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Journal of Structural Biology

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https://read.qxmd.com/read/30876891/structures-of-full-length-plasma-kallikrein-bound-to-highly-specific-inhibitors-describe-a-new-mode-of-targeted-inhibition
#1
James R Partridge, Rebeca M Choy, Abel Silva-Garcia, Chul Yu, Zhe Li, Hing Sham, Brian Metcalf
Plasma kallikrein (pKal) is a serine protease responsible for cleaving high-molecular-weight kininogen to produce the pro-inflammatory peptide, bradykinin. Unregulated pKal activity can lead to hereditary angioedema (HAE) following excess bradykinin release. HAE attacks can lead to a compromised airway that can be life threatening. As there are limited agents for prophylaxis of HAE attacks, there is a high unmet need for a therapeutic agent for regulating pKal with a high degree of specificity. Here we present crystal structures of both full-length and the protease domain of pKal, bound to two very distinct classes of small-molecule inhibitors: compound 1, and BCX4161...
March 12, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30872095/mbir-a-cryo-et-3d-reconstruction-method-that-effectively-minimizes-missing-wedge-artifacts-and-restores-missing-information
#2
Rui Yan, Singanallur V Venkatakrishnan, Jun Liu, Charles A Bouman, Wen Jiang
Cryo-Electron Tomography (cryo-ET) has become an essential technique in revealing cellular and macromolecular assembly structures in their native states. However, due to radiation damage and the limited tilt range, cryo-ET suffers from low contrast and missing wedge artifacts, which limits the tomograms to low resolution and hinders further biological interpretation. In this study, we applied the Model-Based Iterative Reconstruction (MBIR) method to obtain tomographic 3D reconstructions of experimental cryo-ET datasets and demonstrated the advantages of MBIR in contrast improvement, missing wedge artifacts reduction, missing information restoration, and subtomogram averaging compared with other reconstruction approaches...
March 11, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30858049/intercellular-pathways-from-the-vasculature-to-the-forming-bone-in-the-zebrafish-larval-caudal-fin-possible-role-in-bone-formation
#3
Anat Akiva, Or Nelkenbaum, Andreas Schertel, Karina Yaniv, Steve Weiner, Lia Addadi
The pathway of ion supply from the source to the site of bone deposition in vertebrates is thought to involve transport through the vasculature, followed by ion concentration in osteoblasts. The cells deposit a precursor mineral phase in vesicles, which are then exocytosed into the extracellular matrix. We observed that the entire skeleton of zebrafish larvae, is labelled within minutes after injection of calcein or FITC-dextran into the blood. This raised the possibility that there is an additional pathway of solute transport that can account for the rapid labelling...
March 8, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30849471/an-unusual-disordered-alveolar-bone-material-in-the-upper-furcation-region-of-minipig-mandibles-a-3d-hierarchical-structural-study
#4
Raquel Maria, Yehonatan Ben-Zvi, Katya Rechav, Eugenia Klein, Ron Shahar, Steve Weiner
Teeth are subjected to compressive loads during mastication. Under small loads the soft tissue periodontal ligament (PDL) deforms most. However when the loads increase and the PDL is highly compressed, the tooth and the alveolar bone supporting the tooth, begin to deform. Here we report on the structure of this alveolar bone in the upper furcation region of the first molars of mature minipigs. Using light microscopy and scanning electron microscopy (SEM) of bone cross-sections, we show that this bone is hypermineralized, containing abundant small pores around 1-5 μm in diameter, lacunae around 10-20 μm as well as larger spaces...
March 5, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30836197/residue-co-evolution-helps-predict-interaction-sites-in-%C3%AE-helical-membrane-proteins
#5
Bo Zeng, Peter Hönigschmid, Dmitrij Frishman
Many integral membrane proteins, just like their globular counterparts, form either transient or permanent multi-subunit complexes to fulfill specific cellular roles. Although numerous interactions between these proteins have been experientially determined, the structural coverage of the complexes is very low. Therefore, the computational identification of the amino acid residues involved in the interaction interfaces is a crucial step towards the functional annotation of all membrane proteins.Here, we present MBPred, a sequence-based method for predicting the interface residues in transmembrane proteins...
March 2, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30825649/conformational-plasticity-of-the-veev-macro-domain-is-important-for-binding-of-adp-ribose
#6
Garyfallia I Makrynitsa, Dioni Ntonti, Konstantinos D Marousis, Maria Birkou, Minos-Timotheos Matsoukas, Sam Asami, Detlef Bentrop, Nicolas Papageorgiou, Bruno Canard, Bruno Coutard, Georgios A Spyroulias
Venezuelan equine encephalitis virus (VEEV) is a new world alphavirus which can be involved in several central nervous system disorders such as encephalitis and meningitis. The VEEV genome codes for 4 non-structural proteins (nsP), of which nsP3 contains a Macro domain. Macro domains (MD) can be found as stand-alone proteins or embedded within larger proteins in viruses, bacteria and eukaryotes. Their most common feature is the binding of ADP ribose (ADPr), while several macro domains act as ribosylation writers, erasers or readers...
February 27, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30822456/electron-cryo-tomography-of-vestibular-hair-cell-stereocilia
#7
Zoltan Metlagel, Jocelyn F Krey, Junha Song, Mark F Swift, William J Tivol, Rachel A Dumont, Jasmine Thai, Alex Chang, Helia Seifikar, Niels Volkmann, Dorit Hanein, Peter G Barr-Gillespie, Manfred Auer
High-resolution imaging of hair-cell stereocilia of the inner ear has contributed substantially to our understanding of auditory and vestibular function. To provide three-dimensional views of the structure of stereocilia cytoskeleton and membranes, we developed a method for rapidly freezing unfixed stereocilia on electron microscopy grids, which allowed subsequent 3D imaging by electron cryo-tomography. Structures of stereocilia tips, shafts, and tapers were revealed, demonstrating that the actin paracrystal was not perfectly ordered...
February 26, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30822455/crystal-structure-and-mutational-analyses-of-ribokinase-from-arabidopsis-thaliana
#8
Pyeoung-Ann Kang, Juntaek Oh, Haehee Lee, Claus-Peter Witte, Sangkee Rhee
Nitrogen remobilization is a key issue in plants. Recent studies in Arabidopsis thaliana have revealed that nucleoside catabolism supplies xanthine, a nitrogen-rich compound, to the purine ring catabolic pathway, which liberates ammonia from xanthine for reassimilation into amino acids. Similarly, pyrimidine nuclosides are degraded and the pyrimidine bases are fully catabolized. During nucleoside hydrolysis, ribose is released, and ATP-dependent ribokinase (RBSK) phosphorylates ribose to ribose-5'-phosphate to allow its entry into central metabolism recycling the sugar carbons from nucleosides...
February 26, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30802506/structural-characterization-of-the-%C3%AE-n-acetylglucosaminidase-a-key-enzyme-in-the-pathogenesis-of-sanfilippo-syndrome-b
#9
Gabriel Birrane, Anne-Laure Dassier, Alla Romashko, Dianna Lundberg, Kevin Holmes, Thomas Cottle, Angela W Norton, Bohong Zhang, Michael F Concino, Muthuraman Meiyappan
Mucopolysaccharidosis III B (MPS III-B) is a rare lysosomal storage disorder caused by deficiencies in Alpha-N-acetylglucosaminidase (NAGLU) for which there is currently no cure, and present treatment is largely supportive. Understanding the structure of NAGLU may allow for identification of novel therapeutic targets for MPS III-B. Here we describe the first crystal structure of human NAGLU, determined to a resolution of 2.3 Å. The crystal structure reveals a novel homotrimeric configuration, maintained primarily by hydrophobic and electrostatic interactions via domain II of three contiguous domains from the N- to C-terminus...
February 23, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30794865/using-focus-ion-beam-to-prepare-crystal-lamella-for-electron-diffraction
#10
Heng Zhou, Zhipu Luo, Xueming Li
Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the electron crystallographic method on large protein crystals with micrometer or larger sizes. Here, we used the focused ion beam (FIB) equipped on the scanning electron microscope (SEM) to mill a large crystal to thin lamella. The influences of the milling on the crystal lamella were observed and investigated, including radiation damage on the crystal surface during the FIB imaging, deformation of the thin crystal lamella, and variation in the diffraction intensities under electron radiation...
February 19, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30769148/structure-of-g57w-mutant-of-human-%C3%AE-s-crystallin-and-its-involvement-in-cataract-formation
#11
Khandekar Jishan Bari, Shrikant Sharma, Kandala V R Chary
A recently identified mutant of human γS-crystallin, G57W is associated with dominant congenital cataracts, the familial determinate of childhood blindness worldwide. To investigate the structural and functional changes that mediate the effect of this cataract-related mutant to compromise eye lens transparency and cause lens opacification in children, we recently reported complete sequence-specific resonance assignments of γS-G57W using a suite of heteronuclear NMR experiments. As a follow up, we have determined the 3D structure of γS-G57W and studied its conformational dynamics by solution NMR spectroscopy...
February 12, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30753894/characterization-of-the-molecular-properties-of-ktrc-a-second-rck-domain-that-regulates-a-ktr-channel-in-bacillus-subtilis
#12
Rita Rocha, Celso M Teixeira-Duarte, João M P Jorge, João Henrique Morais-Cabral
RCK (regulating conductance of K+ ) domains are common regulatory domains that control the activity of eukaryotic and prokaryotic K+ channels and transporters. In bacteria these domains play roles in osmoregulation, regulation of turgor and membrane potential and in pH homeostasis. Whole-genome sequencing unveiled RCK gene redundancy, however the biological role of this redundancy is not well understood. In Bacillus subtilis, there are two closely related RCK domain proteins (KtrA and KtrC) that regulate the activity of the Ktr cation channels...
February 9, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30742897/crystal-structures-of-aminotransferases-aro8-and-aro9-from-candida-albicans-and-structural-insights-into-their-properties
#13
Agnieszka Kiliszek, Wojciech Rypniewski, Kamila Rząd, Sławomir Milewski, Iwona Gabriel
Aminotransferases catalyze reversibly the transamination reaction by a ping-pong bi-bi mechanism with pyridoxal 5'-phosphate (PLP) as a cofactor. Various aminotransferases acting on a range of substrates have been reported. Aromatic transaminases are able to catalyze the transamination reaction with both aromatic and acidic substrates. Two aminotransferases from C. albicans, Aro8p and Aro9p, have been identified recently, exhibiting different catalytic properties. To elucidate the multiple substrate recognition of the two enzymes we determined the crystal structures of an unliganded CaAro8p, a complex of CaAro8p with the PLP cofactor bound to a substrate, forming an external aldimine, CaAro9p with PLP in the form of internal aldimine, and CaAro9p with a mixture of ligands that have been interpreted as results of the enzymatic reaction...
February 8, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30742896/enhancement-of-tomogram-interpretability-using-the-locked-self-rotation-function
#14
Andrei Fokine, Baldeep Khare, Yingyuan Sun, Michael G Rossmann
The interpretation of cryo-electron tomograms of macromolecular complexes can be difficult because of the large amount of noise and because of the missing wedge effect. Here it is shown how the presence of rotational symmetry in a sample can be utilized to enhance the quality of a tomographic analysis. The orientation of symmetry axes in a sub-tomogram can be determined using a locked self-rotation function. Given this knowledge, the sub-tomogram density can then be averaged to improve its interpretability...
February 8, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30742895/structural-and-functional-insights-into-the-role-of-a-cupin-superfamily-isomerase-in-the-biosynthesis-of-choi-moiety-of-aeruginosin
#15
Xiaoting Qiu, Wenjun Zhu, Weikai Wang, Haixiao Jin, Peng Zhu, Rongyu Zhuang, Xiaojun Yan
The 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety is a hallmark of aeruginosins, a class of cyanobacterial derived bioactive linear tetrapeptides that possess antithrombotic activity. The biosynthetic pathway of Choi has yet to be resolved. AerE is a cupin superfamily enzyme that was shown to be involved in the biosynthesis of Choi, but its exact role remains unclear. This study reports the functional characterization and structural analyses of AerE. Enzymatic observation reveals that AerE can dramatically accelerate 1,3-allylic isomerization of the non-aromatic decarboxylation product of prephenate, dihydro-4-hydroxyphenylpyruvate (H2 HPP)...
February 8, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30690142/consideration-of-sample-motion-in-cryo-tomography-based-on-alignment-residual-interpolation
#16
Jose-Jesus Fernandez, Sam Li, David A Agard
Recently, it has been shown that the resolution in cryo-tomography could be improved by considering the sample motion in tilt-series alignment and reconstruction, where a set of quadratic polynomials were used to model this motion. One requirement of this polynomial method is the optimization of a large number of parameters, which may limit its practical applicability. In this work, we propose an alternative method for modeling the sample motion. Starting from the standard fiducial-based tilt-series alignment, the method uses the alignment residual as local estimates of the sample motion at the 3D fiducial positions...
January 25, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30685338/breaking-the-long-standing-morphological-paradigm-individual-prisms-in-the-pearl-oyster-shell-grow-perpendicular-to-the-c-axis-of-calcite
#17
Y Dauphin, E Zolotoyabko, A Berner, E Lakin, C Rollion-Bard, J P Cuif, P Fratzl
Cross-sections of calcitic prismatic layers in mollusk shells, cut perpendicular to growth direction, reveal well-defined polygonal shapes of individual "grains" clearly visible by light and electron microscopy. For several kinds of shells, it was shown that the average number of edges in an individual prism approaches six during the growth process. Taking into account the rhombohedral symmetry of calcite, often presented in hexagonal axes, all this led to the long-standing opinion that calcitic prisms grow along the c-axis of calcite...
January 24, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30677521/structure-and-electrochemistry-of-proteins-harboring-iron-sulfur-clusters-of-different-nuclearities-part-iv-canonical-non-canonical-and-hybrid-iron-sulfur-proteins
#18
REVIEW
Piero Zanello
A plethora of proteins are able to express iron-sulfur clusters, but have a clear picture of the different types of proteins and the different iron-sulfur clusters they harbor it is not easy. In the last five years we have reviewed structure/electrochemistry of metalloproteins expressing: (i) single types of iron-sulfur clusters (namely: {Fe(Cys)4 }, {[Fe2 S2 ](Cys)4 }, {[Fe2 S2 ](Cys)3 (X)} (X = Asp, Arg, His), {[Fe2 S2 ](Cys)2 (His)2 }, {[Fe3 S4 ](Cys)3 }, {[Fe4 S4 ](Cys)4 } and {[Fe4 S4 ](Sγ Cys )3 (nonthiolate ligand)} cores); (ii) metalloproteins harboring iron-sulfur centres of different nuclearities (namely: [4Fe-4S] and [2Fe-2S], [4Fe-4S] and [3Fe-4S], and [4Fe-4S], [3Fe-4S] and [2Fe-2S] clusters...
January 21, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30660625/3d-reconstruction-of-trypanosoma-cruzi-macrophage-interaction-shows-the-recruitment-of-host-cell-organelles-towards-parasitophorous-vacuoles-during-its-biogenesis
#19
Lissa Catherine Reignault, Carolina de Lima Alcantara, Emile Santos Barrias, Wanderley de Souza
Trypanosoma cruzi has a complex life cycle where two infective developmental stages, known as trypomastigote and amastigote, can be found in the vertebrate host. Both forms can invade a large variety of cellular types and induce the formation of a parasitophorous vacuole (PV), that, posteriorly, disassembles and releases the parasites into the host cell cytoplasm. The biogenesis of T. cruzi PVs has not been analyzed in professional phagocytic cells. We investigated the biogenesis of PVs containing trypomastigotes or amastigotes in peritoneal macrophages...
January 17, 2019: Journal of Structural Biology
https://read.qxmd.com/read/30654136/nadph-dependent-sulfite-reductase-flavoprotein-adopts-an-extended-conformation-unique-to-this-diflavin-reductase
#20
Angela M Tavolieri, Daniel T Murray, Isabel Askenasy, Joseph M Pennington, Lauren McGarry, Christopher B Stanley, M Elizabeth Stroupe
This is the first X-ray crystal structure of the monomeric form of sulfite reductase (SiR) flavoprotein (SiRFP-60) that shows the relationship between its major domains in an extended position not seen before in any homologous diflavin reductases. Small angle neutron scattering confirms this novel domain orientation also occurs in solution. Activity measurements of SiR and SiRFP variants allow us to propose a novel mechanism for electron transfer from the SiRFP reductase subunit to its oxidase metalloenzyme partner that, together, make up the SiR holoenzyme...
January 14, 2019: Journal of Structural Biology
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