Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy.

Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678 cm-1 band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states.

Elucidating the role of structural fluctuations, and intermolecular and vibronic interactions in the spectroscopic response of a bacteriophytochrome.

We present the first comprehensive multiscale computational investigation of Resonance Raman, absorption and Circular Dichroism spectra of the resting state of the Deinococcus radiodurans phytochrome. The spectra are simulated in all their components, namely the energy position and the lineshapes of both the far-red and the blue bands. To achieve such a goal, we have combined a 4.5 µs MD simulation of the solvated dimeric phytochrome with a hybrid quantum mechanics/molecular mechanics (QM/MM) model, which accounts for both electrostatic and mutual polarization effects between the QM and the MM subsystems. A good agreement with experiments is found for all the three spectra. Moreover, we find a transient H-bond network within the binding pocket of the biliverdin chromophore that, unexpectedly, does not significantly affect the spectra. In parallel, we characterize the vibrations that are more strongly coupled to the biliverdin excitation, confirming the important role of the hydrogen-out-of-plane mode of its vinyl C-H together with the expected C[double bond, length as m-dash]C stretching of the double bond involved in the photoisomerization.

Use of smartphone apps to monitor human exposure to solar radiation: Comparison between predicted and measured UV index values.

The Ultra-Violet Index (UVI) is widespread used to communicate the UV radiation intensity to the general public. The knowledge of the UVI value and of its daily variation is essential for many techniques for monitoring the personal exposure to UV radiation. The UVI values are usually provided by the meteorological services and nowadays it is very common to find UVI forecast tools even in smartphone apps. In this paper, with the aim to evaluate the prediction accuracy of six smartphone apps, a measurement campaign of UVI has been carried out. The measurements have been conducted for the site of Pisa (central Italy), using a portable photoradiometer equipped with a UV erythemal irradiance probe (operating range 250-400 nm). The measured UVI values have been compared with the predicted UVI values (using smartphone apps). Bland-Altman and Passing-Bablok methods have been used to compare the data, the comparison has been conducted on the basis of 90 different UVI measurements, taken at different times, different days and different sky conditions. From the comparison between measured and predicted UVI values it has been possible to observe a general poor accuracy of the apps. The percentage deviations between measured and predicted UVI values were quite high and only one app was able to predict more than 70% of the measured data with an average percentage deviation lower than 30%.

[Not Available]. / Valutazione del rischio da esposizione al rumore in un'officina meccanica e scelta dei dispositivi di protezione uditiva.

In this study the authors intended to describe and provide a critical remark of the necessary assessments for the selection of the most appropriate personal protective equipment. This selection has been made with reference to the calculation methods specified in the International Standard UNI EN ISO 9612 and UNI EN 458.

Analogies and Differences in the Photoactivation Mechanism of Bathy and Canonical Bacteriophytochromes Revealed by Multiscale Modeling.

Bacteriophytochromes are light-sensing biological machines that switch between two photoreversible states, Pr and Pfr. Their relative stability is opposite in canonical and bathy bacteriophytochromes, but in both cases the switch between them is triggered by the photoisomerization of an embedded bilin chromophore. We applied an integrated multiscale strategy of excited-state QM/MM nonadiabatic dynamics and (QM/)MM molecular dynamics simulations with enhanced sampling techniques to the Agrobacterium fabrum bathy phytochrome and compared the results with those obtained for the canonical phytochrome Deinococcus radiodurans. Contrary to what recently suggested, we found that photoactivation in both phytochromes is triggered by the same hula-twist motion of the bilin chromophore. However, only in the bathy phytochrome, the bilin reaches the final rotated structure already in the first intermediate. This allows a reorientation of the binding pocket in a microsecond time scale, which can propagate through the entire protein causing the spine to tilt.

Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response.

In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.

Exploring the interaction between a fluorescent Ag(I)-biscarbene complex and non-canonical DNA structures: a multi-technique investigation.

Silver compounds are mainly studied as antimicrobial agents, but they also have anticancer properties, with the latter, in some cases, being better than their gold counterparts. Herein, we analyse the first example of a new Ag(I)-biscarbene that can bind non-canonical structures of DNA, more precisely G-quadruplexes (G4), with different binding signatures depending on the type of G4. Moreover, we show that this Ag-based carbene binds the i-motif DNA structure. Alternatively, its Au(I) counterpart, which was investigated for comparison, stabilises mitochondrial G4. Theoretical in silico studies elucidated the details of different binding modes depending on the geometry of G4. The two complexes showed increased cytotoxic activity compared to cisplatin, overcoming its resistance in ovarian cancer. The binding of these new drug candidates with other relevant biosubstrates was studied to afford a more complete picture of their possible targets. In particular, the Ag(I) complex preferentially binds DNA structures over RNA structures, with higher binding constants for the non-canonical nucleic acids with respect to natural calf thymus DNA. Regarding possible protein targets, its interaction with the albumin model protein BSA was also tested.

Dataset of virtual and real-life visual experiences inside a museum: survey on visual perception with objective and subjective measures.

Occupants' perception of a space depends on their experience [1], [2], [3]. Four kinds of visiting experiences were carried out inside the Natural History Museum of the University of Pisa [4]. The museum is housed, together with the National Museum of the Charterhouse [5], inside the Monumental Charterhouse of Calci, near Pisa. Four of the permanent exhibition halls of the Museum were selected for the survey: Historical Gallery, Mammal's Hall, Ungulates' Gallery and Cetaceans' Gallery. A total of 117 participants were divided into four groups depending on their visiting experience: real-life, or virtual based respectively on videos, photos or computer-generated photorealistic images (renders). Experiences are compared. The comparison comprehends objective data (measured illuminance levels) and subjective data (questionnaire outcomes on the perception of the space). The illuminance levels were measured using a photoradiometer: datalogger Delta Ohm HD2102.2 equipped with LP 471 PHOT probe. The probe was placed 1.20 m above floor level, and it was set to measure vertical illuminance at 10 seconds intervals. To evaluate participants' perception of the space questionnaires were used. The presented data refer to the article: "Perception of light in museum environments: comparison between real-life and virtual visual experiences" [1]. This kind of data provides a base to assess if virtual kinds of experience can be implemented in museum environments as an alternative to the real-life experience, and to understand if such an implementation is detrimental or not in terms of participants' perception of the space. Virtual experiences can be particularly useful for spreading culture, making it accessible even in presence of moving restrictions for people, such as those in force today due to the SARS-CoV-2 emergency.

Drawing data for a 3D historical reconstruction of Shakespeare's first Globe Theatre.

The first Globe Theatre was one of the main outdoor playhouses in London in the early 17th century. Although it was built in 1599 and was destroyed in a fire in 1613, its history has survived to the present day as the theatre that was able to accommodate most of William Shakespeare's plays. Extensively studied during the last century, it has been attempted to be reconstructed several times in different parts of the world, although the information present does not allow for an exact reconstruction. The data presented here have been collected from the various interpretations offered in literature by the main scholars of the first Globe Theatre and re-elaborated according to criteria of coherence with vernacular building techniques and ease and feasibility of construction. What is presented is the methodology probably used by the Globe's carpenter Peter Street to draw the plan and then build the theatre. The data presented were used to provide a virtual reconstruction of the first Globe Theatre, featured in the article " Towards reconstructing the Shakespeare's first Globe Theatre: A virtual model for research and development", published in the Frontiers of Architectural Research by the same authors [1]. The data can be used to confirm, improve, or reconstruct the first Globe, as well as most Elizabethan theatres, similar in type and form.

Exploration of environmental noise in Saharan oases on the basis of urban configurations: City of Biskra datasets.

The scope of this dataset is to explore the acoustic environment on the basis of spatial configurations. To fulfill this objective, two ranges of data were involved. Firstly, urban acoustic data was obtained by setting up 240 stations of measurements based on equivalent continuous A-weighted sound pressure level, across 16 urban zones in Biskra City, Algeria, during working hours. The data was analyzed using geostatistical and interpolation models on a Geographic Information System platform in order to enhance the observations and examine their distribution within the urban area. Secondly, spatial configuration data is based on two indicators: Normalized Angular Integration and Normalized Angular choice. Integration refers to the degree of accessibility ``to-movement'', whereas Choice values depict the urban route hierarchy, or the ``through-movement'' potential. The data includes different values of the global and local scale of the urban structure using several metric radii of 400m, 800m, 1200m, 1600m, 2000m, 2400m and 3200m. A correlation scheme is required in order to validate the effectiveness of this methodological approach. The dataset serves as an insightful reference for further inquiry and policymakers in dealing with sustainable concerns related to soundscape, noise pollution, and urban planning.

Protein control of photochemistry and transient intermediates in phytochromes.

Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded chromophore, triggering large conformational changes in the protein. Despite numerous experimental and computational studies, the role of chromophore-protein interactions in controlling the mechanism and timescale of the process remains elusive. Here, we combine nonadiabatic surface hopping trajectories and adiabatic molecular dynamics simulations to reveal the molecular details of such control for the Deinococcus radiodurans bacteriophytochrome. Our simulations reveal that chromophore photoisomerization proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen bond of the chromophore with a close-by histidine. The resulting photoproduct relaxes to an early intermediate stabilized by a tyrosine, and finally evolves into a late intermediate, featuring a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the active state.

The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation.

Phytochromes are red-light sensing proteins, with important light-regulatory roles in different organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon absorption of light by the embedded bilin chromophore, they undergo structural changes that extend from the chromophore to the protein and finally drive the biological function. Up to now, the underlying mechanism still has to be characterized fully. Here we investigate the Pfr activated form of a bacterial phytochrome, by combining extensive molecular dynamics simulations with a polarizable QM/MM description of the spectroscopic properties, revealing a large structure relaxation in solution, compared to the crystal structure, both in the chromophore-binding pocket and in the overall structure of the phytochrome. Our results indicate that the final opening of the dimeric structure is preceded by an important internal reorganization of the phytochrome specific (PHY) domain involving a bend of the helical spine connecting the PHY domain with the chromophore-binding domain, opening the way to a new understanding of the activation pathway.

Assessing museums' daylighting adequacy without annual measurement campaign: Dataset of a confrontation between measured and simulated illuminance values inside the Cetacean Gallery of the Charterhouse of Calci.

Lighting Cultural Heritage is a complex task: light is necessary for the act of seeing, it can even enhance the visual experience [1,2], in addition proper lighting can significantly cut down energy consumptions [3], but on the same time it has detrimental effects on exhibits, especially daylight. In order to safeguard the exhibits from damages, national and international standards provide specific recommendations for exhibits' exposure, based on their photosensitivity category. These recommendations are the annual luminous exposure(LO) and the Maximum Illuminance Level (Emax), museums' curators have to verify that the display lighting conditions comply with the standards. Historical buildings are often converted into museums but, as their original purpose was different, the lighting conditions are often inadequate (e.g. too much uncontrolled daylight), therefore the lighting conditions' adequacy of the space should be assessed [4]. As the name suggest the annual luminous exposure requires an annual monitoring campaign, unfortunately it often happens that exhibits have been exposed incorrectly for prolonged periods, and therefore it is very important to evaluate the need of a fast intervention. In this casuistry a prolonged measurement campaign is not acceptable. Simulations can help running a great number of analysis while reducing the length and expenses of a measurements campaign, however their previsions must be validated. This paper provides the data acquired through measurements and simulations inside the Cetacean Gallery of the Monumental Charterhouse of Calci, near Pisa (Tuscany Region, Italy). The data comprehends horizontal and vertical illuminance measurements, recorded on December the 6th, and simulations run in Grasshopper with the plugins Honeybee+ and Ladybug. The data are related to the research article entitled "Application of climate-based daylight simulation to assess lighting conditions of space and artworks in historical buildings: the case study of Cetacean Gallery of the Monumental Charterhouse of Calci", published on the Journal of Cultural Heritage [5].

Dye Stabilization and Wavelength Tunability in Lasing Fibers Based on DNA.

Lasers based on biological materials are attracting an increasing interest in view of their use in integrated and transient photonics. Deoxyribonucleic acid (DNA) as optical biopolymer in combination with highly emissive dyes has been reported to have excellent potential in this respect. However, achieving miniaturized lasing systems based on solid-state DNA shaped in different geometries to confine and enhance emission is still a challenge, and the physicochemical mechanisms originating fluorescence enhancement are not fully understood. Herein, a class of wavelength-tunable lasers based on DNA nanofibers is demonstrated, for which optical properties are highly controlled through the system morphology. A synergistic effect is highlighted at the basis of lasing action. Through a quantum chemical investigation, it is shown that the interaction of DNA with the encapsulated dye leads to hindered twisting and suppressed channels for the nonradiative decay. This is combined with effective waveguiding, optical gain, and tailored mode confinement to promote morphologically controlled lasing in DNA-based nanofibers. The results establish design rules for the development of bright and tunable nanolasers and optical networks based on DNA nanostructures.

Sun Exposure of Body Districts: Development and Validation of an Algorithm to Predict the Erythemal Ultra Violet Dose.

Solar Ultra-Violet (UV) radiation has positive and negative effects on human body tissues. Small doses of solar UV radiation are needed by the human skin for the activation of the vitamin D production. Overexposure to solar UV radiation can produce acute and long-term negative effects, such as sunburns and, in the worst cases, cataracts and skin cancers. For this reason, knowing the amount of UV doses received by people is essential to evaluate their risk to UV overexposure and to evaluate the adequate countermeasure to avoid the negative effects. The original contribution of the present study consists in having searched, collected, adapted and processed a series of technical information and analytical relations, developing an algorithm suitable for the calculation of the erythemal UV dose on sloped surfaces exposed to solar radiation, which at the moment is not present in the scientific literature. The results obtained by the algorithm have been compared to the results of a field measurements campaign, carried out in three different Italian sites. Results comparison indicated that measured and calculated values show a sufficient level of agreement, with a mean absolute error equal to 20%.

Binding of model polycyclic aromatic hydrocarbons and carbamate-pesticides to DNA, BSA, micelles and liposomes.

The binding to biosubstrates and micellar systems of pollutants as the polycyclic aromatic hydrocarbon (PAH) derivatives 1-aminopyrene (1-PyNH2) and 1-hydroxymethylpyrene (1-PyMeOH) and the carbamate-pesticides 1-naphthyl-N-methylcarbamate (carbaryl, CA) and methyl benzimidazol-2-ylcarbamate (carbendazim, CBZ) was analysed through an integrated strategy combining spectroscopy and quantum chemistry. As biosubstrates, natural DNA and bovine serum albumin (BSA) were taken into account for a thermodynamic analysis of the binding features through spectrophotometric and spectrofluorometric techniques. In all cases, a strong DNA interaction is present and intercalation is supposed as the major binding mode. For the PAH derivatives, DNA binding is found to be favoured under high salt conditions and BSA static quenching and binding with 1:1 stoichiometry occurs. The molecular structure and optical properties of 1-PyNH2, CA and CBZ together with their intercalated adducts in DNA were studied also by means of quantum chemical approach. The (TD)DFT calculations on intercalated dye/DNA adducts quantitatively reproduce the experimentally observed spectroscopic changes, thus confirming the intercalation hypothesis. The theoretical approach also provides information on the adducts' geometries and on the amount of charge transfer with DNA. Moreover, ultrafiltration tests in the presence of anionic (SDS), cationic (DTAC) and neutral (Triton X) micellar aggregates and liposomes provided insights into lipophilicity and cellular membrane affinity. PAH derivatives show high retention coefficient in all cases, whereas in the case of carbamate-pesticides micellar retention might be significantly reduced and is very limited in the case of liposomes.