The following articles are a selection of those recently accepted for publication in Acta Crystallographica Section D: Biological Crystallography.
See also Forthcoming articles in all IUCr journals.
Synopsis: in vitro neuromuscular studies were performed to demonstrate that suramin neutralizes toxic activity of a PLA2-like proteins corroborating with calorimetric assays. Crystallographic studies demonstrated that the inhibitor binds to the surface of the toxin, obstructing its membrane docking and disruption sites confirming the proposed myotoxic mechanism.
Synopsis: Response from J R Helliwell et al to Shabalin et al (2015)
Synopsis: Response to Shabalin et al.
Synopsis: The high resolution structure of uracil-DNA N-glycosylase (UNG) from D. radiodurans in complex with DNA provides support for a model where DNA compression and minor groove stabilization is crucial for the uracil damage detection mechanism of UNGs.
Synopsis: A method is reported for collecting room temperature data from protein crystals under vacuum by protecting them with a thin graphene layer.
Synopsis: The self-complementary DNA decamer d(GCATGCATGC) crystallizes as an unusual double-folded structure, which serves as the basis for a possible structural model of triplet repeat DNA sequences.
Synopsis: The crystal structure of broadly neutralizing antibodies 8 ANC195 and PGT128 bound to an HIV-1 envelope trimer has been determined. Structural and binding analyses have elucidated the full epitopes for these antibodies in the context of the intact viral glycoprotein, providing improved templates for HIV-1 vaccine design.
Synopsis: Epsilon class glutathione S-transferases (GSTs) are found in invertebrates, including many insects, where they play roles in detoxication of insecticides and development. The crystal structures of two epsilon class GSTs from Drosophila melanogaster are reported and compared to aid in characterization of functional differences between the isozymes.
Synopsis: Crystal structures of two constructs of RC1339/APRc from Rickettsia conorii, consisting of either residues 105-231 or 110-231 followed by a His tag, have been determined in three different crystal forms. The monomer of APRc assumes retropepsin-like fold, but the dimer observed in all crystal forms is entirely different from the canonical dimer of retropepsins.
Synopsis: A structural insight is provided into the mechanism of how a widespread family of bacterial chemotaxis receptors containing the periplasmic tandem-Per-Arnt-Sim (PAS) sensing domain recognize free amino acids, and a model for signal transduction across the membrane is proposed.
Synopsis: The crystal structure of an Rsd-HPr complex was determined in order to reveal the binding interface between Rsd and HPr. A molecular link between global gene regulation and nutrient availability is described.
Synopsis: The catalytic mechanism and low pH optimum of C. bescii family 3 pectate lyase are explained.
Synopsis: A new Rice function approximation for the effect of intensity measurement errors improves the treatment of weak intensity data in calculating log-likelihood-gain scores in crystallographic applications including experimental phasing, molecular replacement and refinement.
Synopsis: ARCIMBOLDO solves the phase problem starting from small model fragments placed in the asymmetric unit. Density modification aids in combining phase information from correct solutions to avoid a combinatorial explosion of sequential searches.
Synopsis: X-ray structural analysis of T. cruzi spermidine synthase was conducted to identify novel inhibitor-binding sites, including an allosteric site, and to elucidate inhibition mechanisms.
Synopsis: High-resolution structures of a variant of an IMPDH enzyme with the regulatory CBS motifs deleted, as well as a point-mutation variant, have been solved and provide new insights into the allosteric behaviour and the octameric structure of the enzyme.
Synopsis: The first crystal structures of an O-demethylase methyltransferase protein in apo, THF-bound and MTHF-bound forms are reported. A conserved asparagine residue position is altered in favour of a putative proton-relay network.
Synopsis: Time-lapse crystal structures of human H-chain ferritin loaded with iron show the distribution of the substrate metal ion within the catalytic site. Comparison of these data with previously determined X-ray structures of R. catesbeiana M ferritin points to a number of shared and unshared features of the active sites of the two proteins that contribute to the ongoing debate on the possible existence of a universal mechanism for iron oxidation in all ferritins.
Synopsis: The structural changes associated with conformational switching in a copper-sensing metalloregulator are revealed. These highlight the importance of charge distribution in regulating DNA binding.
Synopsis: The efficiency of the Phantom Derivative method, in its non ab initio variant, has been checked by using the phases obtained via molecular-replacement methods as a starting point.
Synopsis: The structure of the complex of NO66 and Rpl8 was solved in the native state and NO66 recognizes the consensus motif NHXH . Tetramerization is required for efficient substrate binding and catalysis by NO66.
Synopsis: The REVAN pipeline for automatic protein crystal structure solution via molecular replacement and density-guided optimization algorithms is described.
Synopsis: The crystal structure of the 34 kDa F-actin-bundling protein ABP34 from D. discoideum is reported.
Synopsis: The crystal structure of RNA polymerase I in an alternative crystal form at 5.5 Å resolution with three dimers in a pseudo-heptagonal helical arrangement is reported. The angle between the monomers in the three dimers differs markedly from that in previously reported high-resolution structures.
Synopsis: Crystal structures of P. falciparum HAD1 in complex with three different substrates were solved in order to understand how cap-domain movement enables diverse substrate recognition by this sugar phosphatase.
Synopsis: Some interesting aspects of domain swapping, which is a unique method of protein oligomerization, are addressed, with the aim of understanding the role of interfaces and hinge regions in domain swapping.
Synopsis: Serial crystallography generates partial reflections from still diffraction images. Partialities are estimated with EVAL ray-tracing simulations, thereby improving merged reflection data to a similar quality as conventional rotation data.
Synopsis: Many small-molecule compounds have been shown to bind the peripheral anionic site (PAS) of acetylcholinesterase, but only a few have been shown by X-ray crystallography to induce specific structural changes in the enzyme. Here, an unexpected conformational change observed in the PAS upon the binding of an experimental bis-imidazolium oxime nerve-agent antidote is reported and the observed structures are correlated with measured binding and reactivation kinetics.
Synopsis: ARCIMBOLDO solves the phase problem through massive combination of small fragments and density modification. The use and performance of the single-workstation implementation is described.
Synopsis: Data collection with a tailored 50 µm diameter X-ray beam at 4.6 keV ( = 2.69 Å) at the newly established EMBL beamline P13 at PETRA III, allowed the crystal structure determination of the Cdc23Nterm homodimer (65.4 kDa, 12 Cys and 10 Met) by sulfur SAD phasing at 3.1 Å resolution while overcoming crystal twinning.
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