CH-π hydrogen bonds in biological macromolecules Nishio, Motohiro; Umezawa, Yoji; Fantini, Jacques ...
Physical chemistry chemical physics : PCCP,
07/2014, Letnik:
16, Številka:
25
Journal Article
Recenzirano
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP ...themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
XDSAPP is a Tcl/Tk‐based graphical user interface for the easy and convenient processing of diffraction data sets using XDS. It provides easy access to all XDS functionalities, automates the data ...processing and generates graphical plots of various data set statistics provided by XDS. By incorporating additional software, further information on certain features of the data set, such as radiation decay during data collection or the presence of pseudo‐translational symmetry and/or twinning, can be obtained. Intensity files suitable for CCP4, CNS and SHELX are generated.
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.
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.
Prolidase – A protein with many faces Wilk, Piotr; Wątor, Elżbieta; Weiss, Manfred S.
Biochimie,
April 2021, 2021-Apr, 2021-04-00, 20210401, Letnik:
183
Journal Article
Recenzirano
Prolidase is a metal-dependent peptidase specialized in the cleavage of dipeptides containing proline or hydroxyproline on their C-termini. Prolidase homologues are found in all kingdoms of life. The ...importance of prolidase in human health is underlined by a rare hereditary syndrome referred to as Prolidase Deficiency. A growing number of studies highlight the importance of prolidase in various other human conditions, including cancer. Some recent studies link prolidase’s activity-independent regulatory role to tumorigenesis. Furthermore, the enzyme or engineered variants have some applications in biotechnology. In this short review, we aim to highlight different aspects of the protein the importance of which is increasingly recognized over the last years.
Today the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that successfully pass clinical trials. At the ...heart of the screening for fragments binding to a specific target, crystallography delivers structural information essential for subsequent drug design. While it is common to search for bound ligands in electron densities calculated directly after an initial refinement cycle, we raise the important question whether this strategy is viable for fragments characterized by low affinities. Here, we describe and provide a collection of high-quality diffraction data obtained from 364 protein crystals treated with diverse fragments. Subsequent data analysis showed that ∼25% of all hits would have been missed without further refining the resulting structures. To enable fast and reliable hit identification, we have designed an automated refinement pipeline that will inspire the development of optimized tools facilitating the successful application of fragment-based methods.
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•Reliable fragment hit identification requires phase improvement through refinement•The modeling of water molecules particularly enhances fragment electron densities•364 diffraction datasets are provided for the design and validation of new methods•An automated procedure was developed to streamline structural refinement
Schiebel et al. describe a large collection of diffraction data obtained from protein crystals treated with 364 different fragment molecules. An automated structural refinement of these datasets suggests that more complete refinement enables detection of additional fragments binding in the target's active site.
Secretory proteins are used by pathogenic bacteria to manipulate the host systems and compete with other microorganisms, thereby enabling their survival in their host. Similar to other bacteria, ...secretory proteins of Mycobacterium tuberculosis also play a pivotal role in evading immune response within hosts, thereby leading to acute and latent tuberculosis infection. Prokaryotes have several classes of bacterial secretory systems out of which the Sec and Tat pathways are the most conserved in Mtb to transport proteins across the cytoplasmic membrane. Here, we report the crystal structure of a secretory protein, Rv0398c determined to 1.9 Å resolution. The protein comprises a core of antiparallel β sheets surrounded by α helices adopting a unique β sandwich fold. Structural comparison with other secretory proteins in Mtb and other pathogenic bacteria reveals that Rv0398c may be secreted via the Sec pathway. Our structural and in silico analyses thus provide mechanistic insights into the pathway adopted by Mtb to transport out secretory protein, Rv0398c which will facilitate the invasion to the host immune system.
•The crystal structure of the secretory protein Rv0398c was determined to 1.9 Å resolution.•The protein consists of a core of antiparallel β sheets surrounded by α helices adopting a unique β sandwich fold.•In silico analysis reveals that the protein is exported via the Sec pathway of Mtb.
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.
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.
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.
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.
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.
ClinicalTrials.gov, NCT01187134 . Registered on 23 August 2010.
Global indicators of the quality of diffraction data are presented and discussed, and are evaluated in terms of their performance with respect to various tasks. Based on the results obtained, it is ...suggested that some of the conventional indicators still in use in the crystallographic community should be abandoned, such as the nominal resolution dmin or the merging R factor Rmerge, and replaced by more objective and more meaningful numbers, such as the effective optical resolution deff,opt and the redundancy‐independent merging R factor Rr.i.m.. Furthermore, it is recommended that the precision‐indicating merging R factor Rp.i.m. should be reported with every diffraction data set published, because it describes the precision of the averaged measurements, which are the quantities normally used in crystallography as observables.
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