Morphological development of Pleurochyrsis carterae coccoliths examined by cryo-electron tomography
Publication date: Available online 1 February 2020Source: Journal of Structural BiologyAuthor(s): J.M. Walker, B. Marzec, N. Ozaki, D. Clare, F. NudelmanAbstractCoccolithophores are single-celled marine algae that produce calcified scales called coccoliths. Each scale is composed of anvil-shaped single crystals of calcite that are mechanically interlocked, constituting a remarkable example of the multi-level construction of mineralized structures. Coccolith formation starts with the nucleation of rhombohedral crystals on an organic substrate called base plate. The crystals then grow preferentially along specific directions...
Source: Journal of Structural Biology - February 2, 2020 Category: Biology Source Type: research
In situ electron microscopy characterization of intracellular ion pools in mineral forming microalgae
Publication date: Available online 22 January 2020Source: Journal of Structural BiologyAuthor(s): Yuval Kadan, Lior Aram, Eyal Shimoni, Smadar Levin-Zaidman, Shilo Rosenwasser, Assaf GalAbstractThe formation of coccoliths, intricate calcium carbonate scales that cover the cells of unicellular marine microalgae, is a highly regulated biological process. For decades, scientists have tried to elucidate the cellular, chemical, and structural mechanisms that control the precise mineralogy and shape of the inorganic crystals. Transmission electron microscopy was pivotal in characterizing some of the organelles that orchestrate t...
Source: Journal of Structural Biology - January 23, 2020 Category: Biology Source Type: research
A structural entropy index to analyse local conformations in Intrinsically Disordered Proteins
In this study, we used an ensemble of disordered proteins (or regions) and, we applied a structural alphabet to analyse their local conformation. This structural alphabet, namely Protein Blocks, had been efficiently used to highlight rigid local domains within flexible regions and so discriminates deformability and mobility concepts. Using an entropy index derived from this structural alphabet, we underlined its interest to measure these local dynamics, and to quantify, for the first time, continuum states from rigidity to flexibility and finally disorder. We also highlight non-disordered regions in the ensemble of disorde...
Source: Journal of Structural Biology - January 22, 2020 Category: Biology Source Type: research
Higher-Order Oligomerization of a Chimeric αβγ Bifunctional Diterpene Synthase with Prenyltransferase and Class II Cyclase Activities is Concentration-Dependent
Publication date: Available online 21 January 2020Source: Journal of Structural BiologyAuthor(s): Trey A. Ronnebaum, Kushol Gupta, David W. ChristiansonAbstractThe unusual diterpene (C20) synthase copalyl diphosphate synthase from Penicillium verruculosum (PvCPS) is the first bifunctional terpene synthase identified with both prenyltransferase and class II cyclase activities in a single polypeptide chain with αβγ domain architecture. The C-terminal prenyltransferase αdomain generates geranylgeranyl diphosphate which is then cyclized to form copalyl diphosphate at the N-terminal βγ domain interface. We now demonstrate...
Source: Journal of Structural Biology - January 21, 2020 Category: Biology Source Type: research
A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1
Publication date: Available online 18 January 2020Source: Journal of Structural BiologyAuthor(s): Junha Song, Roma Patterson, Zoltan Metlagel, Jocelyn F. Krey, Samantha Hao, Linshanshan Wang, Brian Ng, Salim Sazzed, Julio Kovacs, Willy Wriggers, Jing He, Peter G. Barr-Gillespie, Manfred AuerAbstractElectron cryo-tomography allows for high-resolution imaging of stereocilia in their native state. Because their actin filaments have a higher degree of order, we imaged stereocilia from mice lacking the actin crosslinker plastin 1 (PLS1). We found that while stereocilia actin filaments run 13 nm apart in parallel for long d...
Source: Journal of Structural Biology - January 20, 2020 Category: Biology Source Type: research
Structures of catalytic cycle intermediates of the Pyrococcus furiosus methionine adenosyltransferase demonstrate negative cooperativity in the archaeal orthologues
Publication date: Available online 18 January 2020Source: Journal of Structural BiologyAuthor(s): Claudia Minici, Laura Mosca, Concetta Paola Ilisso, Giovanna Cacciapuoti, Marina Porcelli, Massimo DeganoAbstractMethionine adenosyltransferases catalyse the biosynthesis of S-adenosylmethionine, the primary methyl group donor in biochemical reactions, through the condensation of methionine and ATP. Here, we report the structural analysis of the Pyrococcus furiosus methionine adenosyltransferase (PfMAT) captured in the unliganded, substrate- and product-bound states. The conformational changes taking place during the enzymatic...
Source: Journal of Structural Biology - January 20, 2020 Category: Biology Source Type: research
Cryo-EM structures of cardiac thin filaments reveal the 3D architecture of troponin
This study provides a structural basis for understanding the molecular mechanism of actomyosin system.Graphical abstract (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - January 18, 2020 Category: Biology Source Type: research
Clearing, immunofluorescence, and confocal microscopy for the three-dimensional imaging of murine testes and study of testis biology
Publication date: Available online 10 January 2020Source: Journal of Structural BiologyAuthor(s): Jason A. Kaufman, Monica J. Castro, Saul A. Ruiz, Garilyn M. Jentarra, Bernardo Chavira, Jose R. Rodriguez-SosaGraphical abstractClearing and immunofluorescence of whole samples from murine testes for their subsequent three-dimensional reconstruction by confocal microscopy. (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - January 11, 2020 Category: Biology Source Type: research
In situ 3D visualization of biomineralization matrix proteins
Publication date: Available online 9 January 2020Source: Journal of Structural BiologyAuthor(s): Oliver R.B. Thomas, Kay L. Richards, Steven Petrou, Blaine R. Roberts, Stephen E. SwearerAbstractCalcium biominerals occur in all major animal phyla, and through biomolecular control, exhibit such diverse structures as exoskeletons, shells, bones, teeth and earstones (otoliths). Determining the three-dimensional expression of key biomineral proteins, however, has proven challenging as typical protein identification methods either lose spatial resolution during dissolution of the mineral phase or are costly and limited to two-di...
Source: Journal of Structural Biology - January 9, 2020 Category: Biology Source Type: research
Outside Front Cover
Publication date: 1 January 2020Source: Journal of Structural Biology, Volume 209, Issue 1Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - January 7, 2020 Category: Biology Source Type: research
Editorial Board
Publication date: 1 January 2020Source: Journal of Structural Biology, Volume 209, Issue 1Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - January 7, 2020 Category: Biology Source Type: research
Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening
Publication date: Available online 3 January 2020Source: Journal of Structural BiologyAuthor(s): J.L. Vilas, J. Vargas, M. Martinez, E. Ramirez-Aportela, R. Melero, A. Jimenez-Moreno, E. Garduño, P. Conesa, R. Marabini, D. Maluenda, J.M. Carazo, C.O.S. SorzanoAbstractThe analysis of structure factors in 3D cryo-EM Coulomb potential maps and their “enhancement” at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accomplish this enhancement is by means of the...
Source: Journal of Structural Biology - January 5, 2020 Category: Biology Source Type: research
Journal of Structural Biology – Paper of the Year 2019
Publication date: Available online 23 December 2019Source: Journal of Structural BiologyAuthor(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - December 24, 2019 Category: Biology Source Type: research
Inverse Folding with RNA-As-Graphs Produces a Large Pool of Candidate Sequences with Target Topologies
We present an RNA-As-Graphs (RAG) based inverse folding algorithm, RAG-IF, to design novel RNA sequences that fold onto target tree graph topologies. The algorithm can be used to enhance our recently reported computational design pipeline (Jain et. al, NAR 2018). The RAG approah reresents RNA secondary structures as tree and dual graphs, where RNA loops and helices are coarse-grained as vertices and edges, opening the usage of graph theory methods to study, predict, and design RNA structures. Our recently developed computational pipeline for design utilizes graph partitioning (RAG-3D) and atomic fragment assembly (F-RAG) t...
Source: Journal of Structural Biology - December 24, 2019 Category: Biology Source Type: research
Cryo-EM reveals an asymmetry in a novel single-ring viral chaperonin
Publication date: Available online 21 December 2019Source: Journal of Structural BiologyAuthor(s): Tatiana B. Stanishneva-Konovalova, Pavel I. Semenyuk, Lidia P. Kurochkina, Evgeny B. Pichkur, Alexander L. Vasilyev, Mikhail V. Kovalchuk, Mikhail P. Kirpichnikov, Olga S. SokolovaAbstractChaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants). However...
Source: Journal of Structural Biology - December 21, 2019 Category: Biology Source Type: research
