solvents. Moreover, formation of an isomer that competes with the photochromic cycle in solution is also observed.

The hydroquinone family of photochromic Schiff bases has been studied by means of stationary and time-resolved spectroscopic absorption and emission techniques in the UV-Vis spectral range in the temporal range from 100 fs to 1 h. The studies have revealed that besides the ultrafast excited state intramolecular proton transfer reaction there is also another deactivation channel from the initially excited state. For the symmetric molecule with two intramolecular hydrogen bonds, the efficiency of the proton transfer reaction has been found to be at least ten times reduced when compared to that of the asymmetric molecule with one intramolecular hydrogen bond. The long-lived transient species absorbing in the UV range and coexisting with the photochrome have been observed in differently interacting solvents. Evidence for different conformers of almost all of the tautomers involved in the photochromic cycle has been also found.

The spectral and photophysical behavior of four fluorescent 9-oxo-imidazo[1,2-a]purine derivatives containing pyridyl, pyridylphenyl, phenyl, and biphenylyl substituents at the C(6) position of the tricyclic skeleton is described. The studies were performed in several aprotic and protic organic solvents using absorption spectroscopy as well as steady-state and time-resolved fluorescence spectroscopy. The results are also presented of TDDFT calculations on singlet-singlet excitation energies and oscillator strengths for two models of 9-oxo-imidazo[1,2-a]purine, with phenyl or pyridyl substituents, both in the gas phase and in methanol solution. While the derivatives with aryl substituents did not show any significant dependence of their static and dynamic fluorescence properties on the nature of the solvent, the compounds containing a pyridine residue exhibited a remarkable reduction of their fluorescence quantum yields and lifetimes in the alcoholic solutions. The solute-solvent hydrogen-bonding interaction in the first excited singlet state is responsible for the fast radiationless decay rates determined for pyridyl- and pyridylphenyl-substituted compounds in protic solvents. The results of experimental and theoretical studies show that the hydrogen of the alcohols' hydroxyl group and the nitrogen atom of the pyridine moiety are involved in the interaction. The fluorescence-quenching experiments performed for the pyridyl-substituted 9-oxo-imidazo[1,2-a]purine derivative using trifluoroethanol, methanol, and butanol as quenchers revealed that the quenching efficiencies, expressed by the Stern-Volmer quenching constants, correlate with the H-bond donating abilities of the alcohols. The quenching is a dynamic process, and the H-bonded complex formed is nonfluorescent. The experimentally determined and the calculated values of the dipole moment change associated with the electronic excitation indicate that the excited S(1) states of all of the molecules studied in this work have an intramolecular charge-transfer character and that electronic charge is transferred to the C(6) substituent upon excitation. Thus, the ability of the pyridyl substituent nitrogen atom to act as an H-bond acceptor in the excited S(1) state is enhanced. The 6-pyridyl-9-oxo-imidazo[1,2-a]purine presents a novel fluorophore, which, besides its medical applications, may be useful as a sensor of hydroxyl groups in microorganized systems.

Quantum chemical density functional theory (DFT) calculations and spectral data were employed to investigate the possibility of the excited-state double proton transfer (ESDPT) in lumichrome crystals. The calculations in a lumichrome dimer predict a transfer of a proton in the first excited state, leading to a cation-anion pair. The presently reported X-ray structure of 1,3-dimethyllumichrome and its complex solid-state luminescence indicate that also in this molecule intermolecular hydrogen bonds might be involved in the photophysics. The long-wavelength emission in lumichrome crystals peaked at 530 nm is attributed to excited-state proton transfer, whereas a wider emission band in methylated lumichrome derivatives peaked at 560 nm is attributed to ions formed upon photoexcitation of the crystals.

Experimental time-resolved spectral and photon counting kinetic results confirm formation of an isoalloxazinic excited state via excited-state double proton transfer (ESDPT) catalyzed by a carboxylic acid molecule that forms a hydrogen-bond complex with the parent alloxazine molecule. This isoalloxazinic tautomer manifests itself as a distinct long-lived emissive species formed only in such alloxazine derivatives that were not substituted at the N1 nitrogen atom, being a product of the excited-state reaction occurring from the alloxazinic excited state. Theoretical calculations support the idea that the ESDPT occurs by the concerted mechanism. The calculated activation barrier in the excited state is much lower than the same barrier in the ground state and even disappears for the HOMO-1 to LUMO excitation, which explains the fact that the reaction takes place in the excited-state only. The reaction rate estimated from the emission kinetics is ca. 1.4 x 10(8) dm3 mol(-1) s(-1) in ethanolic solutions of lumichrome with added acetic acid.

Interactions of tyrosine and phenylalanine analogues with beta-cyclodextrin have been examined in terms of structural features of the ligand such as the separation of the charged amino group and aromatic ring, the presence of additional functional group attached to the amino or phenyl ring, and the presence of a charge on amino or carboxyl group, and steric effects using steady-state and time-resolved fluorescence spectroscopy and microcalorimetry. The studied aromatic amino acids possess low binding constant to beta-cyclodextrin, diversified with respect to the presence or absence of a substituent in para position of the phenyl ring. However, calculated, based on the global analysis of the fluorescence intensity decays, binding constants do not allow to estimate unequivocally the influence of the distance between the charged groups and phenol/phenyl ring on the inclusion complex stability because of their low diversification.

Photophysical properties of tyrosine and its derivatives with free and blocked functional groups were studied by steady state and time-resolved fluorescence spectroscopy and global analysis in organic solvents, such as methanol, 2-propanol, tetrahydrofuran (THF), and dimethylsulfoxide (DMSO). The mono-exponential fluorescence intensity decays were observed for all tyrosine derivatives in THF and DMSO solutions, whereas in alcohols some derivatives have bi-exponential decays. The rotamer population calculated from 1H nuclear magnetic resonance spectroscopy in DMSO does not correspond to the pre-exponential factors obtained from fluorescence spectroscopy. Moreover in the case of DMSO, the strong interaction of this solvent with the hydroxyl group of the fluorophore's phenol ring causes substantial changes in the fluorescence and nonradiative rate constants of tyrosine derivatives compared with those of tyrosine with a blocked hydroxyl group, Tyr(Me). The steady state and time-resolved fluorescence measurements in pure organic solvents and water-organic solvent mixtures indicate that the fluorescence quenching of the phenol chromophore of tyrosine by an acetyl or amide group or both depends on the polarity of the solvent used as well as the ability of the solvent to form hydrogen bonds with functional groups of tyrosine.

The steady-state and time-resolved fluorescence spectroscopy was applied to determine the influence of an alkyl substituent(s) (methyl or ethyl, n-propyl, iso-propyl, n-butyl, sec-butyl, or t-butyl) on amide nitrogen atom on photophysical properties of tyrosine and N-acetyltyrosine amides in water. Generally, the amide group strongly quenches the fluorescence of tyrosine, however, the size and number of substituents on amide nitrogen atom modify the quenching process only in small degree. The fluorescence intensity decays of all amides studied are bi-exponential. The contribution of both components (alphai) to the fluorescence decay undergoes irregular change. An introduction of alkyl substituent on amide nitrogen atom causes an increase of the fluorescence lifetime of tyrosine derivative compared to the unsubstituted amide for both N-acetyltyrosine and tyrosine with the protonated amino group. Calculated, basing on the fluorescence quantum yield (QY) and average lifetime, the radiative rate constants (kf) are similar, which indicates that the substituent(s) does not have substantial influence on radiative process of the deactivation of the excited state of the phenol chromophore for all compounds studied regardless the amino group status as well as the number and type of substituent (linear or branched). The comparison of the ground-state rotamer populations of tyrosine amides and N-acetyltyrosine amides with different alkyl substituent on amide nitrogen atom obtained from 1H NMR with the value of pre-exponential factors indicates that not the rotamer populations, but specific hydration of a whole molecule of the amino acid including chromophore and amino acid moiety, seems to be the main reason of the heterogenous fluorescence intensity decay of tyrosine derivatives.

The analgesic activity of opioid peptides is mainly connected with their affinity and selectivity for the mu-receptors. The biological activity of cyclic opioid analogues depends on mutual orientation and conformational freedom of aromatic pharmacophore groups at positions 1 and 4. The distance and distance distributions between chromophores at positions 1 [Phe(p-NO(2)), p-nitrophenylalanine] and 4 [Nal, beta-(2-naphthyl)alanine], which constitute an energy donor-acceptor pair, were calculated based on measured fluorescence intensity decays of a donor (Nal). The influence of the solvent and configuration of the residues at position 2 and 3 on donor-acceptor distance distribution and mobility of pharmacophore groups at position 1 and 4 in cyclic enkephalin analogues are discussed., (Copyright 2001 John Wiley & Sons, Inc.)