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Current Opinion in Structural Biology

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https://www.readbyqxmd.com/read/28801059/editorial-overview-cryo-electron-microscopy-exciting-advances-in-cryoem-herald-a-new-era-in-structural-biology
#1
EDITORIAL
Wah Chiu, Kenneth H Downing
No abstract text is available yet for this article.
August 8, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28787658/atomic-cryo-em-structures-of-viruses
#2
REVIEW
Wen Jiang, Liang Tang
During the development of single particle cryo-EM in past five decades, icosahedral viruses have led the resolution progress owing to their large mass and high symmetry. Many technical advances in cryo-EM were first established with viruses. Since reaching ∼4Å resolution in 2008, it has become a relatively routine task to solve the atomic structure of isolated viruses. The future of structural virology will be increasingly focused on remaining challenges including solving structures of jumbo viruses, intermediate functional states during assembly, maturation, and infection, and in situ structures...
August 5, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28787627/live-and-let-die-insights-into-pseudoenzyme-mechanisms-from-structure
#3
REVIEW
James M Murphy, Peter D Mace, Patrick A Eyers
Pseudoenzymes were first described more than 50 years ago, when it was recognised that a subset of proteins that are structurally homologous to active enzymes lack amino acids necessary for catalytic activity. Recently, interest in pseudoenzymes has surged as it has become apparent that they constitute ∼10% of proteomes and perform essential metabolic and signalling functions that can be experimentally distinguished from catalytic outputs of enzymes. Here, we highlight recent structural studies of pseudoenzymes, which have revealed the molecular basis for roles as allosteric regulators of conventional enzymes, as molecular switches and integrators, as hubs for assembling protein complexes, and as competitors of substrate availability and holoenzyme assembly...
August 5, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28743025/rna-polymerase-i-and-iii-similar-yet-unique
#4
REVIEW
Heena Khatter, Matthias K Vorländer, Christoph W Müller
The majority of non-protein-coding RNAs present in eukaryotic cells comprises rRNAs, tRNAs and U6 snRNA that are involved in protein biosynthesis and are synthesized by DNA-dependent-RNA polymerase I and III. The transcription cycle (initiation, elongation and termination) has similar principles in all three nuclear RNA polymerases with specific features that are reflected back in their structures. Recently, owing to the 'resolution revolution' in electron cryo-microscopy, there has been a significant advancement in the understanding of these molecular machines...
July 22, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28735108/structural-biology-outside-the-box-inside-the-cell
#5
REVIEW
Jürgen M Plitzko, Benjamin Schuler, Philipp Selenko
Recent developments in cellular cryo-electron tomography, in-cell single-molecule Förster resonance energy transfer-spectroscopy, nuclear magnetic resonance-spectroscopy and electron paramagnetic resonance-spectroscopy delivered unprecedented insights into the inner workings of cells. Here, we review complementary aspects of these methods and provide an outlook toward joint applications in the future.
July 20, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28735107/integrative-modelling-of-cellular-assemblies
#6
REVIEW
Agnel Praveen Joseph, Guido Polles, Frank Alber, Maya Topf
A wide variety of experimental techniques can be used for understanding the precise molecular mechanisms underlying the activities of cellular assemblies. The inherent limitations of a single experimental technique often requires integration of data from complementary approaches to gain sufficient insights into the assembly structure and function. Here, we review popular computational approaches for integrative modelling of cellular assemblies, including protein complexes and genomic assemblies. We provide recent examples of integrative models generated for such assemblies by different experimental techniques, especially including data from 3D electron microscopy (3D-EM) and chromosome conformation capture experiments, respectively...
July 20, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28734135/folding-while-bound-to-chaperones
#7
REVIEW
Scott Horowitz, Philipp Koldewey, Frederick Stull, James Ca Bardwell
Chaperones are important in preventing protein aggregation and aiding protein folding. How chaperones aid protein folding remains a key question in understanding their mechanism. The possibility of proteins folding while bound to chaperones was reintroduced recently with the chaperone Spy, many years after the phenomenon was first reported with the chaperones GroEL and SecB. In this review, we discuss the salient features of folding while bound in the cases for which it has been observed and speculate about its biological importance and possible occurrence in other chaperones...
July 19, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28732250/structural-biology-of-telomerase-and-its-interaction-at-telomeres
#8
REVIEW
Yaqiang Wang, Juli Feigon
Telomerase is an RNP that synthesizes the 3' ends of linear chromosomes and is an important regulator of telomere length. It contains a single long non-coding telomerase RNA (TER), telomerase reverse transcriptase (TERT), and other proteins that vary among organisms. Recent progress in structural biology of telomerase includes reports of the first cryo-electron microscopy structure of telomerase, from Tetrahymena, new crystal structures of TERT domains, telomerase RNA structures and models, and identification in Tetrahymena telomerase holoenzyme of human homologues of telomere-associated proteins that have provided a more unified view of telomerase interaction at telomeres as well as insights into the role of telomerase RNA in activity and assembly...
July 18, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28686957/on-the-state-of-crystallography-at-the-dawn-of-the-electron-microscopy-revolution
#9
REVIEW
Matthew K Higgins, Susan M Lea
While protein crystallography has, for many years, been the most used method for structural analysis of macromolecular complexes, remarkable recent advances in high-resolution electron cryo-microscopy led to suggestions that 'the revolution will not be crystallised'. Here we highlight the current success rate, speed and ease of modern crystallographic structure determination and some recent triumphs of both 'classical' crystallography and the use of X-ray free electron lasers. We also outline fundamental differences between structure determination using X-ray crystallography and electron microscopy...
July 4, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28675835/new-insights-into-influenza-a-specificity-an-evolution-of-paradigms
#10
REVIEW
Ye Ji, Yohanna Jb White, Jodi A Hadden, Oliver C Grant, Robert J Woods
Understanding the molecular origin of influenza receptor specificity is complicated by the paucity of quantitative affinity measurements, and the qualitative and variable nature of glycan array data. Further obstacles arise from the varied impact of viral glycosylation and the relatively narrow spectrum of biologically relevant receptors present on glycan arrays. A survey of receptor conformational properties is presented, leading to the conclusion that conformational entropy plays a key role in defining specificity, as does the newly reported ability of biantennary receptors that terminate in Siaα2-6Gal sequences to form bidentate interactions to two binding sites in a hemagglutinin trimer...
July 1, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28675816/expanding-the-boundaries-of-cryo-em-with-phase-plates
#11
REVIEW
Radostin Danev, Wolfgang Baumeister
Phase plates have long been considered as a means for improving the performance of cryo-electron microscopy (cryo-EM). But practical limitations, such as a short lifespan or cumbersome usage have prevented their widespread adoption. The recently developed Volta phase plate overcomes most of the practical issues and it is now commercially available. Results from both, electron cryo-tomography (cryo-ET) and single particle analysis (SPA), have demonstrated the benefits of using a phase plate. In CET phase plates have helped to visualize cellular ultrastructure in unprecedented detail...
July 1, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28648726/taking-the-measure-of-microed
#12
REVIEW
Jose A Rodriguez, David S Eisenberg, Tamir Gonen
It is now possible to routinely determine atomic resolution structures by electron cryo-microscopy (cryoEM), facilitated in part by the method known as micro electron-diffraction (MicroED). Since its initial demonstration in 2013, MicroED has helped determine a variety of protein structures ranging in molecular weight from a few hundred Daltons to several hundred thousand Daltons. Some of these structures were novel while others were previously known. The resolutions of structures obtained thus far by MicroED range from 3...
June 22, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28646653/cryo-em-beyond-the-microscope
#13
REVIEW
Lesley A Earl, Veronica Falconieri, Jacqueline Ls Milne, Sriram Subramaniam
The pace at which cryo-EM is being adopted as a mainstream tool in structural biology has continued unabated over the past year. Initial successes in obtaining near-atomic resolution structures with cryo-EM were enabled to a large extent by advances in microscope and detector technology. Here, we review some of the complementary technical improvements that are helping sustain the cryo-EM revolution. We highlight advances in image processing that permit high resolution structure determination even in the presence of structural and conformational heterogeneity...
June 21, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28628789/challenges-and-opportunities-in-the-high-resolution-cryo-em-visualization-of-microtubules-and-their-binding-partners
#14
REVIEW
Eva Nogales, Elizabeth H Kellogg
As non-crystallizable polymers, microtubules have been the target of cryo-electron microscopy (cryo-EM) studies since the technique was first established. Over the years, image processing strategies have been developed that take care of the unique, pseudo-helical symmetry of the microtubule. With recent progress in data quality and data processing, cryo-EM reconstructions are now reaching resolutions that allow the generation of atomic models of microtubules and the factors that bind them. These include cellular partners that contribute to microtubule cellular functions, or small ligands that interfere with those functions in the treatment of cancer...
June 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28628788/cryo-em-structures-of-human-%C3%AE-secretase
#15
REVIEW
Guanghui Yang, Rui Zhou, Yigong Shi
γ-secretase, a membrane-embedded aspartate protease, catalyzes peptide bond hydrolysis of a large variety of type I integral membrane proteins exemplified by amyloid precursor protein (APP). Cleavage of APP leads to formation of β-amyloid plaque, which is a hallmark of Alzheimer's disease (AD). Over 200 AD-associated mutations are mapped to presenilin 1 (PS1), the catalytic component of γ-secretase. In the past three years, several cryo-electron microscopy (cryo-EM) structures of human γ-secretase have been determined at near atomic resolutions...
June 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28624569/readers-writers-and-erasers-of-n-6-methylated-adenosine-modification
#16
REVIEW
Baixing Wu, Li Li, Ying Huang, Jinbiao Ma, Jinrong Min
N(6)-methyladenosine (m(6)A) as the most prevalent internal modification in mammalian RNAs has been increasingly realized as an important reversible mark that participates in various biological processes and cancer pathogenesis. In this review, we discuss the catalytic mechanisms of MT-A70 domain family proteins for mediating adenosine N(6)-methylation, the removal of this RNA mark by members of ALKB homologue domain family proteins, and the recognition of these m(6)A-modified RNAs by YTH domain family proteins...
June 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28624735/advances-in-high-resolution-cryo-em-of-oligomeric-enzymes
#17
REVIEW
Janet Vonck, Deryck J Mills
Recent advances in cryo-electron microscopy instrumentation and software have made it possible to obtain atomic resolution structures of macromolecular complexes with a small amount of material at low concentration and without the need for crystallisation. Oligomeric enzymes are particularly well suited for this technique because of their symmetry and often large size or rigid structure and can be used to explore the limits of the technique. Conformational changes can reach their full extent in solution, not hampered by crystal contacts, and multiple conformations in a sample can be separated computationally...
June 15, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28624568/towards-a-mechanistic-understanding-of-core-promoter-recognition-from-cryo-em-studies-of-human-tfiid
#18
REVIEW
Eva Nogales, Avinash B Patel, Robert K Louder
TFIID is a critical component of the eukaryotic transcription pre-initiation complex (PIC) required for the recruitment of RNA Pol II to the start site of protein-coding genes. Within the PIC, TFIID's role is to recognize and bind core promoter sequences and recruit the rest of the PIC components. Due to its size and its conformational complexity, TFIID poses a serious challenge for structural characterization. The small amounts of purified TFIID that can be obtained by present methods of purification from endogenous sources has limited structural studies to cryo-EM visualization, which requires very small amounts of sample...
June 15, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28618351/structure-of-ip3r-channel-high-resolution-insights-from-cryo-em
#19
REVIEW
Mariah R Baker, Guizhen Fan, Irina I Serysheva
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ubiquitously expressed intracellular Ca(2+) channels and the major mediators of cellular Ca(2+) signals generated by the release of Ca(2+) ions from intracellular stores in response to a variety of extracellular stimuli. Despite established physiological significance and proven involvements of IP3R channels in many human diseases, detailed structural basis for signal detection by these ion channels and their gating remain obscure. Recently, single particle electron cryomicroscopy (cryo-EM) has yielded a long-awaited near-atomic resolution structure of the entire full-length type 1 IP3R...
June 12, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28609682/cryo-em-of-bacterial-pili-and-archaeal-flagellar-filaments
#20
REVIEW
Edward H Egelman
Recent advances in cryo-electron microscopy (cryo-EM) have opened up the possibility that a large class of biological structures, helical polymers, may now be readily reconstructed at near-atomic resolution. This will have a huge impact, since most of these structures are unlikely to be crystallized. This review focuses on new cryo-EM studies involving three classes of bacterial pili (chaperone-usher, mating, and Type IV) as well as on archaeal flagellar filaments. While it has long been known that one domain within archaeal flagellar filaments is homologous to a domain within bacterial Type IV pilins, the new studies shed light on how homologous and even highly conserved subunits can pack together in different ways with only small changes in sequence...
June 10, 2017: Current Opinion in Structural Biology
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