A methodology using Gaussian-based density map approximation to assess sets of cryo-electron microscopy density maps
This article presents a methodology to assess a set of density maps, as used in the Blind Assessment Phase of the 2015/2016 Map Challenge (EMDataBank Validation Challenges). The synthetic and experimental cryo-electron microscopy (cryo-EM) density maps obtained by different single particle analysis protocols and by different participants, submitted in the Challenge Phase for assessment, were analyzed with this methodology and the obtained results are presented and discussed here. The goal of using such a methodology was to blindly identify the density maps with globally similar structural information, meaning the maps with...
Source: Journal of Structural Biology - July 20, 2018 Category: Biology Source Type: research

Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency
Publication date: Available online 19 July 2018Source: Journal of Structural BiologyAuthor(s): Catherine Bougault, Isabel Ayala, Waldemar Vollmer, Jean-Pierre Simorre, Paul SchandaAbstractThe bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeniety, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spin...
Source: Journal of Structural Biology - July 20, 2018 Category: Biology Source Type: research

Modulation of calcium oxalate dihydrate growth by phosphorylated osteopontin peptides
Publication date: Available online 17 July 2018Source: Journal of Structural BiologyAuthor(s): Yung-Ching Chien, Ahmad Mansouri, Wenge Jiang, Saeed R. Khan, Jeffrey J. Gray, Marc D. McKeeAbstractOsteopontin (OPN) is a significant component of kidney stone matrix and a key modulator of stone formation. Here, we investigated the effects of different phosphorylated states of a synthesized peptide of OPN (the ASARM peptide; acidic, serine- and aspartate-rich motif) on calcium oxalate dihydrate (COD) crystals, a major mineral phase of kidney stones. In vitro, phosphorylated OPN-ASARM peptides strongly inhibited COD crystal grow...
Source: Journal of Structural Biology - July 18, 2018 Category: Biology Source Type: research

Crystal structure of saposin D in an open conformation
Publication date: Available online 17 July 2018Source: Journal of Structural BiologyAuthor(s): Ahmad Gebai, Alexei Gorelik, Bhushan NagarAbstractSaposins are accessory proteins that aid in the degradation of sphingolipids by hydrolytic enzymes. Their structure usually comprises four α-helices arranged in various conformations including an open, V-shaped form that is generally associated with the ability to interact with membranes and/or enzymes to accentuate activity. Saposin D is required by the lysosomal hydrolase, acid ceramidase, which breaks down ceramide into sphingosine and free fatty acid, to display optimal ...
Source: Journal of Structural Biology - July 18, 2018 Category: Biology Source Type: research

Map Challenge Assessment: Fair comparison of single particle cryoEM reconstructions
Publication date: Available online 17 July 2018Source: Journal of Structural BiologyAuthor(s): J. Bernard HeymannAbstractCryo-electron microscopy (cryoEM) is capable of achieving near-atomic resolution of biomolecular structures due to recent advances in hardware. Despite the long history of image processing software development for cryoEM, uncertainty about best practices and validation remains. The Map Challenge was therefore designed to test the current state of single particle reconstruction. As the first such challenge, the participants were given the freedom to analyze the cases in whichever way they wanted. Therefor...
Source: Journal of Structural Biology - July 18, 2018 Category: Biology Source Type: research

Improved sample dispersion in cryo-EM using “perpetually-hydrated” graphene oxide flakes
Publication date: Available online 18 July 2018Source: Journal of Structural BiologyAuthor(s): Martin Cheung, Hidehito Adaniya, Cathal Cassidy, Masao Yamashita, Kun-Lung Li, Seita Taba, Tsumoru ShintakeAbstractFor many macromolecular complexes, the inability to uniformly disperse solubilized specimen particles within vitreous ice films precludes their analysis by cryo-electron microscopy (cryo-EM). Here, we introduce a sample preparation process using “perpetually-hydrated” graphene oxide flakes as particle support films, and report vastly improved specimen dispersion. The new method introduced in this study in...
Source: Journal of Structural Biology - July 18, 2018 Category: Biology Source Type: research

Evaluation System and Web Infrastructure for the Second Cryo-EM Model Challenge
Publication date: Available online 12 July 2018Source: Journal of Structural BiologyAuthor(s): Andriy Kryshtafovych, Paul D. Adams, Catherine L. Lawson, Wah ChiuAbstractAn evaluation system and a web infrastructure were developed for the second cryo-EM model challenge. The evaluation system includes tools to validate stereo-chemical plausibility of submitted models, check their fit to the corresponding density maps, estimate their overall and per-residue accuracy, and assess their similarity to reference cryo-EM or X-ray structures as well as other models submitted in this challenge. The web infrastructure provides a conve...
Source: Journal of Structural Biology - July 13, 2018 Category: Biology Source Type: research

A simple and robust procedure for preparing graphene-oxide cryo-EM grids
Publication date: Available online 11 July 2018Source: Journal of Structural BiologyAuthor(s): Eugene Palovcak, Feng Wang, Shawn Q. Zheng, Zanlin Yu, Sam Li, Miguel Betegon, David Bulkley, David A. Agard, Yifan ChengAbstractGraphene oxide (GO) sheets have been used successfully as a supporting substrate film in several recent cryogenic electron-microscopy (cryo-EM) studies of challenging biological macromolecules. However, difficulties in preparing GO-covered holey carbon EM grids have limited their widespread use. Here, we report a simple and robust method for covering holey carbon EM grids with GO sheets and demonstrate ...
Source: Journal of Structural Biology - July 12, 2018 Category: Biology Source Type: research

Studying assembly of the BAM complex in native membranes by cellular solid-state NMR spectroscopy
Publication date: Available online 29 November 2017Source: Journal of Structural BiologyAuthor(s): Cecilia Pinto, Deni Mance, Manon Julien, Mark Daniels, Markus Weingarth, Marc BaldusAbstractSignificant progress has been made in obtaining structural insight into the assembly of the β-barrel assembly machinery complex (BAM). These crystallography and electron microscopy studies used detergent as a membrane mimetic and revealed structural variations in the central domain, BamA, as well as in the lipoprotein BamC. We have used cellular solid-state NMR spectroscopy to examine the entire BamABCDE complex in native outer me...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Coiled-coil oligomerization controls localization of the plasma membrane REMORINs
Publication date: Available online 23 February 2018Source: Journal of Structural BiologyAuthor(s): Denis Martinez, Anthony Legrand, Julien Gronnier, Marion Decossas, Paul Gouguet, Olivier Lambert, Mélanie Berbon, Loris Verron, Axelle Grélard, Veronique Germain, Antoine Loquet, Sébastien Mongrand, Birgit HabensteinAbstractREMORINs are nanodomain-organized proteins located in the plasma membrane and involved in cellular responses in plants. The dynamic assembly of the membrane nanodomains represents an essential tool of the versatile membrane barriers to control and modulate cellular functions. Neverthel...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Interplay between membrane curvature and protein conformational equilibrium investigated by solid-state NMR
Publication date: Available online 1 March 2018Source: Journal of Structural BiologyAuthor(s): Shu Y. Liao, Myungwoon Lee, Mei HongAbstractMany membrane proteins sense and induce membrane curvature for function, but structural information about how proteins modulate their structures to cause membrane curvature is sparse. We review our recent solid-state NMR studies of two virus membrane proteins whose conformational equilibrium is tightly coupled to membrane curvature. The influenza M2 proton channel has a drug-binding site in the transmembrane (TM) pore. Previous chemical shift data indicated that this pore-binding site i...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Amyloid structure of high-order assembly of Leucine-rich amelogenin revealed by solid-state NMR
Publication date: Available online 28 March 2018Source: Journal of Structural BiologyAuthor(s): Cheng-Wei Ma, Jing Zhang, Xing-Qi Dong, Jun-Xia LuAbstractHigh-order assemblies of amelogenin, the major protein in enamel protein matrix, are believed to act as the template for enamel mineral formation. The Leucine-rich amelogenin (LRAP) is a natural splice-variant of amelogenin, a functional protein in vivo, containing conserved domains of amelogenin. In this work, we showed LRAP aggregates hierarchically into assemblies with various sizes including scattered beads, beads-on-a-string and gel-like precipitations in the presenc...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Comparison of the 3D Structures of Mouse and Human α-Synuclein Fibrils by Solid-State NMR and STEM
Publication date: Available online 17 April 2018Source: Journal of Structural BiologyAuthor(s): Songhwan Hwang, Pascal Fricke, Maximilian Zinke, Karin Giller, Joseph S. Wall, Dietmar Riedel, Stefan Becker, Adam LangeAbstractIntra-neuronal aggregation of α-synuclein into fibrils is the molecular basis for α -synucleinopathies, such as Parkinson’s disease. The atomic structure of human α -synuclein (hAS) fibrils was recently determined by Tuttle et al. using solid-state NMR (ssNMR). The previous study found that hAS fibrils are composed of a single protofilament. Here, we have investigated the structu...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Protein-Solvent Interfaces in Human Y145Stop Prion Protein Amyloid Fibrils Probed by Paramagnetic Solid-State NMR Spectroscopy
Publication date: Available online 18 April 2018Source: Journal of Structural BiologyAuthor(s): Darryl Aucoin, Yongjie Xia, Theint Theint, Philippe S. Nadaud, Krystyna Surewicz, Witold K. Surewicz, Christopher P. JaroniecAbstractThe C-terminally truncated Y145Stop variant of prion protein (PrP23-144), which is associated with heritable PrP cerebral amyloid angiopathy in humans and also capable of triggering a transmissible prion disease in mice, serves as a useful in vitro model for investigating the molecular and structural basis of amyloid strains and cross-seeding specificities. Here, we determine the protein-solvent in...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Collagen Gly missense mutations: Effect of residue identity on collagen structure and integrin binding
Publication date: Available online 11 May 2018Source: Journal of Structural BiologyAuthor(s): Yimin Qiu, Arya Mekkat, Hongtao Yu, Sezin Yigit, Samir Hamaia, Richard W. Farndale, David L. Kaplan, Yu-Shan Lin, Barbara BrodskyAbstractGly missense mutations in type I collagen, which replace a conserved Gly in the repeating (Gly-Xaa-Yaa)n sequence with a larger residue, are known to cause Osteogenesis Imperfecta (OI). The clinical consequences of such mutations range from mild to lethal, with more serious clinical severity associated with larger Gly replacement residues. Here, we investigate the influence of the identity of the...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Effects of flexibility of the α2 chain of type I collagen on collagenase cleavage
This study indicates that α2(I) homotrimers are susceptible to MMP-1, proves that the presence of an α1(I) chain is not a requirement for α2(I) cleavage, and supports the importance of local unfolding of α2(I) in collagenase cleavage. (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Atomic structure of a rationally engineered gene delivery vector, AAV2.5
Publication date: Available online 18 May 2018Source: Journal of Structural BiologyAuthor(s): Matthew Burg, Claire Rosebrough, Lauren M. Drouin, Antonette Bennett, Mario Mietzsch, Paul Chipman, Robert McKenna, Duncan Sousa, Mark Potter, Barry Byrne, R. Jude Samulski, Mavis Agbandje-McKennaAbstractAAV2.5 represents the first structure-guided in-silico designed Adeno-associated virus (AAV) gene delivery vector. This engineered vector combined the receptor attachment properties of AAV serotype 2 (AAV2) with the muscle tropic properties of AAV1, and exhibited an antibody escape phenotype because of a modified antigenic epitope...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Mechanical variations in proteins with large-scale motions highlight the formation of structural locks
Publication date: Available online 28 May 2018Source: Journal of Structural BiologyAuthor(s): Sophie Sacquin-MoraAbstractProtein function depends just as much on flexibility as on structure, and in numerous cases, a protein’s biological activity involves transitions that will impact both its conformation and its mechanical properties. Here, we use a coarse-grain approach to investigate the impact of structural changes on protein flexibility. More particularly, we focus our study on proteins presenting large-scale motions. We show how calculating directional force constants within residue pairs, and investigating thei...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Know your detergents: A case study on detergent background in negative stain electron microscopy
Publication date: Available online 29 May 2018Source: Journal of Structural BiologyAuthor(s): Theresa Gewering, Dovile Januliene, Anne B. Ries, Arne MoellerAbstractElectron cryo-microscopy (cryo-EM) of purified macromolecular complexes is now providing 3D-structures at near-atomic resolution (Kühlbrandt, 2014). Cryo-EM can tolerate heterogeneous specimens, however, high-resolution efforts demand highly optimized samples. Therefore, significant pre-screening and evaluation is essential before a final dataset can be obtained.While cryo-EM is comparably slow and requires access to expensive high-end electron microscopes,...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

The protofilament architecture of a de novo designed coiled coil-based amyloidogenic peptide
Publication date: Available online 29 May 2018Source: Journal of Structural BiologyAuthor(s): Mônica Santos de Freitas, Raheleh Rezaei Araghi, Enrico Brandenburg, Jork Leiterer, Franziska Emmerling, Kristin Folmert, Ulla I.M. Gerling-Driessen, Benjamin Bardiaux, Christoph Böttcher, Kevin Pagel, Anne Diehl, Hans v. Berlepsch, Hartmut Oschkinat, Beate KokschAbstractAmyloid fibrils are polymers formed by proteins under specific conditions and in many cases they are related to pathogenesis, such as Parkinson’s and Alzheimer’s diseases. Their hallmark is the presence of a β-sheet structure. High reso...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Biochemical characterization of the skeletal matrix of the massive coral, Porites australiensis – The saccharide moieties and their localization
Publication date: Available online 30 May 2018Source: Journal of Structural BiologyAuthor(s): Takeshi Takeuchi, Laurent Plasseraud, Isabelle Ziegler-Devin, Nicolas Brosse, Chuya Shinzato, Noriyuki Satoh, Frédéric MarinAbstractTo construct calcium carbonate skeletons of sophisticated architecture, scleractinian corals secrete an extracellular skeletal organic matrix (SOM) from aboral ectodermal cells. The SOM, which is composed of proteins, saccharides, and lipids, performs functions critical for skeleton formation. Even though polysaccharides constitute the major component of the SOM, its contribution to cora...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Plasmin-driven fibrinolysis in a quasi-two-dimensional nanoscale fibrin matrix
Publication date: Available online 30 May 2018Source: Journal of Structural BiologyAuthor(s): Tímea Feller, Jolán Hársfalvi, Csilla Csányi, Balázs Kiss, Miklós KellermayerAbstractFibrin plays a fundamentally important role during hemostasis. To withstand the shear forces of blood flow and prevent embolisation, fibrin monomers form a three-dimensional polymer network that serves as an elastic scaffold for the blood clot. The complex spatial hierarchy of the fibrin meshwork, however, severely complicates the exploration of structural features, mechanical properties and molecular chan...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Spectral comparisons of mammalian cells and intact organelles by solid-state NMR
Publication date: Available online 30 May 2018Source: Journal of Structural BiologyAuthor(s): Sabrina H. Werby, Lynette CegelskiAbstractWhole-cell protein profiling, spatial localization, and quantification of activities such as gene transcription and protein translation are possible with modern biochemical and biophysical techniques. Yet, addressing questions of overall compositional changes within a cell – capturing the relative amounts of protein and ribosomal RNA levels and lipid content simultaneously – would require extractions and purifications with caveats due to isolation yields and detection methods. ...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud
Publication date: Available online 1 June 2018Source: Journal of Structural BiologyAuthor(s): Michael A. Cianfrocco, Indrajit Lahiri, Frank DiMaio, Andres E. LeschzinerAbstractAccess to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have developed tools that will submit cryo-EM analysis routines and atomic model building jobs directly to Amazon Web Services (AWS) from a local computer or laptop. These new software tools (“cryoem-cloud-tools”) have incorporated optimal data movement, security, and cost-saving strategie...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Solid-state NMR analysis of the sodium pump Krokinobacter rhodopsin 2 and its H30A mutant
This study is complemented by data from time-resolved optical spectroscopy. (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Reductive power of the archaea right-handed coiled coil nanotube (RHCC-NT) and incorporation of mercury clusters inside protein cages
Publication date: Available online 5 June 2018Source: Journal of Structural BiologyAuthor(s): Matthew McDougall, Kevin McEleney, Olga Francisco, Benchmen Trieu, Efehi Kelly Ogbomo, Gregg Tomy, Jörg StetefeldAbstractCoiled coils are well described as powerful oligomerization motifs and exhibit a large diversity of functions, including gene regulation, cell division, membrane fusion and drug extrusion. The archaea S-layer originated right-handed coiled coil –RHCC-NT- is characterized by extreme stability and is free of cysteine and histidine moieties. In the current study, we have followed a multidisciplinary appr...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Identification of a novel tetrameric structure for human apolipoprotein-D
Publication date: Available online 6 June 2018Source: Journal of Structural BiologyAuthor(s): Claudia S. Kielkopf, Jason K.K. Low, Yee-Foong Mok, Surabhi Bhatia, Tony Palasovski, Aaron J. Oakley, Andrew E. Whitten, Brett Garner, Simon H.J. BrownAbstractApolipoprotein-D is a 25 kDa glycosylated member of the lipocalin family that folds into an eight-stranded β-barrel with a single adjacent α-helix. Apolipoprotein-D specifically binds a range of small hydrophobic ligands such as progesterone and arachidonic acid and has an antioxidant function that is in part due to the reduction of peroxidised lipids by methion...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Structural and biochemical characterization of SpoIIIAF, a component of a sporulation-essential channel in Bacillus subtilis
Publication date: Available online 7 June 2018Source: Journal of Structural BiologyAuthor(s): N. Zeytuni, K.A. Flanagan, L.J. Worrall, S.C. Massoni, A.H. Camp, N.C.J. StrynadkaAbstractEnvironmental stress factors initiate the developmental process of sporulation in some Gram-positive bacteria including Bacillus subtilis. Upon sporulation initiation the bacterial cell undergoes a series of morphological transformations that result in the creation of a single dormant spore. Early in sporulation, an asymmetric cell division produces a larger mother cell and smaller forespore. Next, the mother cell septal membrane engulfs the ...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

High resolution crystal structure of substrate-free human neprilysin
Publication date: Available online 12 June 2018Source: Journal of Structural BiologyAuthor(s): Stephen Moss, Vasanta Subramanian, K. Ravi AcharyaAbstractNeprilysin is a transmembrane M13 zinc metalloprotease responsible for the degradation of several biologically active peptides including insulin, enkephalin, substance P, bradykinin, endothelin-1, neurotensin and amyloid-β. The protein has received attention for its role in modulating blood pressure responses with its inhibition producing an antihypertensive response. To date, several inhibitor bound crystal structures of the human neprilysin extracellular domain have...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

PSF correction in soft x-ray tomography
Publication date: Available online 13 June 2018Source: Journal of Structural BiologyAuthor(s): Axel Ekman, Venera Weinhardt, Jian-Hua Chen, Gerry McDermott, Mark A. Le Gros, Carolyn LarabellAbstractIn this manuscript, we introduce a linear approximation of the forward model of soft x-ray tomography (SXT), such that the reconstruction is solvable by standard iterative schemes. This linear model takes into account the three-dimensional point spread function (PSF) of the optical system, which consequently enhances the reconstruction data. The feasibility of the model is demonstrated on both simulated and experimental data, ba...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Detection of single alpha-helices in large protein sequence sets using hardware acceleration
Publication date: Available online 13 June 2018Source: Journal of Structural BiologyAuthor(s): Ákos Kovács, Dániel Dudola, László Nyitray, Gábor Tóth, Zoltán Nagy, Zoltán GáspáriAbstractSingle alpha-helices (SAHs) are increasingly recognized as important structural and functional elements of proteins. Comprehensive identification of SAH segments in large protein datasets was largely hindered by the slow speed of the most restrictive prediction tool for their identification, FT_CHARGE on common hardware. We have previously implemented an FPGA-based...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Analytical symmetry detection in protein assemblies. II. Dihedral and cubic symmetries
Publication date: Available online 15 June 2018Source: Journal of Structural BiologyAuthor(s): Guillaume Pagès, Sergei GrudininAbstractProtein assemblies are often symmetric, as this organization has many advantages compared to individual proteins. Complex protein structures thus very often possess high-order symmetries. Detection and analysis of these symmetries has been a challenging problem and no efficient algorithms have been developed so far. This paper presents the extension of our cyclic symmetry detection method for higher-order symmetries with multiple symmetry axes. These include dihedral and cubic, i.e.,...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Characterization of inter-crystallite peptides in human enamel rods reveals contribution by the Y allele of amelogenin
Publication date: Available online 28 June 2018Source: Journal of Structural BiologyAuthor(s): Catherine Rathsam, Ramin M Farahani, Peter G Hains, Valentina A Valova, Nattida Charadram, Hans Zoellner, Michael Swain, Neil HunterAbstractProteins of the inter-rod sheath and peptides within the narrow inter-crystallite space of the rod structure are considered largely responsible for visco-elastic and visco-plastic properties of enamel. The present study was designed to investigate putative peptides of the inter-crystallite space. Entities of 1-6 kDa extracted from enamel rods of erupted permanent teeth were analysed by mass s...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Processing Apoferritin with the Appion Pipeline
Publication date: Available online 30 June 2018Source: Journal of Structural BiologyAuthor(s): Scott Stagg, Joshua H. MendezAbstractThe 3DEM map challenge provided an opportunity to test different algorithms and workflows for processing single particle cryo-EM data. We were interested in testing whether we could use the standard Appion workflow with minimal manual intervention to achieve similar or better resolution than other challengers. Another question we were interested in testing was what the influence of particle sorting and elimination would be on the resolution and quality of 3D reconstructions. Since apoferritin ...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Structural basis for partition of the cyclodipeptide synthases into two subfamilies
Publication date: July 2018Source: Journal of Structural Biology, Volume 203, Issue 1Author(s): Gabrielle Bourgeois, Jérôme Seguin, Morgan Babin, Pascal Belin, Mireille Moutiez, Yves Mechulam, Muriel Gondry, Emmanuelle SchmittAbstractCyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides that can be further used for the synthesis of diketopiperazines. It was shown that CDPSs fall into two subfamilies, NYH and XYP, characterized by the presence of specific sequence signatures. However, current understanding of CDPSs only comes from stud...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Cep120 promotes microtubule formation through a unique tubulin binding C2 domain
Publication date: July 2018Source: Journal of Structural Biology, Volume 203, Issue 1Author(s): Ashwani Sharma, Samuel F. Gerard, Natacha Olieric, Michel O. SteinmetzAbstractCentrioles are microtubule-based structures that play essential roles in cell division and cilia biogenesis. Cep120 is an important protein for correct centriole formation and mutations in the Cep120 gene cause severe human diseases like Joubert syndrome and complex ciliopathies. Here, we show that Cep120 contains three consecutive C2 domains that are followed by a coiled-coil dimerization domain. Surprisingly, unlike the classical C2 domains, all thre...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design
Publication date: July 2018Source: Journal of Structural Biology, Volume 203, Issue 1Author(s): Jan Ludwiczak, Adam Jarmula, Stanislaw Dunin-HorkawiczAbstractComputational protein design is a set of procedures for computing amino acid sequences that will fold into a specified structure. Rosetta Design, a commonly used software for protein design, allows for the effective identification of sequences compatible with a given backbone structure, while molecular dynamics (MD) simulations can thoroughly sample near-native conformations. We benchmarked a procedure in which Rosetta design is started on MD-derived structural ensemb...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Topology of interaction between titin and myosin thick filaments
Publication date: July 2018Source: Journal of Structural Biology, Volume 203, Issue 1Author(s): Miklós Kellermayer, Dominik Sziklai, Zsombor Papp, Brennan Decker, Eszter Lakatos, Zsolt MártonfalviAbstractTitin is a giant protein spanning between the Z- and M-lines of the sarcomere. In the A-band titin is associated with the myosin thick filament. It has been speculated that titin may serve as a blueprint for thick-filament formation due to the super-repeat structure of its A-band domains. Accordingly, titin might provide a template that determines the length and structural periodicity of the thick filament. H...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Exploring applications of crowdsourcing to cryo-EM
Publication date: July 2018Source: Journal of Structural Biology, Volume 203, Issue 1Author(s): Jacob Bruggemann, Gabriel C. Lander, Andrew I. SuAbstractExtraction of particles from cryo-electron microscopy (cryo-EM) micrographs is a crucial step in processing single-particle datasets. Although algorithms have been developed for automatic particle picking, these algorithms generally rely on two-dimensional templates for particle identification, which may exhibit biases that can propagate artifacts through the reconstruction pipeline. Manual picking is viewed as a gold-standard solution for particle selection, but it is too...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

αCGRP, another amyloidogenic member of the CGRP family
Publication date: July 2018Source: Journal of Structural Biology, Volume 203, Issue 1Author(s): Paraskevi L. Tsiolaki, Georgia I. Nasi, Fotis A. Baltoumas, Nikolaos N. Louros, Vassiliki Magafa, Stavros J. Hamodrakas, Vassiliki A. IconomidouAbstractThe Calcitonin-gene related peptide (CGRP) family is a group of peptide hormones, which consists of IAPP, calcitonin, adrenomedullin, intermedin, αCGRP and βCGRP. IAPP and calcitonin have been extensively associated with the formation of amyloid fibrils, causing Type 2 Diabetes and Medullary Thyroid Carcinoma, respectively. In contrast, the potential amyloidogenic prop...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Editorial Board
Publication date: July 2018Source: Journal of Structural Biology, Volume 203, Issue 1Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Gaussian-input Gaussian mixture model for representing density maps and atomic models
Publication date: July 2018Source: Journal of Structural Biology, Volume 203, Issue 1Author(s): Takeshi KawabataAbstractA new Gaussian mixture model (GMM) has been developed for better representations of both atomic models and electron microscopy 3D density maps. The standard GMM algorithm employs an EM algorithm to determine the parameters. It accepted a set of 3D points with weights, corresponding to voxel or atomic centers. Although the standard algorithm worked reasonably well; however, it had three problems. First, it ignored the size (voxel width or atomic radius) of the input, and thus it could lead to a GMM with a ...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Ionic stress induces fusion of mitochondria to 3-D networks: An electron tomography study
Publication date: Available online 2 July 2018Source: Journal of Structural BiologyAuthor(s): Philip Steiner, Manja Luckner, Hubert Kerschbaum, Gerhard Wanner, Ursula Lütz-MeindlAbstractMitochondria are central organelles for energy supply of cells and play an important role in maintenance of ionic balance. Consequently mitochondria are highly sensitive to any kind of stress to which they mainly response by disturbance of respiration, ROS production and release of cytochrome c into the cytoplasm. Many of the physiological and molecular stress reactions of mitochondria are well known, yet there is a lack of information...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Variability of the core geometry in parallel coiled-coil bundles
Publication date: Available online 2 July 2018Source: Journal of Structural BiologyAuthor(s): Krzysztof Szczepaniak, Jan Ludwiczak, Aleksander Winski, Stanislaw Dunin-HorkawiczAbstractIn protein modelling and design, an understanding of the relationship between sequence and structure is essential. Using parallel, homotetrameric coiled-coil structures as a model system, we demonstrated that machine learning techniques can be used to predict structural parameters directly from the sequence. Coiled coils are regular protein structures, which are of great interest as building blocks for assembling larger nanostructures. They a...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Elemental composition and ultrafine structure of the skeleton in shell-bearing protists—A case study of phaeodarians and radiolarians
Publication date: Available online 3 July 2018Source: Journal of Structural BiologyAuthor(s): Yasuhide Nakamura, Izumi Iwata, Rie S. Hori, Naomi Uchiyama, Akihiro Tuji, Masaki J. Fujita, Daiske Honda, Hiroaki OhfujiAbstractCross-sections were prepared by ultramicrotome (UM) and focused ion beam (FIB) system in order to examine the skeletal structure of ecologically and geologically important shell-bearing protists: phaeodarians and radiolarians. The elemental composition of the skeleton was clarified by the energy dispersive X-ray spectroscopy, suggesting that the skeletons of both groups are mainly made of amorphous silic...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Routine Determination of Ice Thickness for Cryo-EM Grids
We describe the methods as implemented into the Leginon/Appion data collection workflow, along with some examples from test cases. Routine monitoring of ice thickness should prove helpful for optimizing sample preparation, data collection, and data processing. (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Single particle reconstruction and validation using Bsoft for the map challenge
Publication date: Available online 5 July 2018Source: Journal of Structural BiologyAuthor(s): J. Bernard HeymannAbstractThe Bsoft package is aimed at processing electron micrographs for the determination of the three-dimensional structures of biological specimens. Recent advances in hardware allow us to solve structures to near atomic resolution using single particle analysis (SPA). The Map Challenge offered me an opportunity to test the ability of Bsoft to produce reconstructions from cryo-electron micrographs at the best resolution. I also wanted to understand what needed to be done to work towards full automation with v...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Optimal data-driven parameterization of coiled coils
Publication date: Available online 9 July 2018Source: Journal of Structural BiologyAuthor(s): Dmytro Guzenko, Sergei V. StrelkovAbstractα-helical coiled coils (CCs) represent an important, highly regular protein folding motif. To date, many thousands of CC structures have been determined experimentally. Their geometry is usually modelled by theoretical equations introduced by F. Crick that involve a predefined set of parameters. Here we have addressed the problem of efficient CC parameterization from scratch by performing a statistical evaluation of all available CC structures. The procedure is based on the principal...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Structure of the DNA-binding domain of human myelin-gene regulatory factor reveals its potential protein-DNA recognition mode
Publication date: August 2018Source: Journal of Structural Biology, Volume 203, Issue 2Author(s): Baohua Chen, Yun Zhu, Sheng Ye, Rongguang ZhangAbstractMyelin-gene regulatory factor (MYRF) is a membrane-bound transcription factors, which is responsible for the differentiation of oligodendrocytes and myelination of central nervous system. Followed by a self-cleavage by the intramolecular chaperone auto-processing (ICA) domain, DNA-binding domain (DBD) of MYRF is released from the endoplasmic reticulum (ER) and was then translocated to the nucleus to regulate gene expression. In present work, we have solved the crystal stru...
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research

Editorial Board
Publication date: August 2018Source: Journal of Structural Biology, Volume 203, Issue 2Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - July 11, 2018 Category: Biology Source Type: research