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Modification of the electronic structure of quantum matter by ad atom deposition allows for directed fundamental design of electronic and magnetic properties. This concept is utilized in the present work in order to tune the surface electronic structure of magnetic topological insulators based on MnBi2Te4. The topological bands of these systems are typically strongly electron-doped and hybridized with a manifold of surface states that places the salient topological states out of reach of electron transport and practical applications. In this work, micro-focused angle-resolved photoemission spectroscopy (microARPES) provides direct access to the termination-dependent dispersion of MnBi2Te4and MnBi4Te7during in situ deposition of rubidium atoms. The resulting band structure changes are found to be highly complex, encompassing coverage-dependent am-bipolar doping effects, removal of surface state hybridization and the collapse of a surface state band gap. In addition, a doping-dependent band bending is found to give rise to tunable quantum well states. This wide range of observed electronic structure modifications could provide new ways to exploit the topological states and the rich surface electronic structures of manganese bismuthtellurides.

The mitochondrial outer membrane creates a diffusion barrier between the cytosol and mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in theGDAP1gene are linked to the most common human peripheral neuropathy, Charcot-Marie-Tooth disease (CMT). GDAP1 is a distant member of the glutathione-S-transferase (GST) superfamily, with unknown enzymatic properties or functions at the molecular level. The structure of the cytosol-facing GST-like domain has been described, but there is no consensus on how the protein interacts with the mitochondrial outer membrane. Here, we describe a model for GDAP1 assembly on the membrane using peptides vicinal to the GDAP1 transmembrane domain. We used oriented circular dichroism spectroscopy (OCD) with synchrotron radiation to study the secondary structure and orientation of GDAP1 segments at the outer and inner surfaces of the outer mitochondrial membrane. These experiments were complemented by small-angle X-ray scattering, providing the first experimental structural models for full-length human GDAP1. The results indicate that GDAP1 is bound into the membraneviaa single transmembrane helix, flanked by two peripheral helices interacting with the outer and inner leaflet of the mitochondrial outer membrane in different orientations. Impairment of such interactions could be a mechanism for CMT in the case of missense mutations affecting these segments instead of the GST-like domain.

This study investigated the emulsifying and antioxidant activity of 10 peptides derived from seaweed, methanotrophic bacteria, and potatoes, which were identified as emulsifiers using quantitative proteomics and predictive bioinformatics. The factors (e.g., interfacial properties, secondary structure, net charge) behind the dualfunctionality of peptides were characterized and related to peptides’ ability to provide physical and oxidative stability in 5 % fish oil-in-water emulsions during 10 days of storage. The secondary structure of some of the peptides changed from highly disordered to more α-helical (GIIPATILEFLEGQLQEVDNNKDAR and GIIPGTILEFLEGQLQK) or β-strand (VGFACSGSAQTYLSFEGDNTGRGEEEVAI, ELQVSARVTLEIEL, KVKINETVEIKGKFHV, RSPQKKESDMMKATKFAVVLMAAGLTVGCA) structures when adsorbed at the oil-water interface in comparison, Innovation Fund Denmark (Grant no.: 7045-00021B)

Funding Information: L.V.S.D., A.S.B., and M.H.F.B. acknowledge support from the Brazilian agencies Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). L.V.S.D., A.S.B., and M.H.F.B. also acknowledge Prof. Carlos de Carvalho for computational support at LFTC-DFis-UFPR and at LCPAD-UFPR. The authors acknowledge the beam time at the ISA synchrotron, Aarhus University, Denmark. The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) CALIPSO under grant agreement n° 312284. P.L.V. acknowledges the Portuguese National Funding Agency (FCT) through research grant CEFITEC (UIDB/00068/2020), as well as his visiting professor position at Federal University of Paraná, Curitiba, Brazil. This contribution is also based upon work from the COST Action CA18212-Molecular Dynamics in the GAS phase (MD-GAS), supported by COST (European Cooperation in Science and Technology). Publisher Copyright: © 2023 The Authors. Published by American Chemical Society. High-resolution photoabsorption cross-sections in the 3.7-10.8 eV energy range are reinvestigated for nitromethane (CH3NO2), while for nitroethane (C2H5NO2), they are reported for the first time. New absorption features are observed for both molecules which have been assigned to vibronic excitations of valence, Rydberg, and mixed valence-Rydberg characters. In comparison with nitromethane, nitroethane shows mainly broad absorption bands with diffuse structures, which can be interpreted as a result of the side-chain effect contributing to an increased number of internal degrees of freedom. New theoretical quantum chemical calculations performed at the time-dependent density functional theory (TD-DFT) level were used to qualitatively help interpret the recorded photoabsorption spectra. From the photoabsorption cross-sections, photolysis lifetimes in the terrestrial atmosphere have been obtained for both compounds. Relevant internal conversion from Rydberg to valence character is noted for both molecules, while the nuclear dynamics of CH3NO2 and C2H5NO2 along the C-N reaction coordinate have been evaluated through potential energy curves at the TD-DFT level of theory, showing that the pre-dissociative character is more prevalent in nitromethane than in nitroethane. publishersversion published

The UV absorbance bands of 1,4-distyrylbenzene (1,4-Bis[(E)-2-phenylethenyl]benzene, DSB) are investigated by Synchrotron Radiation Linear Dichroism (SRLD) spectroscopy using stretched polyethylene as an anisotropic solvent. The observed polarization data provide information on the transition moment directions of the observed spectral features. The investigation covers the range 15000–58000 cm–1 (667–172 nm), thereby providing new information on the transitions of DSB in the vacuum UV region. The observed spectrum is characterized by four main band systems centered at 27600, 41000, 49800, and 57500 cm–1 (362, 244, 201, and 174 nm). In general, the observed bands and their polarization directions are well predicted by the results of quantum chemical calculations using Time-Dependent Density Functional Theory (TD–DFT) with the functional CAM-B3LYP, and with the semi-empirical all-valence-electrons method LCOAO.

Protein science 32(2), e4567 (2023). doi:10.1002/pro.4567, DNA-binding proteins from starved cells (Dps) are small multifunctional nanocages expressed by prokaryotes in acute oxidative stress conditions or during the starvation-induced stationary phase, as a bacterial defense mechanism. Dps proteins protect bacterial DNA from damage by either direct binding or by removing precursors of reactive oxygen species from solution. The DNA-binding properties of most Dps proteins studied so far are related to their unordered, flexible, N- and C-terminal extensions. In a previous work, we revealed that the N-terminal tails of Deinoccocus grandis Dps shift from an extended to a compact conformation depending on the ionic strength of the buffer and detected a novel high-spin ferrous iron center in the proximal ends of those tails. In this work, we further explore the conformational dynamics of the protein by probing the effect of divalent metals binding to the tail by comparing the metal-binding properties of the wild-type protein with a binding site-impaired D34A variant using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism, and small-angle X-ray scattering. The N-terminal ferrous species was also characterized by Mössbauer spectroscopy. The results herein presented reveal that the conformation of the N-terminal tails is altered upon metal binding in a gradual, reversible, and specific manner. These observations may point towards the existence of a regulatory process for the DNA-binding properties of Dps proteins through metal binding to their N- and/or C-terminal extensions., Published by Protein Society, Bethesda, Md.

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A synchrotron-based photoionization spectrum up to 27 eV represents a considerable improvement in resolution over early He(I) and He(II) spectra. Symmetry-adapted coupled cluster calculations of the ionic state sequence give the sequence of state vertical ionization energies (VIE) as 12B2 < 12B1 < 12A2 < 22B1 < 12A1. Generally, these symmetry-adapted cluster configuration interactions VIE match reasonably well with the experimental spectrum over this wide energy range. Density functional calculations of the corresponding adiabatic terms (AIE) were also performed. Higher energy ionic states were determined by complete active space self-consistent field methods; these include all π-ionizations and some σ-ionic states. These were analyzed by Franck–Condon (FC) procedures and compared with an experiment. The spectral onset is complex, where two states, later shown to be the 12B2 and 12B1 states, are strongly overlapping. The superposition of the FC vibrational structure in the 12B2 and 12B1 states accounts for most of the peaks arising at the onset of the photoelectron spectra. However, the small separation between these two ionic states makes vibronic interaction fairly inevitable. In the absence of Herzberg–Teller analyses for ionic states, we have sought and determined a transition state between the 12B2 and 12B1 states, showing that vibronic coupling does occur. The lack of degradation in the vibrational envelope of the higher of the two states contrasts with our previous work on the halogenobenzenes, where overlapping state envelopes led to considerable widening of the line width at half-height of the higher energy states.

C4F7N is a promising candidate for the replacement of sulfur hexafluoride as an insulating medium, and it is important to understand the chemical changes initiated in the molecule by collision with free electrons, specifically the formation of neutral fragments. The first step of neutral fragmentation is electronic excitation, yet neither the absorption spectrum in the vacuum ultraviolet (VUV) region nor the electron energy loss spectrum have previously been reported. Here, we experimentally probed the excited states by VUV photoabsorption spectroscopy and electron energy loss spectroscopy (EELS). We found that the distribution of states populated upon electron impact with low-energy electrons is significantly different from that following photoabsorption. This difference was confirmed and interpreted with ab initio modeling of both VUV and EELS spectra. We propose here a new computational protocol for the simulation of EELS spectra combining the Born approximation with approximate forms of correlated wave functions, which allows us to calculate the (usually very expensive) scattering cross sections at a cost similar to the calculation of oscillator strengths. Finally, we perform semi-classical non-adiabatic dynamics simulations to investigate the possible neutral fragments of the molecule formed through electron-induced neutral dissociation. We show that the product distribution is highly non-statistical.

We describe the commissioning of a new electron–ion coincidence spectrometer used to diagnose the photon beam from a plane grating monochromator beamline at the ASTRID2 synchrotron radiation facility. The spectrometer allows determination of the absolute photon intensity by calibration to the photoabsorption cross sections of known gases, such as the rare gases Ar, Kr, and Xe presented here. The spectrometer operates at very low pressure (∼10−8–10−9 mbar) and—due to the coincidence electron–ion detection scheme—the detector efficiencies can be determined routinely; hence, the spectrometer can be recalibrated swiftly. By variation of a single potential of the spectrometer, the content of higher order radiation in the monochromatized synchrotron radiation can be analyzed. The layout and operation of the synchrotron radiation beamline at ASTRID2 and its additional photon diagnostic units are additionally described.

The surface of a carboxylate-enriched octuple mutant of Bacillus subtilis lipase A (8M) is chemically anionized to produce core (8M)-shell (cationic polymer surfactants) bionanoconjugates in protein liquid form, which are termed anion-type biofluids. The resultant lipase biofluids exhibit a 2.5-fold increase in hydrolytic activity when compared with analogous lipase biofluids based on anionic polymer surfactants. In addition, the applicability of the anion-type biofluid using Myoglobin (Mb) that is well studied in anion-type solvent-free liquid proteins is evaluated. Although anionization resulted in the complete unfolding of Mb, the active α-helix level is partially recovered in the anion-type biofluids, and the effect is accentuated in the cation-type Mb biofluids. These highly active anion-type solvent-free liquid enzymes exhibit increased thermal stability and provide a new direction in solvent-free liquid protein research.

The secondary structure of whey protein concentrate hydrolysate (WPCH), used as an emulsifier in oil delivery systems, was investigated using Synchrotron Radiation Circular Dichroism (SRCD). The effect of pH on the conformation of peptides in solution and adsorbed at the oil/water interface, as well as the thermal stability of the systems was studied. Furthermore, oil-loaded microcapsules were produced by spray-drying or electrospraying to investigate the influence of encapsulating agents (glucose syrup, maltodextrin) and drying technique on the secondary structure of WPCH at the oil/water interface. Enzymatic hydrolysis resulted in peptides with a highly unordered structure (~60% turns and unordered regions) in solution. However, WPCH adsorption onto the oil/water interface increased the α-helical content resulting in an improved thermal stability. The encapsulating agents and spray-drying process did not modify the conformation of WPCH at the oil/water interface. Nonetheless, electrospraying affected the SRCD spectra obtained for WPCH adsorbed at the oil/water interface., I + D + i project CTQ2017-87076-R MCIN/AEI/10.13039/501100011033 PRE2018-084861 730872, European Commission

Encapsulins are protein nanocages capable of harboring smaller proteins (cargo proteins) within their cavity. The function of the encapsulin systems is related to the encapsulated cargo proteins. The Myxococcus xanthus encapsulin (EncA) naturally encapsulates ferritin-like proteins EncB and EncC as cargo, resulting in a large iron storage nanocompartment, able to accommodate up to 30,000 iron atoms per shell. In the present manuscript we describe the binding and protection of circular double stranded DNA (pUC19) by EncA using electrophoretic mobility shift assays (EMSA), atomic force microscopy (AFM), and DNase protection assays. EncA binds pUC19 with an apparent dissociation constant of 0.3 ± 0.1 µM and a Hill coefficient of 1.4 ± 0.1, while EncC alone showed no interaction with DNA. Accordingly, the EncAC complex displayed a similar DNA binding capacity as the EncA protein. The data suggest that initially, EncA converts the plasmid DNA from a supercoiled to a more relaxed form with a beads-on-a-string morphology. At higher concentrations, EncA self-aggregates, condensing the DNA. This process physically protects DNA from enzymatic digestion by DNase I. The secondary structure and thermal stability of EncA and the EncA−pUC19 complex were evaluated using synchrotron radiation circular dichroism (SRCD) spectroscopy. The overall secondary structure of EncA is maintained upon interaction with pUC19 while the melting temperature of the protein (Tm) slightly increased from 76 ± 1 °C to 79 ± 1 °C. Our work reports, for the first time, the in vitro capacity of an encapsulin shell to interact and protect plasmid DNA similarly to other protein nanocages that may be relevant in vivo.

A new synchrotron-based photoionization spectrum of 6,6-dimethylfulvene shows significant vibrational fine structure (VFS), in contrast to previous studies; this was successfully analysed by Franck-Condon (FC) methods. The sequence of ionic states in the range 7 to 19 eV has been determined by both symmetry adapted cluster configuration interaction and density functional methods, especially using the long-range corrected version of the Becke three-parameter hybrid functional (B3LYP) using the Coulomb-attenuating method (CAM-B3LYP). Both lead to reliable theoretical values for both the calculated vertical and adiabatic ionization energies. The FC profile for the lowest ionization energy (IE1, X2A2) shows extensive VFS which is analysed successfully. The second IE (A2B1) shows truncated structure owing to overlap with IE1.

DNA-binding proteins from starved cells (Dps) are members of the ferritin family of proteins found in prokaryotes, with hollow rounded cube-like structures, composed of 12 equal subunits. These protein nanocages are bifunctional enzymes that protect the cell from the harmful reaction of iron and peroxide (Fenton reaction), thus preventing DNA damage by oxidative stress. Ferrous ions are oxidized at specific iron-binding sites in the presence of the oxidant and stored in its cavity that can accommodate up to ca. 500 iron atoms. DNA-binding properties of Dps are associated with the N-terminal, positive charge rich, extensions that can promote DNA binding and condensation, apparently by a cooperative binding mechanism. Here, we describe the binding and protection activities of Marinobacter hydrocarbonoclasticus Dps using Electrophoretic Mobility Shift Essays (EMSA), and synchrotron radiation circular dichroism (SRCD) spectroscopy. While no DNA condensation was observed in the tested conditions, it was possible to determine a Dps–DNA complex formation with an apparent dissociation constant of 6.0 ± 1.0 µM and a Hill coefficient of 1.2 ± 0.1. This interaction is suppressed by the inclusion of a single negative charge in the N-terminal region by point mutation. In Dps proteins containing a ferric mineral core (above 96 Fe/protein), DNA binding was impaired. SRCD data clearly showed that no significant modification existed either in secondary structure or protein stability of WT, Q14E variant and core containing proteins. It was, however, interesting to note that, in our experimental conditions, thermal denaturation induced protein aggregation that caused artifacts in thermal denaturation curves, which were dependent on radiation flux and vertical arrangement of the CD cell.

We report a comprehensive study on the electronic excited states of tetrafluoro-1,4-benzoquinone, through high-resolution vacuum ultraviolet photoabsorption spectroscopy and time-dependent density functional theory calculations performed within the nuclear ensemble approach. Absolute cross section values were experimentally determined in the 3.8-10.8 eV energy range. The present experimental results represent the highest resolution data yet reported for this molecule and reveal previously unresolved spectral structures. The interpretation of the results was made in close comparison with the available data forpara-benzoquinone [Joneset al.,J. Chem. Phys., 2017,146, 184303]. While the dominant absorption features for both molecules arise from analogous π* ← π transitions, some remarkable differences have been identified. The perfluoro effect manifests in different ways: shifts in band positions and cross sections, appearance of features associated with excitations to σ CF* orbitals, and spectrum broadening by quenching of either vibrational or Rydberg progressions. The level of agreement between experiment and theory is very satisfactory, yet that required the inclusion of nuclear quantum effects in the calculations. We have also discussed the role of temperature on the absorption spectrum, as well as the involvement of core-excited resonances in promoting dissociative electron attachment reactions in the 3-5 eV range.

Many experimental parameters determine the chemical and physical properties of interstellar ice analogues, each of which may influence the molecular synthesis that occurs in such ices. In part 1, James et al., RSC Adv., 2020, 10, 37517, we demonstrated the effects that the stoichiometric mixing ratio had on the chemical and physical properties of CO2 : NH3 mixtures and the impact on molecular synthesis induced by thermal processing. Here, in part 2, we extend this to include 1 keV electron irradiation at 20 K of several stoichiometric mixing ratios of CO2 : NH3 ices followed by thermal processing. We demonstrate that not all stoichiometric mixing ratios of CO2 : NH3 ice form the same products. Not only did the 4 : 1 ratio form a different residue after thermal processing, but O3 was observed after electron irradiation at 20 K, which was not observed in the other ratios. For the other ratios, the residue formed from a thermal reaction similar to the work shown in Part 1. However, conversion of ammonium carbamate to carbamic acid was hindered due to electron irradiation at 20 K. Our results demonstrate the need to systematically investigate stoichiometric mixing ratios to better characterise the chemical and physical properties of interstellar ice analogues to further our understanding of the routes of molecular synthesis under different astrochemical conditions.

Encapsulins are protein nanocages capable of harboring smaller proteins (cargo proteins) within their cavity. The function of the encapsulin systems is related to the encapsulated cargo proteins. The

Membrane-mediated assembly has been well characterised for toxic amyloid species such as the amyloid-β peptide implicated in Alzheimer's disease. However, little is known about the membrane-mediated assembly of functional-amyloid forming peptides, recently identified as a natural storage state for neuropeptide hormones in vivo. Here, we study the aggregation of somatostatin-14 (SST-14) co-incubated with model lipid membranes. Atomic force microscopy (AFM) studies confirmed that nanofibrils formed in the presence of various lipid membranes display reduced fibrillogenesis and promote the formation of non-fibrillar oligomers. Both circular dichroism (CD) and intrinsic tryptophan fluorescence studies confirmed interaction between the peptide and the lipid bilayer; this interaction appears to drive changes in membrane-mediated aggregation kinetics. We show that both the surface charge of the membrane and chain packing drive changes in the electrostatic and hydrophobic interactions between the peptide and the membrane, and hence the rate of assembly. The similarities in the effect of the lipid membrane on aggregation of functional amyloids and the more well studied toxic amyloids suggest strong aggregation modifying lipid bilayer interactions are a ubiquitous feature of all amyloid fibrils and highlight the need for further investigation as to why this leads to toxicity in some systems and not others.

The interplay between multiple chromophores in nucleic acids and photosynthetic proteins gives rise to complex electronic phenomena and largely governs the de-excitation dynamics. Electronic coupling between bases in the excited states of single strands of DNA and RNA may extend over several bases and likely protects nucleic acids from harmful UV damage. Here we report on the coupling between bases in single RNA strands of cytosine and find that the excited state is delocalized over up to five bases at neutral pH, where all bases are non-protonated (i.e. neutral). Delocalization is over four bases at 278 nm excitation, while it involves five bases at shorter wavelengths of 188 nm and 201 nm. This is in contrast to only nearest-neighbour interactions for corresponding DNA strands as previously reported. The current results seemingly corroborate earlier findings of larger spatial communication in RNA than in DNA strands of adenine, but there is no obvious link between the overall structure of strands and delocalization lengths. RNA cytosine strands form a tight helix, while comparatively, adenine strands show less tight packing, also compared to their DNA counterparts, and yet exhibit even higher delocalisation.

This work was part of PROVIDE (Protein valorization through informatics, hydrolysis, and separation) project, which is supported by Innovation Fund Denmark (Grant No.: 7045-00021B) . We acknowledge ISA, Centre for Storage Ring Facilities in Aarhus, Denmark, for granting the beam time (Grant No.: ISA-20-1005) . We thank Lis Berner for her help in the lab with the production and physicochemical characterization of the emulsions. We also acknowledge the companies involved and provided the original samples used as source materials: KMC Kartoffelmelcentralen amba (Brande, Denmark) , AKV Langholt amba (Langholt, Denmark) , CP Kelco (Lille Skensved, Denmark) , Unibio A/S (Odense, Denmark) , and Lihme Protein Solutions (Kgs. Lyngby, Denmark) ., In this study, we used a combination of quantitative proteomics and bioinformatic prediction for identifying novel antioxidant peptides. Thirty-five peptides from potato, seaweed, microbial, and spinach proteins were investigated. Based on high DPPH radical scavenging activity (IC50 ≤ 16 mg/mL), metal chelation activity, isoelectric point, and high relative abundance in the parent protein sources, 11 peptides were selected. Lipid oxidation retardation was evaluated in 5% fish oil-in-water emulsions stabilized with Tween 20, where emulsion physical stability was unaffected by peptide addition. The secondary structure of selected peptides was similar in the aqueous solution and emulsions, as confirmed by synchrotron radiation circular dichroism spectroscopy. The emulsions containing the selected peptides had lower levels of hydroperoxides and volatile compounds during storage compared to the control (without peptide). This study contributes to elucidating the effect of antioxidant peptides in emulsions and demonstrates the ability of quantitative proteomics and bioinformatics prediction to identify peptides with strong antioxidant properties., Innovation Fund Denmark 7045-00021B, ISA, Centre for Storage Ring Facilities in Aarhus, Denmark ISA-20-1005

A synchrotron-based photoionization spectrum of azulene shows a significant additional vibrational fine structure when compared to previous studies. This spectrum was successfully analyzed by using Franck–Condon (FC) methods. Previously reported zero-kinetic-energy electron spectra for azulene have been reinterpreted in FC terms, leading to some alternative assignments to the earlier work. The sequence of ionic states has been determined by using ab initio configuration interaction (CI) methods, leading to reliable theoretical values for both the calculated adiabatic ionization energy (AIE) and vertical ionization energy (VIE). VIEs were calculated by both symmetry-adapted cluster (SAC-CI), together with Green’s function (GF) and Tamm–Dancoff approximation (TDA), and single excitation CI methods; AIEs for highest states of each symmetry were determined by open-shell self-consistent field (SCF) methods at the restricted Hartree–Fock level. Complete active space SCF was used for the pairs of 12A2 + 22A2 and 12B1 + 22B1 states, each of which occurs as antisymmetric and symmetric (higher energy) combinations. The combined ionic state sequences (AIE and VIE) from these methods are 12A2 < 12B1 < 22A2 < 22B1. The photoelectron spectrum (PES) shows a series of broadbands above 11 eV, each of which is attributed to more than one ionization. The calculated PES sequence of states of up to 19 eV shows that the SAC-CI and GF results are in almost exact agreement. The internal spacing of the bands is best reproduced by the simpler GF and TDA methods. States involving simultaneous ionization and electronic excitation are considered by both SAC-CI and TDA methods.

Interactions between proteins and single-stranded DNA (ssDNA) are crucial for many fundamental biological processes, including DNA replication and genetic recombination. Thus, understanding detailed mechanisms of these interactions is necessary to uncover regulatory rules occurring in all living cells. The RNA-binding Hfq is a pleiotropic bacterial regulator that mediates many aspects of nucleic acid metabolism. The protein notably mediates mRNA stability and translation efficiency by using stress-related small regulatory RNA as cofactors. In addition, Hfq helps to compact double-stranded DNA. In this paper, we focused on the action of Hfq on ssDNA. A combination of experimental methodologies, including spectroscopy and molecular imaging, has been used to probe the interactions of Hfq and its amyloid C-terminal region with ssDNA. Our analysis revealed that Hfq binds to ssDNA. Moreover, we demonstrate for the first time that Hfq drastically changes the structure and helical parameters of ssDNA, mainly due to its C-terminal amyloid-like domain. The formation of the nucleoprotein complexes between Hfq and ssDNA unveils important implications for DNA replication and recombination.

We investigate for the first time the gas-phase lowest-lying valence, Rydberg and ionic electronic states of 2,4,6-trichloroanisole (TCA) using synchrotron radiation for photoabsorption and photoelectron spectroscopy. The high-resolution vacuum ultraviolet photoabsorption spectrum, in the 4.0-10.8 eV energy-range, has been measured with absolute photoabsorption cross-sections and, thanks to novel ab initio calculations of the vertical energies and oscillator strengths, an assignment of the electronic transitions is comprehensively reported. The assignment of weak vibrational features in the absorption bands of TCA reveal that the ring and C-Cl stretching modes are mainly active. In the photoelectron spectrum the lowest 18 ionic bands, between 8 and 30 eV, have been observed and assigned using the first set of calculated valence and outer valence vertical ionisation energies. Finally, the measured absolute photoabsorption cross sections have also been used to estimate the photolysis lifetime of TCA in the upper stratosphere (20-50 km). Crown Copyright (C) 2021 Published by Elsevier Ltd. All rights reserved.

Ices are widely present in the cold regions across the Universe, for instance, in the interstellar medium as mantles on interstellar and circumstellar dust and on the surfaces of small bodies of the Solar System - beyond the distance around 3-5 AU known as the “snowline" (i.e. at temperatures below 150-170 K). The continuous energetic processing of icy objects in the Solar System induces physical and chemical changes within the ice. Laboratory experiments that simulate energetic processing (ions, photons, and electrons) of ices are therefore essential for interpreting and directing future astronomical observations. Here we provide vacuum ultraviolet (VUV) and UV-Vis photoabsorption spectroscopic data of pristine and energetically processed (electron irradiated) space-related ices. Experiments were performed using a custom-made Portable Astrochemistry Chamber (PAC), which has a base pressure of 10-9 mbar. Photoabsorption spectra of ices were measured at the AU-UV beam line of the ASTRID2 synchrotron light source at Aarhus University in Denmark (see Eden et al. 2006; Palmer et al. 2015). We present the results of three series of experiments: one dedicated to the study of nitrogen- and oxygen-rich ices (Ioppolo et al., 2020); the other one to the spectroscopic study of carbonic acid as formed and destroyed under conditions relevant to space (Ioppolo et al., 2021); and the third one to the study of photoabsorption spectra of O2 ice, both pure and mixed with other species (Migliorini et al, 2021). Results are discussed in light of their relevance to various astrophysical environments, e.g., the icy moons of Saturn and Jupiter. Laboratory VUV-UV-vis spectra of ices can help their future identification on the surface of icy objects in the Solar System by the upcoming Jupiter ICy moons Explorer mission and on interstellar dust by the James Webb Space Telescope spacecraft. This research was partly supported by the Italian Space Agency (Grant ASI-INAF n. 2018-25-HH-0). REFERENCES: Eden, S., Limão-Vieira, P., Hoffmann, S. V., & Mason, N. J. 2006, Chem. Phys., 323, 313 Ioppolo, S., Kanuchova Z., James, R.L., Dawes, A., Jones, N.C., Hoffmann, S.V., Mason, N.J., Strazzulla, G. 2020, Astron. Astrophys. 641, A154 Ioppolo, S., Kanuchova Z., James, R.L., Dawes, A., Ryabov, A., Dezalay, J., Jones, N.C., Hoffmann, S.V., Mason, N.J., Strazzulla, G. 2021, Astron. Astrophys. 645, A172 Migliorini, A., Kanuchova Z., Ioppolo, S., Jones, N.C., Hoffmann, S.V., Tosi, F., Piccioni, G., Barbieri, M. 2021, Icarus, submitted Palmer, M. H., Ridley, T., Hoffmann, S. V., et al. 2015, J. Chem. Phys., 142, 134302

The electronic spectrum of tetrathiafulvalene (TTF) oriented in a polyethylene film is characterized experimentally using synchrotron radiation linear dichroism from the near-UV to the vacuum-UV region to 56,500 cm–1 (177 nm). The non-planar TTF molecule is shown to have electronic transitions of significant intensity polarized along all three molecular symmetry axes. A procedure for processing linear dichroic data to obtain partial absorbance curves representing different polarization directions is exemplified. The overlapping contributions to eight individual spectral features are furthermore interpreted by the aid of time-dependent density functional theory using CAM-B3LYP/6-311++G(3df,3pd) with geometry optimized at the B3LYP / 6-311++G(3df,3pd) level within the C2v point group. Additional calculations using larger basis sets as well as other long-range corrected functionals (LC-ωPBE and ωB97XD) yielded similar results. The planar conformer with D2h symmetry is also considered and it is discussed that rapid equilibration via this transition state may contribute to the diffuse nature of some features of the electronic spectrum. The TTF molecule is a dynamic and 3-dimensional chromophore, and these characteristics may serve as a basis for understanding the optical properties of the numerous TTF-based materials finding applications in supramolecular chemistry, molecular electronics and beyond.

PTDC/FIS‐ AQM/31281/2017 PD/00193/2012 We report absolute photoabsorption cross sections for gas‐phase 2‐ and 5‐ bromopyrimidine in the 3.7–10.8 eV energy range, in a joint theoretical and experimental study. The measurements were carried out using high‐resolution vacuum ultraviolet synchrotron radiation, with quantum chemical calculations performed through the nuclear ensemble approach in combination with time‐dependent density functional theory, along with additional Franck–Condon Herzberg–Teller calculations for the first absorption band (3.7–4.6 eV). The cross sections of both bromopyrimidines are very similar below 7.3 eV, deviating more substantially from each other at higher energies. In the 7.3–9.0 eV range where the maximum cross‐section is found, a single and broad band is observed for 5‐bromopyrimidine, while more discernible features appear in the case of 2‐bromopyrimidine. Several π* ← π transitions account for the most intense bands, while weaker ones are assigned to transitions involving the nitrogen and bromine lone pairs, the antibonding σ*Br orbital, and the lower‐lying Rydberg states. A detailed comparison with the available photo‐absorption data of bromobenzene is also reported. We have found significant differences regarding the main absorption band, which is more peaked in bromobenzene, becoming broader and shifting to higher energies in both bromopyrimidines. In addition, there is a significant suppression of vibrational structures and of Rydberg states in the pair of isomers, most noticeably for 2‐bromopyrimidine. publishersversion published

3-Bromopyruvic acid (3BP) is a potential anti-cancer drug, the action of which on cellular metabolism is not yet entirely clear. The presence of a bromine atom suggests that it is also reactive towards low-energy electrons, which are produced in large quantities during tumour radiation therapy. Detailed knowledge of the interaction of 3BP with secondary electrons is a prerequisite to gain a complete picture of the effects of 3BP in different forms of cancer therapy. Herein, dissociative electron attachment (DEA) to 3BP in the gas phase has been studied both experimentally by using a crossed-beam setup and theoretically through scattering and quantum chemical calculations. These results are complemented by a vacuum ultraviolet absorption spectrum. The main fragmentation channel is the formation of Br − close to 0 eV and within several resonant features at 1.9 and 3–8 eV. At low electron energies, Br − formation proceeds through σ* and π* shape resonances, and at higher energies through core-excited resonances. It is found that the electron-capture cross-section is clearly increased compared with that of non-brominated pyruvic acid, but, at the same time, fragmentation reactions through DEA are significantly altered as well. The 3BP transient negative ion is subject to a lower number of fragmentation reactions than those of pyruvic acid, which indicates that 3BP could indeed act by modifying the electron-transport chains within oxidative phosphorylation. It could also act as a radio-sensitiser.

The formation of a mature myelin sheath in the vertebrate nervous system requires specific protein-membrane interactions. Several myelin-specific proteins are involved in stacking lipid membranes into multilayered structures around axons, and misregulation of these processes may contribute to chronic demyelinating diseases. Two key proteins in myelin membrane binding and stacking are the myelin basic protein (MBP) and protein zero (P0). Other factors, including Ca 2+ , are important for the regulation of myelination. We studied the effects of ionic strength and Ca 2+ on the membrane interactions of MBP and the cytoplasmic domain of P0 (P0ct). MBP and P0ct bound and aggregated negatively charged lipid vesicles, while simultaneously folding, and both ionic strength and calcium had systematic effects on these interactions. When decreasing membrane net negative charge, the level and kinetics of vesicle aggregation were affected by both salt and Ca 2+ . The effects on lipid membrane surfaces by ions can directly affect myelin protein-membrane interactions, in addition to signalling effects in myelinating glia.

The UV absorbance bands of dibenzo-p-dioxin (dibenzo-1,4-dioxin, DD) are investigated by synchrotron radiation linear dichroism (SRLD) spectroscopy on molecular samples aligned in stretched polyethylene. The investigation covers the range 58,000–30,000 cm−1 (170–330 nm), thereby providing new information on the transitions of DD in the vacuum UV region. The observed polarization data enable experimental symmetry assignments of the observed transitions, leading to revision of previously published assignments by Ljubic and Sabljic (J. Phys. Chem. A 109 (2005) 8209-8217). In general, the experimental spectra are well predicted by the results of quantum chemical calculations using time-dependent density functional theory (TD–DFT). The observed absorbance in the region 58,000–55,000 cm−1 (170–180 nm) in the vacuum UV is almost entirely short-axis polarized, in pleasing agreement with the predicted spectrum.

Photoabsorption spectra of isoflurane and sevoflurane have been measured with synchrotron radiation over the photon range 5.0–10.8 eV. Low-lying excited singlet valence and Rydberg states are investigated and the assignments supported by quantum chemical calculations, the latter also helping to identify the triplet states. This provides the first comprehensive investigation of all excited electronic states up to the first ionisation energy. The Rydberg series converging to the ionisation energy limits are identified according to the magnitude of the quantum defects. The measured absolute cross-sections have been used to calculate the photolysis lifetimes of isoflurane and sevoflurane in the Earth’s atmosphere.

The response of CueR towards environmental changes in solution was investigated. CueR is a bacterial metal ion selective transcriptional metalloregulator protein, which controls the concentration of copper ions in the cell. Although several articles have been devoted to the discussion of the structural and functional features of this protein, CueR has not previously been extensively characterized in solution. Here, we studied the effect of change in pH, temperature, and the presence of specific or non-specific binding partners on the secondary structure of CueR with circular dichroism (CD) spectroscopy. A rather peculiar reversible pH-dependent secondary structure transformation was observed, elucidated and supplemented with pKa estimation by PROPKA and CpHMD simulations suggesting an important role of His(76) and His(94) in this process. CD experiments revealed that the presence of DNA prevents this structural switch, suggesting that DNA locks CueR in the α-helical-rich form. In contrast to the non-cognate metal ions HgII, CdII and ZnII, the presence of the cognate AgI ion affects the secondary structure of CueR, most probably by stabilizing the metal ion and DNA-binding domains of the protein.

Iron–sulfur centers are widespread in living organisms, mostly performing electron transfer functions, either in electron transfer chains or as part of multi-enzymatic complexes, while being also present in enzyme active sites, handling substrate catalysis. Rubredoxin is the simplest iron–sulfur containing protein constituted by a single polypeptide chain of 50 to 60 amino acids, of which four cysteine residues are responsible for metal binding in a tetrahedral coordination sphere. In this manuscript we explore the structure and stability of both apo- and holo-forms of a Rubredoxin from Marinobacter hydrocarbonoclasticus using Synchrotron Radiation Circular Dichroism (SRCD) in combination with other biochemical and spectroscopic techniques. The results are consistent with a holo-protein form containing a monomeric iron center with UV–visible maxima at 760, 578, 494, 386, 356 and 279 nm, an intense EPR resonance with a g value around 4.3 and Mossbauer spectroscopy parameters of δ equal to 0.69 mm/s and ΔEQ equal to 3.25 mm/s, for the ferrous reconstituted state. SRCD data, obtained for the first time for the apo-form, show a quite defined structure with ∆e maximum at 191 nm and minima at 203 and 231 nm. Most significantly, the presence of isosbestic points at 189 and 228 nm made the interconversion between the two stable apo- and holo-form solution structures clear. SRCD temperature dependence data shows that for both forms the denaturation process proceeds through an intermediate species.

The growing global threat of antimicrobial resistance, combined with the slowed development of novel antibiotics, has resulted in a critical need for new antimicrobial therapies. Naturally occurring antimicrobial peptides (AMPs) can act as highly potent, broad-spectrum antibiotics which may be less likely to engender resistance in target organisms. However, their susceptibility to proteolysis and lack of specificity necessitates the use of a drug delivery vehicle to both protect the AMP from chemical degradation and provide a platform for further functionalization, enabling the development of targeted delivery and release systems. In this study, we have used lipid-based inverse bicontinuous cubic phase nanoparticles (cubosomes) as delivery vehicles for six different antimicrobial peptides. The phase stability, morphology, and peptide loading efficiency of the nanoparticles were characterized and rationalized according to lipid composition, buffer conditions, as well as peptide charge and hydrophobicity. The AMP loading efficiency within cubosomes was increased significantly through simple manipulation of electrostatic charge. Minimum inhibitory concentration (MIC) values were determined for formulations with high loading efficiency against Staphylococcus aureus, Bacilus cereus, Escherichia coli, and Pseudomonas aeruginosa. Encapsulation within a lipid nanocarrier was shown to increase antimicrobial activity for some formulations. We anticipate that the further development of these peptide loaded cubosomes will enable the design of potent and targeted antibiotic therapies.

Layer-by-layer films of poly (allylamine hydrochloride) (PAH) and graphene oxide (GO) were characterized, looking at growth with the number of bilayers, morphology, and electrical properties. The PAH/GO films revealed a linear increase in absorbance with the increase in the number of deposited bilayers, allowing the determination that 10.7 ± 0.1 mg m−2 of GO is adsorbed per unit of area of each bilayer. GO absorption bands at 146, 210, 247 and 299 nm, assigned to π-π* and n-π* transitions in the aromatic ring (phenol) and of the carboxylic group, respectively, were characterized by vacuum ultraviolet spectroscopy. The morphological characterization of these films demonstrated that they are not completely uniform, with a bilayer thickness of 10.5 ± 0.7 nm. This study also revealed that the films are composed of GO and/or PAH/GO fibers and that GO is completely adsorbed on top of PAH. The electrical properties of the films reveal that PAH/GO films present a semiconductor behavior. In addition, a slight decrease in conduction was observed when films were prepared in the presence of visible light, likely due to the presence of oxygen and moisture that contributes to the damage of GO molecules. publishersversion published

International audience; We investigated the role of the interfacial properties of ten synthetic potato peptides (previously identified by bioinformatics) to physically and oxidatively stabilize 5 wt% fish oil-in-water emulsions (pH 7). Peptides alpha 10, alpha 12, gamma 1, gamma 75 and gamma 76 adopted a predominantly a-helical conformation (48-57%) at the interface leading to poor inter-peptides interactions as well as weak and stretchable interfaces (E-d* < 12mN/m). Peptides beta 22, beta 27, gamma 36 and gamma 38 displayed a significantly higher degree of interfacial inter-peptide interaction, resulting in stiff and solid-like interfaces (E-d*, = 35 - 45 mN/m). beta 22 and gamma 36 peptides re-arranged at the interface adopting a highly beta-strand structure (63-65%). Emulsions stabilized with all peptides showed high physical stability during one week (D-3,D-2 at day 1 = 0.134-0.175 mu m), except from the ones stabilized with beta 27 that had creaming after day 1, or beta 22 that destabilized during storage. Emulsions stabilized with peptides exhibiting negative surface charge at pH 7 (alpha 12, beta 22, gamma 1, 775, gamma 76, gamma 36 and 740) (zeta potential: -50.9 to -69.5 mV) showed the lowest oxidative stability due to the attraction of cationic metal ions that catalyzed lipid oxidation. In contrast, emulsions stabilized with peptides having positive surface charge at pH 7 (alpha 10, beta 27 and gamma 38) (zeta potential: 11.6-42.8 mV) showed high oxidative stability (i.e., by repulsion of cationic metal ions), independently of the peptide length, secondary structure at the interface, or viscoelasticity of the interfacial layer. Hence, this work advances our understanding of the relation between interfacial properties of peptide layers and the physicochemical stability of emulsions.

Circularly polarised light (CPL) interacting with interstellar organic molecules might have imparted chiral bias and hence preluded prebiotic evolution of biomolecular homochirality. The l-enrichment of extra-terrestrial amino acids in meteorites, as opposed to no detectable excess in monocarboxylic acids and amines, has previously been attributed to their intrinsic interaction with stellar CPL revealed by substantial differences in their chiroptical signals. Recent analyses of meteoritic hydroxycarboxylic acids (HCAs) – potential co-building blocks of ancestral proto-peptides – indicated a chiral bias toward the l-enantiomer of lactic acid. Here we report on novel anisotropy spectra of several HCAs using a synchrotron radiation electronic circular dichroism spectrophotometer to support the re-evaluation of chiral biomarkers of extra-terrestrial origin in the context of absolute photochirogenesis. We found that irradiation by CPL which would yield l-excess in amino acids would also yield l-excess in aliphatic chain HCAs, including lactic acid and mandelic acid, in the examined conditions. Only tartaric acid would show “unnatural” d-enrichment, which makes it a suitable target compound for further assessing the relevance of the CPL scenario. Enantiomerically-enriched hydroxycarboxylic acids have been found in meteorites, but the possible origin of this asymmetry has not been explored experimentally. Here circular dichroism/anisotropy experiments suggest a common astrochemical mechanism for the generation of enantiomeric excess in hydroxycarboxylic acids and amino acids.

Oral delivery of the protein drug insulin is not currently possible due to rapid degradation of the secondary structure in low pH conditions in the stomach and under the influence of digestive enzymes in the gastrointestinal tract. Effective oral delivery of insulin and other protein- or peptide-based drugs will, therefore, require encapsulation in a material or nanoparticle. Herein we investigate the ability of the lipid bicontinuous cubic phase formed by two lipids, monoolein (MO) and phytantriol (PT), to protect encapsulated insulin from degradation by the enzyme chymotrypsin, typically found in the small intestine. High encapsulation efficiency (>80%) was achieved in both lipid cubic phases with retention of the underlying cubic nanostructure. Release of insulin from the cubic matrix was shown to be diffusion-controlled; the release rate was dependent on the cubic nanostructure and consistent with measured diffusion coefficients for encapsulated insulin. Encapsulation was shown to significantly retard enzymatic degradation relative to that in water, with the protective effect lasting up to 2 h, exemplifying the potential of these materials to protect the encapsulated protein payload during oral delivery.

The spectroscopic properties of chlorophyll (Chl) strongly depend on interactions with other Chl molecules, a fact that nature exploits in light harvesting by photosynthetic proteins. In solution, complex Chl aggregates are formed that depend not only on the solvent, but also on the detailed preparation procedure. Here we report synchrotron radiation circular dichroism (SRCD) spectra of Chlb in methanol (MeOH) and MeOH/H2O mixtures; in the latter, water molecules assist in the formation of Chl aggregates as Chlb is too hydrophobic to dissolve in water. The magnitude of the most prominent CD signal increases up to 100-fold over time (2-15 hours) when the water content is increased from 0 to 50% in volume, the signal is non-conservative (almost exclusively negative), and sensitive to sample preparation. Three different types of signature CD spectra (Types A to C) are identified depending on preparation, and the change in CD signal over time and with temperature is further analyzed with anisotropy spectroscopy (ratio of simultaneously recorded CD to absorption) and principal component analysis (PCA). We show that CD is clearly superior to pure absorption spectroscopy in identifying structural changes, and anisotropy spectroscopy further increases the sensitivity towards smaller structural changes. PCA on temperature dependent CD data show that depending on preparation, and thus the type of aggregate as revealed by the CD signature, either one (Type A) or two chiral species (Type B) are identified in the spectra, further evidencing the complex nature of Chlb aggregates. Furthermore, the CD signal decreases linearly with volume when a sample of Chlb in MeOH/H2O (i.e., a sample of Chlb aggregates) is diluted, which implies that the aggregation process is irreversible: once aggregates are formed, they largely do not revert back to monomers. However, anisotropy spectroscopy reveals that there are small changes in the aggregates, not directly noticeable in CD and absorption. The work presented here demonstrates, compared to absorption spectroscopy, a clear advantage of CD and anisotropy spectroscopy in studying the complex evolution of Chl samples with time and temperature.

The spectroscopic properties of chlorophyll (Chl) strongly depend on interactions with other Chl molecules, a fact that nature exploits in light harvesting by photosynthetic proteins. In solution, complex Chl aggregates are formed that depend not only on the solvent, but also on the detailed preparation procedure. Here we report synchrotron radiation circular dichroism (SRCD) spectra of Chlb in methanol (MeOH) and MeOH/H2O mixtures; in the latter, water molecules assist in the formation of Chl aggregates as Chlb is too hydrophobic to dissolve in water. The magnitude of the most prominent CD signal increases up to 100-fold over time (2-15 hours) when the water content is increased from 0 to 50% in volume, the signal is non-conservative (almost exclusively negative), and sensitive to sample preparation. Three different types of signature CD spectra (Types A to C) are identified depending on preparation, and the change in CD signal over time and with temperature is further analyzed with anisotropy spectroscopy (ratio of simultaneously recorded CD to absorption) and principal component analysis (PCA). We show that CD is clearly superior to pure absorption spectroscopy in identifying structural changes, and anisotropy spectroscopy further increases the sensitivity towards smaller structural changes. PCA on temperature dependent CD data show that depending on preparation, and thus the type of aggregate as revealed by the CD signature, either one (Type A) or two chiral species (Type B) are identified in the spectra, further evidencing the complex nature of Chlb aggregates. Furthermore, the CD signal decreases linearly with volume when a sample of Chlb in MeOH/H2O (i.e., a sample of Chlb aggregates) is diluted, which implies that the aggregation process is irreversible: once aggregates are formed, they largely do not revert back to monomers. However, anisotropy spectroscopy reveals that there are small changes in the aggregates, not directly noticeable in CD and absorption. The work presented here demonstrates, compared to absorption spectroscopy, a clear advantage of CD and anisotropy spectroscopy in studying the complex evolution of Chl samples with time and temperature.

DNA-binding proteins from starved cells (Dps) are members of the ferritin family of proteins found in prokaryotes, with hollow rounded cube-like structures, composed of 12 equal subunits. These protein nanocages are bifunctional enzymes that protect the cell from the harmful reaction of iron and peroxide (Fenton reaction), thus preventing DNA damage by oxidative stress. Ferrous ions are oxidized at specific iron-binding sites in the presence of the oxidant and stored in its cavity that can accommodate up to ca. 500 iron atoms. DNA-binding properties of Dps are associated with the N-terminal, positive charge rich, extensions that can promote DNA binding and condensation, apparently by a cooperative binding mechanism. Here, we describe the binding and protection activities of Marinobacter hydrocarbonoclasticus Dps using Electrophoretic Mobility Shift Essays (EMSA), and synchrotron radiation circular dichroism (SRCD) spectroscopy. While no DNA condensation was observed in the tested conditions, it was possible to determine a Dps-DNA complex formation with an apparent dissociation constant of 6.0 ± 1.0 µM and a Hill coefficient of 1.2 ± 0.1. This interaction is suppressed by the inclusion of a single negative charge in the N-terminal region by point mutation. In Dps proteins containing a ferric mineral core (above 96 Fe/protein), DNA binding was impaired. SRCD data clearly showed that no significant modification existed either in secondary structure or protein stability of WT, Q14E variant and core containing proteins. It was, however, interesting to note that, in our experimental conditions, thermal denaturation induced protein aggregation that caused artifacts in thermal denaturation curves, which were dependent on radiation flux and vertical arrangement of the CD cell.