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The extreme durability of polyethylene terephthalate (PET) debris has rendered it a long-term environmental burden. At the same time, current recycling efforts still lack sustainability. Two recently discovered bacterial enzymes that specifically degrade PET represent a promising solution. First, Ideonella sakaiensis PETase, a structurally well-characterized consensus α/β-hydrolase fold enzyme, converts PET to mono-(2-hydroxyethyl) terephthalate (MHET). MHETase, the second key enzyme, hydrolyzes MHET to the PET educts terephthalate and ethylene glycol. Here, we report the crystal structures of active ligand-free MHETase and MHETase bound to a nonhydrolyzable MHET analog. MHETase, which is reminiscent of feruloyl esterases, possesses a classic α/β-hydrolase domain and a lid domain conferring substrate specificity. In the light of structure-based mapping of the active site, activity assays, mutagenesis studies and a first structure-guided alteration of substrate specificity towards bis-(2-hydroxyethyl) terephthalate (BHET) reported here, we anticipate MHETase to be a valuable resource to further advance enzymatic plastic degradation. Plastic polymer PET degrading enzymes are of great interest for achieving sustainable plastics recycling. Here, the authors present the crystal structures of the plastic degrading bacterial enzymes PETase, MHETase in its apo-form and MHETase bound to a non-hydrolyzable substrate analog.

Protein crystalline frameworks are attractive for biomimetic and nanotechnological studies because they could augment the useful functionalities of numerous proteins through dense packing and uniform orientation. However, their formation and precise structural control is challenging. Here we present novel protein crystalline frameworks with controllable interpenetration. The homotetrameric lectin concanavalin A is crosslinked by predetermined inducing ligands containing monosaccharide and rhodamine groups connected by an oligo(ethylene oxide) spacer. Two non-covalent interactions, that is, sugar–lectin binding and the dimerization of RhB, are responsible for the framework formation. The three-dimensional structure of the framework is fully characterized by X-ray crystallographic methods. For the first time, either interpenetrating or non-interpenetrating frameworks are obtained, and they are controlled by the spacer length of the inducing ligand. Further kinetics and mechanistic investigations reveal that, in the self-assembly process, the carbohydrate–protein binding occurs first, followed by RhB dimerization. This sequence favours rapid crystallization with a high yield when an excess amount of inducing ligand is used. In short, by using well-controlled dual non-covalent interactions, fast and versatile preparation of protein crystalline framework was achieved with high crystallization ratio of the proteins, which may shed light on protein crystallization in near future. Proteins are particularly desirable building blocks for self-assembled biomimetic materials. Here, the authors present crystalline frameworks based on concanavalin A with controllable levels of interpenetration via dual supramolecular interactions.

Although light is a prominent stimulus for smart materials, the application of photoswitches as light-responsive triggers for phase transitions of porous materials remains poorly explored. Here we incorporate an azobenzene photoswitch in the backbone of a metal-organic framework producing light-induced structural contraction of the porous network in parallel to gas adsorption. Light-stimulation enables non-invasive spatiotemporal control over the mechanical properties of the framework, which ultimately leads to pore contraction and subsequent guest release via negative gas adsorption. The complex mechanism of light-gated breathing is established by a series of in situ diffraction and spectroscopic experiments, supported by quantum mechanical and molecular dynamic simulations. Unexpectedly, this study identifies a novel light-induced deformation mechanism of constrained azobenzene photoswitches relevant to the future design of light-responsive materials. The application of photoswitches as light-responsive triggers for phase transitions of porous materials remains poorly explored. Here, the authors report a light-responsive flexible metal-organic framework which undergoes pore contraction upon combined application of light irradiation and adsorption stress via a buckling process of the framework-embedded azobenzene photoswitch.

Understanding the structural and chemical properties of peptide bonds within protein secondary structures is vital for elucidating their roles in protein folding, stability and function. This study examines the distinct characteristics of peptide bonds in α-helices and β-strands using a nonredundant data set comprising 1024 high-resolution protein crystal structures from the Protein Data Bank (PDB). The analysis reveals surprising and intriguing insights into bond lengths, angles, dihedral angles, electron-density distributions and hydrogen bonding within α-helices and β-strands. While the respective bond lengths (CN and CO) do not differ much between helices and strands, the bond angles (∠CNC α and ∠OCN) are significantly larger in strands compared with helices. Furthermore, the peptide dihedral angle (ω) in helices clusters around 180° and follows a sharp Gaussian distribution with a standard deviation of 4.1°. In contrast, the distribution of dihedral angles in strands spans a much wider range, with a more flattened Gaussian peak around 180°. This distinct difference in the distribution of dihedral angles reflects the unique structural characteristics of helices and strands, highlighting their respective conformational preferences. Additionally, if the ratio of the electron-density values (2 mF o − DF c ) at the midpoint of the CO bond and of the CN bond is calculated, a skewed distribution is observed, with the ratio being lower for helices than for strands. Moreover, higher normalized mean atomic displacement parameters (ADPs) for peptide atoms in helices relative to strands suggest increased flexibility or a more dynamic structure within helical regions. Analysis of hydrogen-bond distances between O and N atoms of the main chain reveals larger distances in helices compared with strands, indicative of distinct hydrogen-bonding patterns associated with different secondary structures. All of these observations taken together led us to conclude that peptide bonds in α-helices are different from peptide bonds in β-strands. Overall, α-helical peptide bonds seem to display a more enol-like character. This suggests that peptide oxygen atoms in helices are more likely to be protonated. These findings have several important implications for refining protein structures, particularly in regions susceptible to enol-like transitions or protonation. By recognizing the distinct bond-angle and bond-length variations associated with protonated carbonyl oxygen atoms, current refinement protocols can be adapted to apply more flexible restraints in these regions. This could improve the accuracy of modelling local geometries, where protonation or enol forms lead to subtle structural deviations from the canonical bond parameters typically enforced in refinement strategies.

Fragment screening by crystallography has recently skyrocketed. Multiple synchrotrons have built specialized screening platforms, established workflows, and assembled compound libraries. Crystallographic fragment screening is now widely accessible to groups that had previously not considered the approach. While hundreds of crystallographic fragment-screening campaigns have been conducted in the last few years, most of the underlying data have neither been published nor made publicly accessible. This perspective highlights the importance of establishing effective mechanisms for preserving large and often heterogeneous groups of datasets intrinsic to crystallographic fragment-screening campaigns, thereby ensuring their accessibility for advancing research and enabling applications such as training AI-based models. In the coming years, crystallographic fragment-screening campaigns will deliver massive amounts of data and challenge existing practices and resources. In the article, options are explored for how best to preserve these data for the community to support further research and developments.

Background This study aimed to evaluate the accuracy of procalcitonin (PCT) serum concentrations to diagnose Gram-negative bacteremia and the association of PCT serum concentrations with more specific pathogens and the focus of infection. Methods Secondary analysis of the prospectively collected patient-level dataset from a cluster randomized quality improvement trial was performed. The trial included sepsis patients with organ dysfunction treated in the participating intensive care units from 2011 to 2015. Test performance for the prediction of Gram-negative bacteremia was assessed by receiver operating curve analysis. Independent effects of specific pathogen groups and foci of infection on PCT concentrations were assessed by linear logistic regression models. Results Blood cultures (BC) and PCT concentrations had been taken in 4858 of 6561 documented patients. PCT was significantly higher in Gram-negative bacteremia compared to Gram-positive bacteremia or candidemia ( p  < 0.001). The area under the curve was 0.72 (95% confidence interval 0.71–0.74) for the prediction of Gram-negative bacteremia compared to all other blood culture results including negative blood cultures. The optimized cutoff value was 10 ng/ml (sensitivity 69%, specificity 35%). PCT differed significantly between specific groups of pathogens ( p  < 0.001) with highest concentrations in Escherichia coli , Streptococcus species and other Enterobacteriaceae . PCT was highest in urogenital followed by abdominal infection and lowest in respiratory infection ( p  < 0.001). In a linear regression model, Streptococci, E. coli and other Enterobacteriaceae detected from BC were associated with three times higher PCT values. Urogenital or abdominal foci of infection were associated with twofold increased PCT values independent of the pathogen. Conclusions Serum PCT concentrations are higher in patients with Gram-negative bacteremia than in patients with Gram-positive bacteremia or candidemia. However, the discriminatory power of this difference is too low to guide therapeutic decisions. Variations in PCT serum concentrations are not determined solely by Gram-negative or Gram-positive bacteria but are also affected by distinct groups of pathogens and different foci of infection. Trial registration ClinicalTrials.gov, NCT01187134 . Registered on 23 August 2010.

For a little over a decade now, the Macromolecular Crystallography (MX) group at the Helmholtz-Zentrum Berlin (HZB) has been operating three state-of-the-art synchrotron beamlines for MX at the BESSY II storage ring in Berlin. The three HZB-MX beamlines, BL14.1, BL14.2 and BL14.3, serve a stable and growing user community of currently more than 100 independent research groups from Berlin, Germany and Europe. Every year, the beamlines provide close to 200 days of MX-beamtime. Over time, the HZB-MX beamlines and endstations, in particular BL14.1, have been continually developed and upgraded and, since 2010, they operate as the most productive MX beamlines in Germany. The environment of the beamlines includes various ancillary equipment as well as additional facilities, such as office space adjacent to the beamlines, a sample preparation laboratory, a safety level 1 biology laboratory (HZB-MX BioLab) and all necessary computing resources. In this paper, the current status of the beamlines as well as the ongoing developments are described.

Phytochromes are biliprotein photoreceptors widespread amongst microorganisms and ubiquitous in plants where they control developmental processes as diverse as germination, stem elongation and floral induction through the photoconversion of inactive Pr to the Pfr signalling state. Here we report crystal structures of the chromophore-binding module of soybean phytochrome A, including ~2.2 Å XFEL structures of Pr and Pfr at ambient temperature and high resolution cryogenic structures of Pr. In the Pfr structure, the chromophore is exposed to the medium, the D-ring remaining α-facial following the likely clockwise photoflip. The chromophore shifts within its pocket, while its propionate side chains, their partners as well as three neighbouring tyrosines shift radically. Helices near the chromophore show substantial shifts that might represent components of the light signal. These changes reflect those in bacteriophytochromes despite their quite different signalling mechanisms, implying that fundamental aspects of phytochrome photoactivation have been repurposed for photoregulation in the eukaryotic plant. Phytochrome photoreceptors are master regulators of plant development. This paper describes 3D structures of soybean phytochrome A in both Pr (inactive) and Pfr (signalling) states, revealing changes that might transmit the light signal to the cell.

Since 2003, the Macromolecular Crystallography (MX) group at Helmholtz-Zentrum Berlin (HZB) has been operating three MX beamlines at the BESSY II storage ring in Berlin. These beamlines were established to support the emerging structural genomics initiatives founded in Germany, Europe, and overseas around the turn of the century. Over the past two decades, these beamlines have been continuously developed to enable state-of-the-art diffraction experiments and to provide supporting facilities such as a sample preparation laboratory, a spectroscopy laboratory, a Biosafety Level 1 laboratory and all necessary computing resources for the MX and chemical crystallography user community. Currently, more than 100 independent research groups from the greater Berlin area, Germany, and Europe utilize these beamlines. Over time, more than 4500 Protein Data Bank depositions have been accrued based on data collected at the beamlines. This paper presents historical aspects of the beamlines, their current status including their research output, and future directions.