Abiotic hydrocarbons and carboxylic acids are known to be formed on Earth, notably during the hydrothermal alteration of mantle rocks. Although the abiotic formation of amino acids has been predicted ...both from experimental studies and thermodynamic calculations, its occurrence has not been demonstrated in terrestrial settings. Here, using a multimodal approach that combines high-resolution imaging techniques, we obtain evidence for the occurrence of aromatic amino acids formed abiotically and subsequently preserved at depth beneath the Atlantis Massif (Mid-Atlantic Ridge). These aromatic amino acids may have been formed through Friedel-Crafts reactions catalysed by an iron-rich saponite clay during a late alteration stage of the massif serpentinites. Demonstrating the potential of fluid-rock interactions in the oceanic lithosphere to generate amino acids abiotically gives credence to the hydrothermal theory for the origin of life, and may shed light on ancient metabolisms and the functioning of the present-day deep biosphere.
Abstract
Circular dichroism (CD) spectroscopy is widely used to characterize the secondary structure composition of proteins. To derive accurate and detailed structural information from the CD ...spectra, we have developed the Beta Structure Selection (BeStSel) method (PNAS, 112, E3095), which can handle the spectral diversity of β-structured proteins. The BeStSel webserver provides this method with useful accessories to the community with the main goal to analyze single or multiple protein CD spectra. Uniquely, BeStSel provides information on eight secondary structure components including parallel β-structure and antiparallel β-sheets with three different groups of twist. It overperforms any available method in accuracy and information content, moreover, it is capable of predicting the protein fold down to the topology/homology level of the CATH classification. A new module of the webserver helps to distinguish intrinsically disordered proteins by their CD spectrum. Secondary structure calculation for uploaded PDB files will help the experimental verification of protein MD and in silico modelling using CD spectroscopy. The server also calculates extinction coefficients from the primary sequence for CD users to determine the accurate protein concentrations which is a prerequisite for reliable secondary structure determination. The BeStSel server can be freely accessed at https://bestsel.elte.hu.
Graphical Abstract
Graphical Abstract
Functions of the BeStSel web server for the analysis of protein CD spectra.
Abstract Food-grade titanium dioxide (TiO 2 ) containing a nanoscale particle fraction (TiO 2 -NPs) is approved as a white pigment (E171 in Europe) in common foodstuffs, including confectionary. ...There are growing concerns that daily oral TiO 2 -NP intake is associated with an increased risk of chronic intestinal inflammation and carcinogenesis. In rats orally exposed for one week to E171 at human relevant levels, titanium was detected in the immune cells of Peyer’s patches (PP) as observed with the TiO 2 -NP model NM-105. Dendritic cell frequency increased in PP regardless of the TiO 2 treatment, while regulatory T cells involved in dampening inflammatory responses decreased with E171 only, an effect still observed after 100 days of treatment. In all TiO 2 -treated rats, stimulation of immune cells isolated from PP showed a decrease in Thelper (Th)-1 IFN-γ secretion, while splenic Th1/Th17 inflammatory responses sharply increased. E171 or NM-105 for one week did not initiate intestinal inflammation, while a 100-day E171 treatment promoted colon microinflammation and initiated preneoplastic lesions while also fostering the growth of aberrant crypt foci in a chemically induced carcinogenesis model. These data should be considered for risk assessments of the susceptibility to Th17-driven autoimmune diseases and to colorectal cancer in humans exposed to TiO 2 from dietary sources.
Leonardo da Vinci (1452-1519) is a key artistic and scientific figure of the Renaissance. He is renowned for his science of art, taking advantage of his acute observations of nature to achieve ...striking pictorial results. This study describes the analysis of an exceptional sample from one of Leonardo's final masterpieces: The Virgin and Child with St. Anne (Musée du Louvre, Paris, France). The sample was analyzed at the microscale by synchrotron-based hyperspectral photoluminescence imaging and high-angular X-ray diffraction. The results demonstrate Leonardo's use of two subtypes of lead white pigment, thus revealing how he must have possessed a precise knowledge of his materials; carefully selecting them according to the aesthetical results he aimed at achieving in each painting. This work provides insights on how Leonardo obtained these grades of pigment and proposes new clues regarding the optical and/or working properties he may have tried to achieve.
Electronic circular dichroism (CD) spectroscopy is an important tool for the elucidation of biomolecular structure. This review describes the latest progress and developments in experimental and ...theoretical studies of proteins using CD spectroscopy, including time-resolved measurements, oriented CD, and state-of-the-art experiments using polarized UV light from high-energy synchrotron radiation. Statistical and machine learning methods for the analysis of experimental spectra are surveyed. Computational methods employed to predict CD spectra from structure include ab initio quantum chemistry techniques, time-dependent density functional theory, and exciton theory. We describe recent computations using exciton theory, where we outline the importance of electronic-vibrational coupling and the influence of electrostatics of the protein environment on the electronic transitions in the chromophores responsible for CD signals in the near UV. Improvements in the accuracy of the computational approaches should allow more quantitative studies, applying a combination of experimental data and modeling to a variety of interesting questions.
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Circular dichroism (CD) is an important spectroscopic technique that enables the characterization of protein secondary and tertiary structure. Proteins can undergo changes in their structure when they participate in processes, for example, ligand binding. CD, therefore, can be used to monitor secondary and tertiary structural changes when a protein (receptor) binds to a drug molecule (ligand).
This review describes experimental studies of protein CD and theoretical and computational methods that compute spectra from structure or structure from spectra. CD is a technique that can be used to complement X-ray, NMR, and ultraviolet-visible (UV-vis) experiments on biomolecules and proteins, all of which can be assisted by molecular modeling, which has the capability of computing CD from first principles. A combination of experimental CD and molecular modeling has the capacity to greatly enhance future multi-disciplinary research to expand our knowledge of the structure, function, and dynamics of proteins.
Circular dichroism is a spectroscopic technique that is used to study the structure of proteins and how that structure changes in various biologically important processes. Structural elements are studied using different wavelengths of light: secondary structure (regular, local geometrical arrangements of amino acids) using far ultraviolet; and tertiary structure (including the interactions of aromatic amino acid side chains) using near ultraviolet. This review outlines recent state-of-the-art experimental and theoretical studies of protein circular dichroism.
Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition ...from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structureârich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides.
Significance Circular dichroism (CD) spectroscopy is widely used for protein secondary structure analysis. However, quantitative estimation for β-sheetâcontaining proteins is problematic due to the huge morphological and spectral diversity of β-structures. We show that parallel/antiparallel orientation and twisting of β-sheets account for the observed spectral diversity. Taking into account the twist of β-structures, our method accurately estimates the secondary structure for a broad range of protein folds, particularly for β-sheetârich proteins and amyloid fibrils. Moreover, the method can predict the protein fold down to the topology level following the CATH classification. We provide a general tool for a quick and reliable structure analysis using conventional or synchrotron radiation CD spectroscopy, which is especially useful when X-ray or NMR techniques fail.
The (auto)fluorescence from three diatom strains, Cyclotella meneghiniana (Cm), Phaeodactylum tricornutum 1a (Pt1a), and Phaeodactylum UTex (PtUTex), has been imaged in vivo to submicrometer ...resolution using confocal laser scanning fluorescence (CLSF) microscopy. The diatoms are excited at 473 and 532 nm, energy primarily absorbed by the carotenoid fucoxanthin (Fx) found within the fucoxanthin chlorophyll a/c proteins (FCPs). On the basis of the fluorescence spectra measured in each image voxel, we obtain information about the spatial and energetic distribution of the terminal Chl a emitters, localized in the FCPs and the reaction centers of the PSII protein complexes, and the nature and location of the primary absorbers that are linked to these emitters; 532 nm excites the highly efficient Fx(red) light harvesters, and lesser amounts of Fx(green)s, that are enriched in some FCPs and preferentially transfer energy to PSII, compared to 473 nm, which excites almost equal amounts of all three previously identified sets of Fx--Fx(red), Fx(green) and Fx(blue)--as well as Chl c. The heterogeneous Chl a emission observed from the (C)LSF images indicates that the different Fx's serve different final emitters in P. tricornutum and suggest, at least in C. meneghiniana , a localization of FCPs with relatively greater Fx(red) content at the chloroplast edges, but with overall higher FCP concentration in the interior of the plastid. To better understand our results, the concentration-dependent ensemble-averaged diatom solution spectra are compared to the (auto)fluorescence spectra of individual diatoms, which indicate that pigment packing effects at an intracellular level do affect the diatoms' spectral properties, in particular, concerning a 710 nm emission band apparent under stress conditions. A species-specific response of the spectral signature to the incident light is also discussed in terms of the presence of a silica shell in Cm but not in Pt1a nor PtUTex.
Weight of evidence: Using synchrotron radiation, photo‐fragmentation of an intrinsically disordered protein is probed and compared with classical tandem mass‐spectrometry activation techniques. It ...provides excellent sequence coverage allowing the identification of the protein noncovalent binding sites.
A main challenge in chemotherapy is to determine the in cellulo parameters modulating the drug concentration required for therapeutic action. It is absolutely urgent to understand membrane permeation ...and intracellular concentration of antibiotics in clinical isolates: passing the membrane barrier to reach the threshold concentration inside the bacterial periplasm or cytoplasm is the pivotal step of antibacterial activity. Ceftazidime (CAZ) is a key molecule of the combination therapy for treating resistant bacteria. We designed and synthesized different fluorescent CAZ derivatives (CAZ*, CAZ**) to dissect the early step of translocation-accumulation across bacterial membrane. Their activities were determined on E. coli strains and on selected clinical isolates overexpressing ß-lactamases. The accumulation of CAZ* and CAZ** were determined by microspectrofluorimetry and epifluorimetry. The derivatives were properly translocated to the periplasmic space when we permeabilize the outer membrane barrier. The periplasmic location of CAZ** was related to a significant antibacterial activity and with the outer membrane permeability. This study demonstrated the correlation between periplasmic accumulation and antibiotic activity. We also validated the method for approaching ß-lactam permeation relative to membrane permeability and paved the way for an original matrix for determining "Structure Intracellular Accumulation Activity Relationship" for the development of new therapeutic candidates.
Renal oxalosis is a rare cause of renal failure whose diagnosis can be challenging. Synchrotron deep ultraviolet (UV) fluorescence was assayed to improve oxalosis detection on kidney biopsies spatial ...resolution and sensitivity compared with the Fourier transform infrared microspectroscopy gold standard. The fluorescence spectrum of synthetic mono‐, di‐ and tri‐hydrated calcium oxalate was investigated using a microspectrometer coupled to the synchrotron UV beamline DISCO, Synchrotron SOLEIL, France. The obtained spectra were used to detect oxalocalcic crystals in a case control study of 42 human kidney biopsies including 19 renal oxalosis due to primary (PHO, n = 11) and secondary hyperoxaluria (SHO, n = 8), seven samples from PHO patients who received combined kidney and liver transplants, and 16 controls. For all oxalocalcic hydrates samples, a fluorescence signal is detected at 420 nm. These spectra were used to identify standard oxalocalcic crystals in patients with PHO or SHO. They also revealed micrometric crystallites as well as non‐aggregated oxalate accumulation in tubular cells. A nine‐points histological score was established for the diagnosis of renal oxalosis with 100% specificity (76–100) and a 73% sensitivity (43–90). Oxalate tubular accumulation and higher histological score were correlated to lower estimated glomerular filtration rate and higher urinary oxalate over creatinine ratio.
Synchrotron deep ultraviolet imaging highlighting pathological calcium oxalate detection in kidney is presented.
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