Journal of Structural Biology

ScienceDirect RSS
  • Characterization of the termini of the West Nile virus genome and their interactions with the small isoform of the 2′ 5′-oligoadenylate synthetase family
    [Apr 2015]

    Publication date: Available online 11 April 2015
    Source:Journal of Structural Biology

    Author(s): Soumya Deo , Trushar R. Patel , Grzegorz Chojnowski , Amit Koul , Edis Dzananovic , Kevin McEleney , Janusz M. Bujnicki , Sean A. McKenna

    2′ 5′-Oligoadenylate synthetases (OAS) are interferon-stimulated proteins that act in the innate immune response to viral infection. Upon binding viral double-stranded RNA, OAS enzymes produce 2′-5′-linked oligoadenylates that stimulate RNase L and ultimately slow viral propagation. Truncations/mutations in the smallest human OAS isoform, OAS1, results in susceptibility to West Nile virus (WNV). We have previously demonstrated in vitro the interaction between OAS1 and the 5′-terminal region of the WNV RNA genome. Here we report that the 3′-terminal region is also able to mediate specific interaction with and activation of OAS1. Binding and kinetic experiments identified a specific stem loop within the 3′-terminal region that is sufficient for activation of the enzyme. The solution conformation of the 3′-terminal region was determined by small angle X-ray scattering, and computational models suggest a conformationally restrained structure comprised of a helix and short stem loop. Structural investigation of the 3′-terminal region in complex with OAS1 is also presented. Finally, we show that genome cyclization by base pairing between the 5′- and 3′-terminal regions, a required step for replication, is not sufficient to protect WNV from OAS1 recognition in vitro. These data provide a physical framework for understanding recognition of the highly structured terminal regions of a flaviviral genome by an innate immune enzyme.





    Categories: Journal Articles
  • Different Conformational Dynamics of Various Active States of β-Arrestin1 Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry
    [Apr 2015]

    Publication date: Available online 11 April 2015
    Source:Journal of Structural Biology

    Author(s): Dong Kyun Kim , Youngjoo Yun , Hee Ryung Kim , Min-Duk Seo , Ka Young Chung

    Arrestins have important roles in G protein-coupled receptor (GPCR) signaling including desensitization of GPCRs and G protein-independent signaling. Two major intra-molecular interactions, the polar core and the three-element region, maintain arrestins in the basal conformation by connecting the N- and C-domains. Mutations in these regions that disrupt the polar core (R169E or p44) or the three-element (3A) have been reported to interact with GPCRs in a phosphorylation-independent manner, and thus these mutants are referred to as pre-activated arrestins. On the other hand, deletion of 7 residues in the linker region between N- and C-domains (Δ7) freezes arrestins in the inactive state, which has a much lower binding affinity to GPCRs compared to the wild type form. Although these mutants are widely used for functional studies of arrestins, the conformations of these mutants have not yet been fully elucidated. Here, we analyzed the conformational dynamics of β-arrestin1 with various mutants (R169E, p44, 3A, and Δ7) by hydrogen/deuterium exchange mass spectrometry (HDX-MS). HDX-MS data revealed that pre-activated mutants have more deuterium uptake than the basal state, and also that the regions and degree of increased deuterium uptake differ between pre-activated mutants. Unexpectedly, the inactive mutant also showed increased deuterium uptake in a few regions.





    Categories: Journal Articles
  • Structural basis for regulation of stability and activity in glyceraldehyde-3-phosphate dehydrogenases. Differential scanning calorimetry and molecular dynamics
    [Apr 2015]

    Publication date: Available online 11 April 2015
    Source:Journal of Structural Biology

    Author(s): Olga N. Makshakova , Pavel I. Semenyuk , Mikhail L. Kuravsky , Elena A. Ermakova , Yuriy F. Zuev , Vladimir I. Muronetz

    Tissue specific isoforms of human glyceraldehyde-3-phosphate dehydrogenase, somatic (GAPD) and sperm-specific (GAPDS), have been reported to display different levels of both stability and catalytic activity. Here we apply MD simulations to investigate molecular basis of this phenomenon. The protein is a tetramer where each subunit consists of two domains – catalytic and NAD-binding one. We demonstrated key residues responsible for intersubunit and interdomain interactions. Effect of several residues was studied by point mutations. Overall we considered three mutations (Glu96Gln, Glu244Gln and Asp311Asn) disrupting GAPDS-specific salt bridges. Comparison of calculated interaction energies with calorimetric enthalpies confirmed that intersubunit interactions were responsible for enhanced thermostability of GAPDS whereas interdomain interactions had indirect influence on intersubunit contacts. Mutation Asp311Asn was around 10Å far from the active center and corresponded to the closest natural substitution in the isoenzymes. MD simulations revealed that this residue had slight interaction with catalytic residues but influenced the hydrogen bond net and dynamics in active site. These effects can be responsible for a strong influence of this residue on catalytic activity. Overall, our results provide new insight into glyceraldehyde-3-phosphate dehydrogenase structure–function relationships and can be used for the engineering of mutant proteins with modified properties and for development of new inhibitors with indirect influence on the catalytic site.





    Categories: Journal Articles
  • Conical Fourier shell correlation applied to electron tomograms
    [Apr 2015]

    Publication date: Available online 3 April 2015
    Source:Journal of Structural Biology

    Author(s): C.A. Diebolder , F.G.A. Faas , A.J. Koster , R.I. Koning

    The resolution of electron tomograms is anisotropic due to geometrical constraints during data collection, such as the limited tilt range and single axis tilt series acquisition. Acquisition of dual axis tilt series can decrease these effects. However, in cryo-electron tomography, to limit the electron radiation damage that occurs during imaging, the total dose should not increase and must be fractionated over the two tilt series. Here we set out to determine whether it is beneficial fractionate electron dose for recording dual axis cryo electron tilt series or whether it is better to perform single axis acquisition. To assess the quality of tomographic reconstructions in different directions here we introduce conical Fourier shell correlation (cFSCe/o). Employing cFSCe/o, we compared the resolution isotropy of single-axis and dual-axis (cryo-)electron tomograms using even/odd split data sets. We show that the resolution of dual-axis simulated and cryo-electron tomograms in the plane orthogonal to the electron beam becomes more isotropic compared to single-axis tomograms and high resolution peaks along the tilt axis disappear. cFSCe/o also allowed us to compare different methods for the alignment of dual-axis tomograms. We show that different tomographic reconstruction programs produce different anisotropic resolution in dual axis tomograms. We anticipate that cFSCe/o can also be useful for comparisons of acquisition and reconstruction parameters, and different hardware implementations.





    Categories: Journal Articles
  • Cover 2 - Editorial Board
    [Apr 2015]

    Publication date: April 2015
    Source:Journal of Structural Biology, Volume 190, Issue 1









    Categories: Journal Articles
  • Table of Contents / barcode
    [Apr 2015]

    Publication date: April 2015
    Source:Journal of Structural Biology, Volume 190, Issue 1









    Categories: Journal Articles
  • Structural origin of the drastic modification of second harmonic generation intensity pattern occurring in tail muscles of climax stages xenopus tadpoles
    [Apr 2015]

    Publication date: April 2015
    Source:Journal of Structural Biology, Volume 190, Issue 1

    Author(s): Gaëlle Recher , Pascal Coumailleau , Denis Rouède , François Tiaho

    Second harmonic generation (SHG) microscopy is a powerful tool for studying submicron architecture of muscles tissues. Using this technique, we show that the canonical single frequency sarcomeric SHG intensity pattern (SHG-IP) of premetamorphic xenopus tadpole tail muscles is converted to double frequency (2f) sarcomeric SHG-IP in metamorphic climax stages due to massive physiological muscle proteolysis. This conversion was found to rise from 7% in premetamorphic muscles to about 97% in fragmented muscular apoptotic bodies. Moreover a 66% conversion was also found in non-fragmented metamorphic tail muscles. Also, a strong correlation between predominant 2f sarcomeric SHG-IPs and myofibrillar misalignment is established with electron microscopy. Experimental and theoretical results demonstrate the higher sensitivity and the supra resolution power of SHG microscopy over TPEF to reveal 3D myofibrillar misalignment. From this study, we suggest that 2f sarcomeric SHG-IP could be used as signature of triad defect and disruption of excitation–contraction coupling. As the mechanism of muscle proteolysis is similar to that found in mdx mouse muscles, we further suggest that xenopus tadpole tail resorption at climax stages could be used as an alternative or complementary model of Duchene muscular dystrophy.





    Categories: Journal Articles
  • NMR structure and dynamics of Q4D059, a kinetoplastid-specific and conserved protein from Trypanosoma cruzi
    [Apr 2015]

    Publication date: April 2015
    Source:Journal of Structural Biology, Volume 190, Issue 1

    Author(s): Aracelys López-Castilla , Tirso Pons , José R. Pires

    Q4D059 (UniProt accession number), is an 86-residue protein from Trypanosoma cruzi, conserved in the related kinetoplastid parasites Trypanosoma brucei and Leishmania major. These pathogens are the causal agents of the neglected diseases: Chagas, sleeping sickness and leishmaniases respectively and had recently their genomes sequenced. Q4D059 shows low sequence similarity with mammal proteins and because of its essentiality demonstrated in T. brucei, it is a potential target for anti-parasitic drugs. The 11 hypothetical proteins homologous to Q4D059 are all uncharacterized proteins of unknown function. Here, the solution structure of Q4D059 was solved by NMR and its backbone dynamics was characterized by 15N relaxation parameters. The structure is composed by a parallel/anti-parallel three-stranded β-sheet packed against four helical regions. The structure is well defined by ca. 9 NOEs per residue and a backbone rmsd of 0.50±0.05Å for the representative ensemble of 20 lowest-energy structures. The structure is overall rigid except for N-terminal residues A9 to D11 at the beginning of β1, K38, V39 at the end of helix H3 with rapid motion in the ps–ns timescale and G25 (helix H2), I68 (β2) and V78 (loop 3) undergoing internal motion in the μs–ms timescale. Limited structural similarities were found in protein structures deposited in the PDB, therefore functional inferences based on protein structure information are not clear. Q4D059 adopts a α/β fold that is slightly similar to the ATPase sub-domain IIB of the heat-shock protein 70 (HSP70) and to the N-terminal domain of the ribosomal protein L11.





    Categories: Journal Articles
  • Crystal structure and substrate-binding mode of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8
    [Apr 2015]

    Publication date: April 2015
    Source:Journal of Structural Biology, Volume 190, Issue 1

    Author(s): Takatsugu Miyazaki , Megumi Ichikawa , Hitoshi Iino , Atsushi Nishikawa , Takashi Tonozuka

    Glycoside hydrolase family 63 (GH63) proteins are found in eukaryotes such as processing α-glucosidase I and also many bacteria and archaea. Recent studies have identified two bacterial and one plant GH63 mannosylglycerate hydrolases that act on both glucosylglycerate and mannosylglycerate, which are compatible solutes found in many thermophilic prokaryotes and some plants. Here we report the 1.67-Å crystal structure of one of these GH63 mannosylglycerate hydrolases, Tt8MGH from Thermus thermophilus HB8, which is 99% homologous to mannosylglycerate hydrolase from T. thermophilus HB27. Tt8MGH consists of a single (α/α)6-barrel catalytic domain with two additional helices and two long loops which form a homotrimer. The structures of this protein in complexes with glucose or glycerate were also determined at 1.77- or 2.10-Å resolution, respectively. A comparison of these structures revealed that the conformations of three flexible loops were largely different from each other. The conformational changes may be induced by ligand binding and serve to form finger-like structures for holding substrates. These findings represent the first-ever proposed substrate recognition mechanism for GH63 mannosylglycerate hydrolase.





    Categories: Journal Articles
  • Presence of plicidentine in the oral teeth of the coelacanth Latimeria chalumnae Smith 1939 (Sarcopterygii; Actinistia)
    [Apr 2015]

    Publication date: April 2015
    Source:Journal of Structural Biology, Volume 190, Issue 1

    Author(s): F.J. Meunier , J. Mondéjar-Fernández , F. Goussard , G. Clément , M. Herbin

    The extant coelacanth Latimeria is a sarcopterygian predatory fish with caniniform teeth on its upper and lower jaws. The teeth are constituted of a cone of dentine with an apical cap of enamel, and they are fixed to the osseous component of the jaws by an attachment bone. Internal walls of the tooth base show folds that have been firstly interpreted in the past as radial vascular canals. Three-dimensional visualisation of these foldings using X-ray tomographic techniques and new histological interpretation lead to reconsider these structures as true plicidentine. The folds of the dentine do not invade the whole pulp cavity of the tooth contrary to the plicated condition of most fossil sarcopterygian fishes (e.g., Eusthenopteron, Porolepis, Megalichthys) certain fossil marine reptiles (ichthyosaurs) and extant varanids; in Latimeria they are limited to the lower third to the half of the pulp cavity. The presence of plicidentine in Latimeria’s teeth is proposed to be a plesiomorphic character for sarcopterygians.





    Categories: Journal Articles
  • The insertion domain 1 of class IIA dimeric glycyl-tRNA synthetase is a rubredoxin-like zinc ribbon
    [Apr 2015]

    Publication date: April 2015
    Source:Journal of Structural Biology, Volume 190, Issue 1

    Author(s): Gurmeet Kaur , Srikrishna Subramanian

    The insertion domain 1 (ID1) of class IIA dimeric glycyl-tRNA synthetase (α2GRS) is an appended domain in the core catalytic region of the enzyme. ID1 has been shown to play a role in tRNA aminoacylation, mediating interaction with the acceptor arm of tRNA and diadenosine tetraphosphate (Ap4A) synthesis. Mutations in α2GRS, including those in the ID1 region, have been implicated in distal hereditary motor neuropathy-V (dHMN-V) and Charcot–Marie–Tooth (CMT) disease. Through sequence and structure based evolutionary analysis, we show that ID1 of α2GRS is a rubredoxin-like zinc ribbon domain. The zinc-chelating cysteines of ID1 are well conserved in all archaeal versions of the enzyme and also in several eukaryotes, which most likely have acquired them via horizontal gene transfer from bacteria; but in all other eukaryotes, the zinc-chelating residues are not preserved. ID1 from bacteria display a selective preservation of zinc-binding residues, ranging from complete conservation to complete loss. The ID1 from different organisms harbor variable-sized non-conserved insertions between the two zinc-binding half-sites of the zinc ribbon. Three of the previously identified CMT-associated mutations in α2GRS, viz., human D146N, mouse C157R and human S211F, are located in the zinc ribbon region of ID1. Interestingly, human Asp146 which is implicated in the synthesis of Ap4A, a molecule known to act during neuronal transmission, has also been reported to be mutated in dHMN-V, suggesting a possible link between hereditary motor neuropathy and Ap4A synthesis.





    Categories: Journal Articles
  • CapsidMaps: Protein–protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps
    [Apr 2015]

    Publication date: April 2015
    Source:Journal of Structural Biology, Volume 190, Issue 1

    Author(s): Mauricio Carrillo-Tripp , Daniel Jorge Montiel-García , Charles L. Brooks III , Vijay S. Reddy

    Structural analysis and visualization of protein–protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces. In the case of viruses, structural analysis becomes even more demanding because several interfaces coexist and, in most cases, these are formed by hundreds of contacting residues that belong to multiple interacting coat proteins. CapsidMaps is an interactive analysis and visualization tool that is designed to benefit the structural virology community. Developed as an improved extension of the φ–ψ Explorer, here we describe the details of its design and implementation. We present results of analysis of a spherical virus to showcase the features and utility of the new tool. CapsidMaps also facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity (S)-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application at http://viperdb.scripps.edu.





    Categories: Journal Articles
  • CNS myelin sheath is stochastically built by homotypic fusion of myelin membranes within the bounds of an oligodendrocyte process
    [Apr 2015]

    Publication date: April 2015
    Source:Journal of Structural Biology, Volume 190, Issue 1

    Author(s): Sara Szuchet , Lauren L. Nielsen , Miriam S. Domowicz , Jotham R. Austin II , Dimitrios L. Arvanitis

    Myelin – the multilayer membrane that envelops axons – is a facilitator of rapid nerve conduction. Oligodendrocytes form CNS myelin; the prevailing hypothesis being that they do it by extending a process that circumnavigates the axon. It is pertinent to ask how myelin is built because oligodendrocyte plasma membrane and myelin are compositionally different. To this end, we examined oligodendrocyte cultures and embryonic avian optic nerves by electron microscopy, immuno-electron microscopy and three-dimensional electron tomography. The results support three novel concepts. Myelin membranes are synthesized as tubules and packaged into “myelinophore organelles” in the oligodendrocyte perikaryon. Myelin membranes are matured in and transported by myelinophore organelles within an oligodendrocyte process. The myelin sheath is generated by myelin membrane fusion inside an oligodendrocyte process. These findings abrogate the dogma of myelin resulting from a wrapping motion of an oligodendrocyte process and open up new avenues in the quest for understanding myelination in health and disease.





    Categories: Journal Articles
  • Changes in the micro- and nanostructure of siliceous valves in the diatom Synedra acus under the effect of colchicine treatment at different stages of the cell cycle
    [Apr 2015]

    Publication date: April 2015
    Source:Journal of Structural Biology, Volume 190, Issue 1

    Author(s): Ksenia V. Kharitonenko , Yekaterina D. Bedoshvili , Yelena V. Likhoshway

    The important role of the cytoskeleton in the morphogenesis of siliceous frustule components, which are synthesized within the diatom cells, has been revealed due to experiments with microtubule inhibitors. It has been shown that colchicine entering the diatom cell inhibits polymerization of tubulin, the main protein of microtubules, thereby disrupting the normal processes of biogenic silica deposition and daughter valve morphogenesis. In this study, experiments with a synchronized culture of the pennate diatom Synedra acus have been performed to determine the timing and duration of the formation of various valve components and analyze the effect of colchicine at a subtoxic concentration on the structure of daughter valves at different stages of their morphogenesis. Electron microscopic analysis has revealed several types of micro- and nanoscale anomalies in daughter valve morphology, with their frequency varying depending on the time of colchicine treatment. Laser scanning microscopy of preparations vitally stained with Tubulin Tracker Green has shown that polymerized tubulin at early stages of valve morphogenesis is localized along the periphery of the developing valve. This is evidence for an important role of microtubules in the horizontal growth of the valve at the stage when its general structural pattern is established, including its shape and arrangement of basic micro- and nanostructures. Treatment with a microtubule inhibitor at a certain stage of valve morphogenesis makes it possible to obtain new forms with a specific structure of siliceous components that hold promise for use in nanotechnologies.





    Categories: Journal Articles
  • The leucine-rich amelogenin protein (LRAP) is primarily monomeric and unstructured in physiological solution
    [Apr 2015]

    Publication date: April 2015
    Source:Journal of Structural Biology, Volume 190, Issue 1

    Author(s): Barbara J. Tarasevich , John S. Philo , Nasib Karl Maluf , Susan Krueger , Garry W. Buchko , Genyao Lin , Wendy J. Shaw

    Amelogenin proteins are critical to the formation of enamel in teeth and may have roles in controlling growth and regulating microstructures of the intricately woven hydroxyapatite (HAP). Leucine-rich amelogenin protein (LRAP) is a 59-residue splice variant of amelogenin and contains the N- and C-terminal charged regions of the full-length protein thought to control crystal growth. Although the quaternary structure of full-length amelogenin in solution has been well studied and can consist of self-assemblies of monomers called nanospheres, there is limited information on the quaternary structure of LRAP. Here, sedimentation velocity analytical ultracentrifugation (SV) and small angle neutron scattering (SANS) were used to study the tertiary and quaternary structure of LRAP at various pH values, ionic strengths, and concentrations. We found that the monomer is the dominant species of phosphorylated LRAP (LRAP(+P)) over a range of solution conditions (pH 2.7–4.1, pH 4.5–8, 50mmol/L(mM) to 200mM NaCl, 0.065–2mg/mL). The monomer is also the dominant species for unphosphorylated LRAP (LRAP(−P)) at pH 7.4 and for LRAP(+P) in the presence of 2.5mM calcium at pH 7.4. LRAP aggregates in a narrow pH range near the isoelectric point of pH 4.1. SV and SANS show that the LRAP monomer has a radius of ∼2.0nm and an asymmetric structure, and solution NMR studies indicate that the monomer is largely unstructured. This work provides new insights into the secondary, tertiary, and quaternary structure of LRAP in solution and provides evidence that the monomeric species may be an important functional form of some amelogenins.





    Categories: Journal Articles
  • SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction
    [Apr 2015]

    Publication date: Available online 31 March 2015
    Source:Journal of Structural Biology

    Author(s): Nicha C. Dvornek , Fred J. Sigworth , Hemant D. Tagare

    Single particle reconstruction methods based on the maximum-likelihood principle and the expectation–maximization (E–M) algorithm are popular because of their ability to produce high resolution structures. However, these algorithms are computationally very expensive, requiring a network of computational servers. To overcome this computational bottleneck, we propose a new mathematical framework for accelerating maximum-likelihood reconstructions. The speedup is by orders of magnitude and the proposed algorithm produces similar quality reconstructions compared to the standard maximum-likelihood formulation. Our approach uses subspace approximations of the cryo-electron microscopy (cryo-EM) data and projection images, greatly reducing the number of image transformations and comparisons that are computed. Experiments using simulated and actual cryo-EM data show that speedup in overall execution time compared to traditional maximum-likelihood reconstruction reaches factors of over 300.





    Categories: Journal Articles
  • The bacteriocin AS-48 requires dimer dissociation followed by hydrophobic interactions with the membrane for antibacterial activity
    [Apr 2015]

    Publication date: Available online 27 March 2015
    Source:Journal of Structural Biology

    Author(s): Rubén Cebrián , Manuel Martínez-Bueno , Eva Valdivia , Armando Albert , Mercedes Maqueda , María José Sánchez-Barrena

    The molecular mechanism underlining the antibacterial activity of the bacteriocin AS-48 is not known, and two different and opposite alternatives have been proposed. Available data suggested that the interaction of positively charged amino acids of AS-48 with the membrane would produce membrane destabilization and disruption. Alternatively, it has been proposed that AS-48 activity could rely on the effective insertion of the bacteriocin into the membrane. The biological and structural properties of the AS-48G13K/L40K double mutant were investigated to shed light on this subject. Compared with the wild type, the mutant protein suffered an important reduction in the antibacterial activity. Biochemical and structural studies of AS-48G13K/L40K mutant suggest the basis of its decreased antimicrobial activity. Lipid cosedimentation assays showed that the membrane affinity of AS-48G13K/L40K is 12-fold lower than that observed for the wild type. L40K mutation is responsible for this reduced membrane affinity and thus, hydrophobic interactions are involved in membrane association. Furthermore, the high-resolution crystal structure of AS-48G13K/L40K, together with the study of its dimeric character in solution showed that G13K stabilizes the inactive water-soluble dimer, which displays a reduced dipole moment. Our data suggest that the cumulative effect of these three affected properties reduces AS-48 activity, and point out that the bactericidal effect is achieved by the electrostatically driven approach of the inactive water-soluble dimer towards the membrane, followed by the dissociation and insertion of the protein into the lipid bilayer.





    Categories: Journal Articles
  • Dimeric WH2 repeats of VopF sequester actin monomers into non-nucleating linear string conformations: An X-ray scattering study
    [Apr 2015]

    Publication date: Available online 25 March 2015
    Source:Journal of Structural Biology

    Author(s): Balendu Sankara Avvaru , Julien Pernier , Marie-France Carlier

    VopF and VopL are highly similar virulence-factors of Vibrio cholerae and Vibrio parahaemolyticus respectively that disrupt the host’s actin cytoskeleton, using a unique organization in dimerized WH2 repeats. Association of dimerized WH2 domains with the barbed face of actin confers multifunctional activities to VopF in vitro, including G-actin sequestration and filament nucleation, barbed end tracking and uncapping. Here, small angle X-ray scattering (SAXS) measurements of complexes of VopF with actin and structural modeling reveal that VopF stabilizes linear actin-strings that differ from canonical actin filament architectures but represent non-polymerizable sequestered forms of actin. The results exclude that VopL binds the pointed end of actin filaments in the template filament nucleation mechanism derived from crystallographic studies.





    Categories: Journal Articles
  • Functionalization of biomineral reinforcement in crustacean cuticle: Calcite orientation in the partes incisivae of the mandibles of Porcellio scaber and the supralittoral species Tylos europaeus (Oniscidea, Isopoda)
    [Apr 2015]

    Publication date: Available online 25 March 2015
    Source:Journal of Structural Biology

    Author(s): Julia Huber , Erika Griesshaber , Fitriana Nindiyasari , Wolfgang W. Schmahl , Andreas Ziegler

    In arthropods the cuticle forms an exoskeleton with its physical and chemical properties adapted to functions of distinct skeletal elements. The cuticle of the partes incisivae (PI) in mandibles of terrestrial isopods is a composite of chitin-protein fibrils/fibres and minerals. It consists of an unmineralized tip, a middle region with organic fibrils reinforced mainly with amorphous calcium phosphate and a base region mineralized with amorphous calcium carbonate and calcite. In this study we extend our work on the structure and material properties of the incisive cuticle employing electron backscatter diffraction (EBSD), and investigate calcite orientation patterns in the PI of two terrestrial isopod species from different habitats. We trace small-scale differences in texture sharpness and calcite microstructure, and compare calcite organization and orientation patterns in the PI with those in the tergites of the same isopod species. We observe that in the PI calcite orientation, the degree of crystal alignment, and mode of crystalline domain assemblage is highly varied within short length scales. This contrasts to calcite organization in the tergite cuticle, where calcite has only one specific texture pattern. Such a large range in the variation of calcite organization has not been observed in other carbonate biological hard tissues, such as shells and teeth, where one specific texture and microstructure prevails. Thus, the investigated isopod species are able to control crystallization of the amorphous carbonate precursor in a differential way, most probably related to the function of the individual skeletal element and the animals’ behavior.





    Categories: Journal Articles
  • Structural insight into the oxidation of sinapic acid by CotA laccase
    [Apr 2015]

    Publication date: Available online 20 March 2015
    Source:Journal of Structural Biology

    Author(s): Tian Xie , Zhongchuan Liu , Qian Liu , Ganggang Wang

    Laccases can oxidize plenty of substrates by use of molecular oxygen as the final electron acceptor. The broad substrate spectrum is further expanded by using redox mediators in so-called laccase–mediator systems, but the structural studies on interactions between laccases and natural mediators are still absent. In this study, the crystal structure of CotA/sinapic acid complex is solved, structural comparison has revealed a novel substrate binding mode. The residue of His419 instead of His497 is bonding to the sinapic acid (SA) as the primary electron acceptor. Moreover, the binding of SA leads to 10° rotation on Arg416, our mutagenesis data exhibits that the residue Arg416 is crucial in the oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and syringaldazine (SGZ). Furthermore, oxidation of several phenolic acids and one non-phenolic acid by CotA was investigated. By analyzing interactions between CotA and SA, it is indicated that the presence of methoxy groups in the ortho-position of the phenolic structure is crucial for the substrate recognition by CotA laccase. This work establishes structure–function relationships for laccase–natural mediator system.
    Graphical abstract




    Categories: Journal Articles