Structural insights into thermostabilization of leucine dehydrogenase from its atomic structure by cryo-electron microscopy
Publication date: Available online 10 December 2018Source: Journal of Structural BiologyAuthor(s): Hiroki Yamaguchi, Akiko Kamegawa, Kunio Nakata, Tatsuki Kashiwagi, Toshimi Mizukoshi, Yoshinori Fujiyoshi, Kazutoshi TaniAbstractLeucine dehydrogenase (LDH, EC 1.4.1.9) is a NAD+-dependent oxidoreductase that catalyzes the deamination of branched-chain L-amino acids (BCAAs). LDH of Geobacillus stearothermophilus (GstLDH) is a highly thermostable enzyme that has been applied for the quantification or production of BCAAs. Here the cryo-electron microscopy (cryo-EM) structures of apo and NAD+-bound LDH are reported at 3.0 and 3....
Source: Journal of Structural Biology - December 11, 2018 Category: Biology Source Type: research

Pig enamel revisited – Incremental markings in enamel of wild boars and domestic pigs
Publication date: Available online 22 November 2018Source: Journal of Structural BiologyAuthor(s): Horst Kierdorf, Friederike Breuer, Carsten Witzel, Uwe KierdorfAbstractThe nature and periodicity of incremental markings in pig enamel is currently debated. To broaden the basis for a correct interpretation of growth marks in pig enamel, we analyzed their periodicity in teeth of wild boars and domestic pigs. For that, the numbers of enamel incremental markings were recorded in ground sections and compared with crown formation times for the respective teeth derived from literature data on tooth development and eruption in Sus...
Source: Journal of Structural Biology - November 30, 2018 Category: Biology Source Type: research

A Local Agreement Filtering Algorithm for Transmission EM Reconstructions
We present LAFTER, an algorithm for de-noising single particle reconstructions from cryo-EM.Single particle analysis entails the reconstruction of high-resolution volumes from tens of thousands of particle images with low individual signal-to-noise. Imperfections in this process result in substantial variations in the local signal-to-noise ratio within the resulting reconstruction, complicating the interpretation of molecular structure. An effective local de-noising filter could therefore improve interpretability and maximise the amount of useful information obtained from cryo-EM maps.LAFTER is a local de-noising algorithm...
Source: Journal of Structural Biology - November 29, 2018 Category: Biology Source Type: research

Structural insights into the catalytic mechanism of 5-methylthioribose 1-phosphate isomerase
Publication date: Available online 22 November 2018Source: Journal of Structural BiologyAuthor(s): Prerana Gogoi, Prerana Mordina, Shankar Prasad KanaujiaAbstract5-Methylthioribose 1-phosphate isomerase (M1Pi) is a crucial enzyme involved in the universally conserved methionine salvage pathway (MSP) where it is known to catalyze the conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P) via a mechanism which remains unspecified till date. Furthermore, although M1Pi has a discrete function, it surprisingly shares high structural similarity with two functionally non-related prot...
Source: Journal of Structural Biology - November 28, 2018 Category: Biology Source Type: research

Metal centers in biomolecular solid-state NMR
Publication date: Available online 28 November 2018Source: Journal of Structural BiologyAuthor(s): José Malanho Silva, Linda Cerofolini, Stefano Giuntini, Vito Calderone, Carlos F.G.C. Geraldes, Anjos L. Macedo, Giacomo Parigi, Marco Fragai, Enrico Ravera, Claudio LuchinatAbstractSolid state NMR (SSNMR) has earned a substantial success in the characterization of paramagnetic systems over the last decades. Nowadays, the resolution and sensitivity of solid state NMR in biological molecules has improved significantly and these advancements can be translated into the study of paramagnetic biomolecules. However, the elec...
Source: Journal of Structural Biology - November 28, 2018 Category: Biology Source Type: research

goCTF: Geometrically optimized CTF determination for single-particle cryo-EM
Publication date: Available online 26 November 2018Source: Journal of Structural BiologyAuthor(s): Min SuAbstractPreferred particle orientation represents a recurring problem in single-particle cryogenic electron microcopy (cryo-EM). A specimen-independent approach through tilting has been attempted to increase particle orientation coverage, thus minimizing anisotropic three-dimensional (3D) reconstruction. However, focus gradient is a critical issue hindering tilt applications from being a general practice in single-particle cryo-EM. The present study describes a newly developed geometrically optimized approach, goCTF, to...
Source: Journal of Structural Biology - November 27, 2018 Category: Biology Source Type: research

Variation in Human Hair Ultrastructure among Three Biogeographic Populations
This study establishes trait patterns in hair morphology and ultrastructure among three biogeographically defined metapopulations to improve the current understanding of human variation in hair form and establish a foundation for future studies on the genetic and developmental bases of phenotypic variation in hair ultrastructure related to genotype.Graphical abstract (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - November 23, 2018 Category: Biology Source Type: research

Structural insights into the catalytic mechanism of methylthioribose-1-phosphate isomerase
Publication date: Available online 22 November 2018Source: Journal of Structural BiologyAuthor(s): Prerana Gogoi, Prerana Mordina, Shankar Prasad KanaujiaAbstractMethylthioribose-1-phosphate isomerase (M1Pi) is a crucial enzyme involved in the universally conserved methionine salvage pathway (MSP) where it is known to catalyze the conversion of methylthioribose-1-phosphate (MTR-1-P) to methylthioribulose-1-phosphate (MTRu-1-P) via a mechanism which remains unspecified till date. Furthermore, although M1Pi has a discrete function, it surprisingly shares high structural similarity with two functionally non-related proteins s...
Source: Journal of Structural Biology - November 23, 2018 Category: Biology Source Type: research

Ex vivo detection of calcium phosphate and calcium carbonate in rat blood serum
Publication date: Available online 22 November 2018Source: Journal of Structural BiologyAuthor(s): Bao-Di Gou, Yang Liu, Yu-Xi Gao, Kun Tang, Lei Zheng, Yi-Dong Zhao, Tian-Lan ZhangAbstractThe total calcium (tCa) in blood serum comprises free Ca2+ ions (fCa), protein-bound calcium (prCa), and complexed calcium by small anions (cCa). The cCa fraction, in addition to fCa, has been indicated to have some physiological activity. However, there is little evidence for the structure of its constituents. Here we report an ex vivo detection of the cCa constituents by synchrotron X-ray absorption near-edge structure spectroscopy. We...
Source: Journal of Structural Biology - November 23, 2018 Category: Biology Source Type: research

Pig enamel revisited - Incremental markings in enamel of wild boars and domestic pigs
Publication date: Available online 22 November 2018Source: Journal of Structural BiologyAuthor(s): Horst Kierdorf, Friederike Breuer, Carsten Witzel, Uwe KierdorfAbstractThe nature and periodicity of incremental markings in pig enamel is currently debated. To broaden the basis for a correct interpretation of growth marks in pig enamel, we analyzed their periodicity in teeth of wild boars and domestic pigs. For that, the numbers of enamel incremental markings were recorded in ground sections and compared with crown formation times for the respective teeth derived from literature data on tooth development and eruption in Sus...
Source: Journal of Structural Biology - November 23, 2018 Category: Biology Source Type: research

Journal of Structural Biology – Paper of the Year 2018
Publication date: Available online 19 November 2018Source: Journal of Structural BiologyAuthor(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - November 21, 2018 Category: Biology Source Type: research

Changing Times: Fluorescence-Lifetime Analysis of Amyloidogenic SF-IAPP Fusion Protein
Publication date: Available online 17 November 2018Source: Journal of Structural BiologyAuthor(s): Olga I Antimonova, Dmitry V Lebedev, Yana A Zabrodskaya, Natalia A Grudinina, Andrey L Timkovsky, Edward Ramsay, Michael M Shavlovsky, Vladimir V EgorovAbstractIn a number of conformational diseases, intracellular accumulation of proteins bearing non-native conformations occurs. The search for compounds that are capable of hindering the formation and accumulation of toxic protein aggregates and fibrils is an urgent task. Present fluorescent methods of fibrils’ detection prevent simple real-time observations. We suppose ...
Source: Journal of Structural Biology - November 18, 2018 Category: Biology Source Type: research

Crystal structure and substrate recognition mechanism of Aspergillus oryzae isoprimeverose-producing enzyme
Publication date: Available online 13 November 2018Source: Journal of Structural BiologyAuthor(s): Tomohiko Matsuzawa, Masahiro Watanabe, Yusuke Nakamichi, Zui Fujimoto, Katsuro YaoiAbstractIsoprimeverose-producing enzymes (IPases) release isoprimeverose (α-d-xylopyranosyl-(1→6)-d-glucopyranose) from the non-reducing end of xyloglucan oligosaccharides. Aspergillus oryzae IPase (IpeA) is classified as a member of the glycoside hydrolase family 3 (GH3); however, it has unusual substrate specificity compared with other GH3 enzymes. Xylopyranosyl branching at the non-reducing ends of xyloglucan oligosaccharides is v...
Source: Journal of Structural Biology - November 14, 2018 Category: Biology Source Type: research

Analysis of a new flavodiiron core structural arrangement in Flv1-ΔFlR protein from Synechocystis sp. PCC6803
Publication date: Available online 14 November 2018Source: Journal of Structural BiologyAuthor(s): Patrícia T. Borges, Célia V. Romão, Lígia M. Saraiva, Vera L. Gonçalves, Maria A. Carrondo, Miguel Teixeira, Carlos FrazãoAbstractFlavodiiron proteins (FDPs) play key roles in biological response mechanisms against oxygen and/or nitric oxide; in particular they are present in oxygenic phototrophs (including cyanobacteria and gymnosperms). Two conserved domains define the core of this family of proteins: a N-terminal metallo-β-lactamase-like domain followed by a C-terminal flavodo...
Source: Journal of Structural Biology - November 14, 2018 Category: Biology Source Type: research

Structural and biochemical characterization of citrate binding to AtPPC3, a plant-type phosphoenolpyruvate carboxylase from Arabidopsis thaliana
Publication date: Available online 9 November 2018Source: Journal of Structural BiologyAuthor(s): Matthew B. Connell, Michael J.Y. Lee, Jerry Li, William C. Plaxton, Zongchao JiaAbstractPhosphoenolpyruvate carboxylase (PEPC) is a tightly regulated cytosolic enzyme situated at a crucial branch point of central plant metabolism. The structure of AtPPC3, a C3 PEPC isozyme of the model plant Arabidopsis thaliana, in complex with the inhibitors aspartate and citrate was solved at 2.2-Å resolution. This represents the first PEPC structure with citrate bound. Aspartate and citrate binding sites are in close proximity (5.1-5...
Source: Journal of Structural Biology - November 11, 2018 Category: Biology Source Type: research

Structural Dissection of Sterol Glycosyltransferase UGT51 from Saccharomyces cerevisiae for Substrate Specificity
This study reported the first sterol glycosyltransferase structure, providing a molecular blueprint for generating tailored sterol glycosyltransferases as potential catalytic elements in synthetic biology.Graphical abstract (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - November 3, 2018 Category: Biology Source Type: research

Asymmetric protein design from conserved supersecondary structures
We report the successful design of a dRP lyase domain fold, which agrees with the experimental NMR structure at atomic accuracy (backbone RMSD of 0.94 Å). Our results show that the residual folding information within conserved fragments, combined with efficient interface-directed sampling, can effectively yield globular proteins with novel sequences and biophysical properties.Graphical abstract (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 26, 2018 Category: Biology Source Type: research

Structural insight into the mechanism of action of antimicrobial peptide BMAP-28(1–18) and its analogue mutBMAP18
We report NMR structure of the BMAP-28(1–18) and its mutated analogue mutBMAP18 in SDS micelles. Structural comparison of the peptides bound to SDS micelles and POPE-POPG vesicles using circular dichroism, suggest that structures in the two lipid preparations are similar. Antimicrobial assays show that even though both these peptides adopt helical conformation, BMAP-28(1–18) is more potent than mutBMAP18 in killing bacterial cells. Our EM images clearly indicate that the peptides target the bacterial cell membrane resulting in leakage of its contents. The structural basis for difference in activity between thes...
Source: Journal of Structural Biology - October 24, 2018 Category: Biology Source Type: research

Structural and biochemical analysis of a NOT1 MIF4G-like domain of the CCR4-NOT complex
We describe a crystal structure of a connector domain of NOT1 from the thermophilic fungus Chaetomium thermophilum (Ct). Comparative structural analysis indicates that this domain adopts a MIF4G-like fold and we have termed it the MIF4G-C domain. Solution scattering studies indicate that the human MIF4G-C domain likely adopts a very similar fold to the Ct MIF4G-C. MIF4G domains have been described to mediate interactions with DEAD-box helicases such as DDX6. However, comparison of the interfaces of the MIF4G-C with the MIF4G domain of NOT1 that interacts with DDX6 reveals key structural differences that explain why the MIF...
Source: Journal of Structural Biology - October 24, 2018 Category: Biology Source Type: research

Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens
Publication date: Available online 23 October 2018Source: Journal of Structural BiologyAuthor(s): Amy E. McGrath, Alexander P. Martyn, Louise R. Whittell, Fay E. Dawes, Jennifer L. Beck, Nicholas E. Dixon, Michael J. Kelso, Aaron J. OakleyAbstractBacterial sliding clamps bind to DNA and act as protein–protein interaction hubs for several proteins involved in DNA replication and repair. The partner proteins all bind to a common pocket on sliding clamps via conserved linear peptide sequence motifs, which suggest the pocket as an attractive target for development of new antibiotics. Herein we report the X-ray crystal st...
Source: Journal of Structural Biology - October 23, 2018 Category: Biology Source Type: research

Investigating HCMV entry into host cells by STEM Tomography
Publication date: Available online 20 October 2018Source: Journal of Structural BiologyAuthor(s): Mohamed E.A. Abdellatif, Christian Sinzger, Paul WaltherAbstractHuman cytomegalovirus (HCMV) entry into susceptible cells is a fast intricate process that is not fully understood. Although, previous studies explored different aspects of this process by means of biochemical and inhibitors assays, a clear morphological characterization of its steps at the ultrastructural level is still lacking. We attempted to characterize those intermediates involved during HCMV entry by developing a methodological approach that resulted in opt...
Source: Journal of Structural Biology - October 21, 2018 Category: Biology Source Type: research

Structure and function of Mycobacterium-specific components of F-ATP synthase subunits α and ε
Publication date: Available online 17 October 2018Source: Journal of Structural BiologyAuthor(s): Nebojša Bogdanović, Lavanya Sundararaman, Neelagandan Kamariah, Anu Tyagi, Shashi Bhushan, Priya Ragunathan, Joon Shin, Thomas Dick, Gerhard GrüberAbstractThe Mycobacterium tuberculosis (Mtb) F1FO-ATP synthase (α3:β3:γ:δ:ε:a:b:b’:c9) is an essential enzyme that supplies energy for both the aerobic growing and the hypoxic dormant stage of the mycobacterial life cycle. Employing the heterologous F-ATP synthase model system αchi3:β3:γ we showed previously, that tr...
Source: Journal of Structural Biology - October 18, 2018 Category: Biology Source Type: research

The structure of DcrB, a lipoprotein from Salmonella enterica, reveals flexibility in the N-terminal segment of the Mog1p/PsbP-like fold
Publication date: Available online 16 October 2018Source: Journal of Structural BiologyAuthor(s): Damien M. Rasmussen, Ross W. Soens, Timothy J. Davie, Cody K. Vaneerd, Basudeb Bhattacharyya, John F. MayAbstractDcrB is an 18 kilodalton lipoprotein that contains a single domain of unknown function. DcrB is found within Enterobacteriaceae, a family of Gram-negative bacteria which includes pathogens that can cause food-borne illness and hospital-acquired infections. In Salmonella enterica serovar Typhimurium, DcrB is up-regulated by conditions that promote the production of known virulence factors. We determined the structure...
Source: Journal of Structural Biology - October 17, 2018 Category: Biology Source Type: research

Structural insight into the mechanism of action of antimicrobial peptide BMAP-28(1-18) and its analogue mutBMAP18
We report NMR structure of the BMAP-28(1-18) and its mutated analogue mutBMAP18 in SDS micelles. Structural comparison of the peptides bound to SDS micelles and POPE-POPG vesicles using circular dichroism, suggest that structures in the two lipid preparations are similar. Antimicrobial assays show that even though both these peptides adopt helical conformation, BMAP-28(1-18) is more potent than mutBMAP18 in killing bacterial cells. Our EM images clearly indicate that the peptides target the bacterial cell membrane resulting in leakage of its contents. The structural basis for difference in activity between these peptides w...
Source: Journal of Structural Biology - October 15, 2018 Category: Biology Source Type: research

Comparing Cryo-EM Structures
Publication date: Available online 13 October 2018Source: Journal of Structural BiologyAuthor(s): Catherine L. Lawson, Wah Chiu (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 13, 2018 Category: Biology Source Type: research

Structural insights into the specificity and catalytic mechanism of mycobacterial nucleotide pool sanitizing enzyme MutT2
Publication date: Available online 9 October 2018Source: Journal of Structural BiologyAuthor(s): Amandeep Singh, Sheikh Mohammad Arif, Pau Biak Sang, Umesh Varshney, M. VijayanAbstractMis-incorporation of modified nucleotides, such as 5-methyl-dCTP or 8-oxo-dGTP, in DNA can be detrimental to genomic integrity. MutT proteins are sanitization enzymes which function by hydrolyzing such nucleotides and regulating the pool of free nucleotides in the cytoplasm. Mycobacterial genomes have a set of four MutT homologs, namely, MutT1, MutT2, MutT3 and MutT4. Mycobacterial MutT2 hydrolyzes 5m-dCTP and 8-oxo-dGTP to their respective m...
Source: Journal of Structural Biology - October 11, 2018 Category: Biology Source Type: research

Using Scipion for Stream Image Processing at Cryo-EM Facilities
We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished. At present, Scipion has been deployed and is in production mode in seven Cryo-EM facilities throughout the world. (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 6, 2018 Category: Biology Source Type: research

Fast Multiscale Reconstruction for Cryo-EM
We present a multiscale reconstruction framework for single-particle analysis (SPA). The representation of three-dimensional (3D) objects with scaled basis functions permits the reconstruction of volumes at any desired scale in the real-space. This multiscale approach generates interesting opportunities in SPA for the stabilization of the initial volume problem or the 3D iterative refinement procedure. In particular, we show that reconstructions performed at coarse scale are more robust to angular errors and permit gains in computational speed. A key component of the proposed iterative scheme is its fast implementation. Th...
Source: Journal of Structural Biology - October 5, 2018 Category: Biology Source Type: research

Structural characterization of the sporulation protein GerM from Bacillus subtilis
Publication date: Available online 25 September 2018Source: Journal of Structural BiologyAuthor(s): Jennyfer Trouve, Ahmed Mohamed, Francisco Leisico, Carlos Contreras-Martel, Bowen Liu, Caroline Mas, David Z. Rudner, Christopher D.A. Rodrigues, Cecile MorlotAbstractThe Gram-positive bacterium Bacillus subtilis responds to starvation by entering a morphological differentiation process leading to the formation of a highly resistant spore. Early in the sporulation process, the cell asymmetrically divides into a large compartment (the mother cell) and a smaller one (the forespore), which will maturate into a resistant spore. ...
Source: Journal of Structural Biology - October 5, 2018 Category: Biology Source Type: research

Map Challenge: Analysis using a Pair Comparison Method based on Fourier Shell Correlation
Publication date: Available online 28 September 2018Source: Journal of Structural BiologyAuthor(s): R. Marabini, M. Kazemi, C.O.S. Sorzano, J.M. CarazoAbstractThis document presents the analysis performed over the Map Challenge dataset using a new algorithm which we refer to as Pair Comparison Method. The new algorithm, which is described in detail in the text, is able to sort reconstructions based on a figure of merit and assigns a level of significance to the sorting. That is, it shows how likely the sorting is due to chance or if it reflects real differences. (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 5, 2018 Category: Biology Source Type: research

DNP NMR of Biomolecular Assemblies
Publication date: Available online 29 September 2018Source: Journal of Structural BiologyAuthor(s): Kristaps Jaudzems, Tatyana Polenova, Guido Pintacuda, Hartmut Oschkinat, Anne LesageAbstractDynamic Nuclear Polarization (DNP) is an effective approach to alleviate the inherently low sensitivity of solid-state NMR (ssNMR) under magic angle spinning (MAS) towards large-sized multi-domain complexes and assemblies. DNP relies on a polarization transfer at cryogenic temperatures from unpaired electrons to adjacent nuclei upon continuous microwave irradiation. This is usually made possible via the addition in the sample of a pol...
Source: Journal of Structural Biology - October 5, 2018 Category: Biology Source Type: research

Tailored disorder in calcite organization in tergite cuticle of the supralittoral isopod Tylos europaeus Arcangeli, 1938
In this study, we investigate structure, chemical composition, mineral organization and local mechanical properties of the anterior and posterior edges of the tergite cuticle in the conglobating beach isopod Tylos europaeus and compare these with the protective dorsal region of the tergites.The distribution of mineral phases at the edges resembles that of dorsal regions of the tergites. At the transition with the unmineralized arthrodial membrane the calcite containing distal exocuticle is replaced by epicuticular material and the subjacent cuticular layers containing amorphous calcium carbonate become enriched with amorph...
Source: Journal of Structural Biology - October 5, 2018 Category: Biology Source Type: research

Crystal structure of a biliverdin-bound phycobiliprotein: interdependence of oligomerization and chromophorylation
Publication date: Available online 1 October 2018Source: Journal of Structural BiologyAuthor(s): Juan Pablo Fuenzalida-Werner, Robert Janowski, Kanuj Mishra, Ina Weidenfeld, Dierk Niessing, Vasilis Ntziachristos, Andre C. StielAbstractSmall, ultra-red fluorescence protein (smURFP) introduces the non-native biliverdin (BV) chromophore to phycobiliproteins (PBPs), allowing them to be used as transgenic labels for in vivo mammalian imaging. Presently, no structural information exists for PBPs bound to the non-native BV chromophore, which limits the further development of smURFP and related proteins as imaging labels or indica...
Source: Journal of Structural Biology - October 5, 2018 Category: Biology Source Type: research

Editorial Board
Publication date: November 2018Source: Journal of Structural Biology, Volume 204, Issue 2Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 5, 2018 Category: Biology Source Type: research

Direct evidence supporting the existence of a helical dislocation in protofilament packing in the intermediate filaments of oxidized trichocyte keratin
Publication date: Available online 21 September 2018Source: Journal of Structural BiologyAuthor(s): R.D. Bruce Fraser, David A.D. ParryAbstractThe X-ray diffraction patterns of quill and hair, as well as other trichocyte keratin appendages, contain meridional reflections that can be indexed on an axial repeat of 470 Å. Unusually, however, many of the expected orders are not observed. A possible explanation, proposed by Fraser and MacRae (1983), was that the intermediate filaments (IF) that constitute the fibrillar component of the filament/matrix texture consist of 4-chain protofilaments arranged on a surface lattice...
Source: Journal of Structural Biology - September 22, 2018 Category: Biology Source Type: research

Structural modulation of a periplasmic sugar-binding protein probes into its evolutionary ancestry
This study also provides the direct structural and functional correlation indicating that divergence of proteins may occur through insertions or deletions of sequences in the already existing SBPs leading to evolution at the functional level.Graphical abstract (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - September 21, 2018 Category: Biology Source Type: research

Automation and assessment of de Novo modeling with pathwalking in near atomic resolution cryoem density maps
Publication date: Available online 17 September 2018Source: Journal of Structural BiologyAuthor(s): Muyuan Chen, Matthew L. BakerAbstractWith the rapidly growing number of macromolecular structures solved to near-atomic resolution using electron cryomicroscopy (cryoEM), map interpretation and model building directly from the density without the use of structural templates has become increasingly important. As part of the 2015/2016 Map and Model Challenge, we attempted to assess our latest de novo modeling tool, Pathwalking, in terms of performance and usability, as well as identify areas for future improvements. In total, ...
Source: Journal of Structural Biology - September 17, 2018 Category: Biology Source Type: research

Assessing the quality of single particle reconstructions by atomic model building
Publication date: Available online 10 September 2018Source: Journal of Structural BiologyAuthor(s): Joshua H. Mendez, Scott M. StaggAbstractThe 2015/2016 Map Challenge challenged cryo-EM practitioners to process a series of publicly available cryo-EM datasets. As part of the challenge, metrics needed to be developed to assess and compare the quality of the different map submissions. The most common metric for assessing maps is determining the resolution by Fourier shell correlation (FSC), but there are well known instances where the resolution can be misleading. In this manuscript, we present a new approach for assessing t...
Source: Journal of Structural Biology - September 11, 2018 Category: Biology Source Type: research

Structural flexibility in the Helicobacter pylori peptidyl-prolyl cis,trans-isomerase HP0175 is achieved through an extension of the chaperone helices
Publication date: Available online 1 September 2018Source: Journal of Structural BiologyAuthor(s): Ayat Yaseen, Gerald F. AudetteAbstractHelicobacter pylori infects the gastric epithelium of half the global population, where infections can persist into adenocarcinomas and peptic ulcers. H. pylori secretes several proteins that lend to its pathogenesis and survival including VacA, CagA, γ-glutamyltransferase and HP0175. HP0175, also known as HpCBF2, classified as a peptidyl-prolyl cis,trans-isomerase, has been shown to induce apoptosis through a cascade of mechanisms initiated though its interaction with toll like rec...
Source: Journal of Structural Biology - September 9, 2018 Category: Biology Source Type: research

Advances in Instrumentation and Methodology for Solid-State NMR of Biological Assemblies
Publication date: Available online 8 September 2018Source: Journal of Structural BiologyAuthor(s): Rachel W. Martin, John E. Kelly, Jessica I. KelzAbstractMany advances in instrumentation and methodology have furthered the use of solid-state NMR as a technique for determining the structure and studying the dynamics of molecules involved in complex biological assemblies. Solid-state NMR does not require large crystals, has no inherent size limit, and with appropriate isotopic labeling schemes, supports solving one component of a complex assembly at a time. It is complementary to cryo-EM, in that it provides local, atomic-le...
Source: Journal of Structural Biology - September 9, 2018 Category: Biology Source Type: research

Polyserine repeats promote coiled coil-mediated fibril formation and length-dependent protein aggregation
Publication date: Available online 6 September 2018Source: Journal of Structural BiologyAuthor(s): Elena Lilliu, Veronica Villeri, Ilaria Pelassa, Federico Cesano, Domenica Scarano, Ferdinando FiumaraAbstractShort polyserine (polyS) repeats are frequently found in proteins and longer ones are produced in neurological disorders such as Huntington disease (HD) owing to translational frameshifting or non-ATG-dependent translation, alongside with polyglutamine (polyQ) and polyalanine (polyA) repeats, forming intracellular aggregates. However, the physiological and pathological structures of polyS repeats are not clearly unders...
Source: Journal of Structural Biology - September 6, 2018 Category: Biology Source Type: research

New software tools in EMAN2 inspired by EMDatabank map challenge
Publication date: Available online 4 September 2018Source: Journal of Structural BiologyAuthor(s): James M. Bell, Muyuan Chen, Tunay Durmaz, Adam C. Fluty, Steven J. LudtkeAbstractEMAN2 is an extensible software suite with complete workflows for performing high-resolution single particle analysis, 2-D and 3-D heterogeneity analysis, and subtomogram averaging, among other tasks. Participation in the recent CryoEM Map Challenge sponsored by the EMDatabank led to a number of significant improvements to the single particle analysis process in EMAN2. A new convolutional neural network particle picker was developed, which dramat...
Source: Journal of Structural Biology - September 5, 2018 Category: Biology Source Type: research

Structural Flexibility in the Helicobacter pylori Peptidyl-prolyl cis, trans-Isomerase HP0175 is achieved through an Extension of the Chaperone Helices
Publication date: Available online 1 September 2018Source: Journal of Structural BiologyAuthor(s): Ayat Yaseen, Gerald AudetteAbstractHelicobacter pylori infects the gastric epithelium of half the global population, where infections can persist into adenocarcinomas and peptic ulcers. H. pylori secretes several proteins that lend to its pathogenesis and survival including VacA, CagA, γ-glutamyltransferase and HP0175. HP0175, also known as HpCBF2, classified as a peptidyl-prolyl cis,trans-isomerase, has been shown to induce apoptosis through a cascade of mechanisms initiated though its interaction with toll like recept...
Source: Journal of Structural Biology - September 1, 2018 Category: Biology Source Type: research

Flexibility of the sec13/31 cage is influenced by the sec31 C-terminal disordered domain
Publication date: Available online 30 August 2018Source: Journal of Structural BiologyAuthor(s): Mohammadreza Paraan, Nilakshee Bhattacharya, Vladimir N. Uversky, Scott M. StaggAbstractIn COPII mediated vesicle formation, Sec13/Sec31 heterotetramers play a role in organizing the membranes into a spherical vesicle. There they oligomerize into a cage that interacts with the other COPII proteins to direct vesicle formation and concentrate cargo into a bud. In this role they must be flexible to accommodate different sizes and shapes of cargo, but also have elements that provide rigidity to help deform the membrane. Here we cha...
Source: Journal of Structural Biology - August 31, 2018 Category: Biology Source Type: research

Editorial Board
Publication date: October 2018Source: Journal of Structural Biology, Volume 204, Issue 1Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - August 29, 2018 Category: Biology Source Type: research

Structural and functional analyses of calcium ion response factors in the mantle of Pinctada fucata
Publication date: Available online 17 August 2018Source: Journal of Structural BiologyAuthor(s): Akihiro Matsuura, Ko Yoshimura, Hiroyuki Kintsu, Takashi Atsumi, Yasushi Tsuchihashi, Takeshi Takeuchi, Noriyuki Satoh, Lumi Negishi, Shohei Sakuda, Tomiko Asakura, Yuki Imura, Etsuro Yoshimura, Michio SuzukiAbstractThe pearl oyster, Pinctada fucata, is cultured for pearl production in Japan. The shell of the pearl oyster consists of calcium carbonate and a small amount of organic matrix. Despite many studies of the shell matrix proteins, the mechanism by which calcium elements are transported from the mantle to the shell remai...
Source: Journal of Structural Biology - August 24, 2018 Category: Biology Source Type: research

A new algorithm for high-resolution reconstruction of Single Particles by Electron Microscopy
Publication date: Available online 24 August 2018Source: Journal of Structural BiologyAuthor(s): C.O.S. Sorzano, J. Vargas, J.M. de la Rosa-Trevín, A. Jiménez, D. Maluenda, R. Melero, M. Martínez, E. Ramírez-Aportela, P. Conesa, J.L. Vilas, R. Marabini, J.M. CarazoAbstractThe Map Challenge organized by the Electron Microscopy Data Bank has prompted the development of an Xmipp high resolution reconstruction protocol (which we will refer to as highres) that is integrated in the software platform Scipion. In this work we describe the details of the image angular alignment and map reconstruction ste...
Source: Journal of Structural Biology - August 24, 2018 Category: Biology Source Type: research

Assessment of Structural Features in Cryo-EM Density Maps using SSE and Side Chain Z-Scores
Publication date: Available online 23 August 2018Source: Journal of Structural BiologyAuthor(s): Grigore Pintilie, Wah ChiuAbstractWe introduce a new method for assessing resolvability of structural features in density maps from Cryo-Electron Microscopy (Cryo-EM) using a fitted model. It calculates Z-scores for secondary structure elements (SSEs) and side chains. Z-scores capture how much larger the cross-correlations score (CCS) is for atoms in such features at their placed location compared to the CCS at displaced positions. Z-scores are larger when the structural features are well-resolved, as confirmed by visual analys...
Source: Journal of Structural Biology - August 23, 2018 Category: Biology Source Type: research

APPLE Picker: Automatic Particle Picking, a Low-Effort Cryo-EM Framework
Publication date: Available online 19 August 2018Source: Journal of Structural BiologyAuthor(s): Ayelet Heimowitz, Joakim Andén, Amit SingerAbstractParticle picking is a crucial first step in the computational pipeline of single-particle cryo-electron microscopy (cryo-EM). Selecting particles from the micrographs is difficult especially for small particles with low contrast. As high-resolution reconstruction typically requires hundreds of thousands of particles, manually picking that many particles is often too time-consuming. While template-based particle picking is currently a popular approach, it may suffer from ...
Source: Journal of Structural Biology - August 20, 2018 Category: Biology Source Type: research

Structural behavior of keratin-associated protein 8.1 in human hair as revealed by a monoclonal antibody
In this study, we generated a monoclonal antibody against human KAP8.1 to analyze the protein’s roles and distribution in the human hair shaft. Using this antibody, we revealed that KAP8.1 was predominantly expressed in discrete regions of the keratinizing zone of the hair shaft cortex. The protein expression patterns paralleled the distribution of KAP8.1 mRNA and suggested that KAP8.1 plays a role associated with cells to control hair curvature. Cross-reactivity among species and epitope analysis indicated that the monoclonal antibody recognized a linear epitope shared among human, mouse, and sheep KAP8.1. The antib...
Source: Journal of Structural Biology - August 18, 2018 Category: Biology Source Type: research