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Current Opinion in Structural Biology

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https://www.readbyqxmd.com/read/28648726/taking-the-measure-of-microed
#1
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
#2
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
#3
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
#4
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/28624735/advances-in-high-resolution-cryo-em-of-oligomeric-enzymes
#5
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/28624569/readers-writers-and-erasers-of-n-6-methylated-adenosine-modification
#6
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 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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28600980/structural-insights-into-ligand-recognition-and-regulation-of-nucleic-acid-sensing-toll-like-receptors
#10
REVIEW
Toshiyuki Shimizu
Toll-like receptors (TLRs) activate the innate immune system in response to invading pathogens. Although nucleic acids are one of the principal TLR ligands, they are not inherently pathogen-specific and, thus, carry the risk of triggering autoimmunity. There are multiple unique regulatory mechanisms aimed at preventing accidental activation of nucleic acid-sensing TLRs. Recent structural studies revealed that different nucleic acid-sensing TLRs have specific modes of recognizing nucleic acids as ligands regulated by diverse regulation mechanism both at the receptor and ligand levels...
June 7, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28600951/structural-mechanism-of-arrestin-activation
#11
REVIEW
Patrick Scheerer, Martha E Sommer
The large and multifunctional family of G protein-coupled receptors (GPCRs) are regulated by a small family of structurally conserved arrestin proteins. In order to bind an active GPCR, arrestin must first be activated by interaction with the phosphorylated receptor C-terminus. Recent years have witnessed major developments in high-resolution crystal structures of pre-active arrestins and arrestin or arrestin-derived peptides in complex with an active GPCR. Although each structure individually offers only a limited snapshot, taken together and interpreted in light of recent complementary functional data, they offer valuable insight into how arrestin is activated by and couples to a phosphorylated active GPCR...
June 7, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28591681/structural-features-of-glycan-recognition-among-viral-pathogens
#12
REVIEW
Sreejesh Shanker, Liya Hu, Sasirekha Ramani, Robert L Atmar, Mary K Estes, B V Venkataram Prasad
Recognition and binding to host glycans present on cellular surfaces is an initial and critical step in viral entry. Diverse families of host glycans such as histo-blood group antigens, sialoglycans and glycosaminoglycans are recognized by viruses. Glycan binding determines virus-host specificity, tissue tropism, pathogenesis and potential for interspecies transmission. Viruses including noroviruses, rotaviruses, enteroviruses, influenza, and papillomaviruses have evolved novel strategies to bind specific glycans often in a strain-specific manner...
June 4, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28591671/mille-viae-in-eukaryotic-mrna-decapping
#13
REVIEW
Eugene Valkov, Stefanie Jonas, Oliver Weichenrieder
Cellular mRNA levels are regulated via rates of transcription and decay. Since the removal of the mRNA 5'-cap by the decapping enzyme DCP2 is generally an irreversible step towards decay, it requires regulation. Control of DCP2 activity is likely effected by two interdependent means: by conformational control of the DCP2-DCP1 complex, and by assembly control of the decapping network, an array of mutually interacting effector proteins. Here, we compare three recent and conformationally distinct crystal structures of the DCP2-DCP1 decapping complex in the presence of substrate analogs and decapping enhancers and we discuss alternative substrate recognition modes for the catalytic domain of DCP2...
June 4, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28587734/editorial-sequences-and-topology
#14
EDITORIAL
R Sowdhamini, Kenji Mizuguchi
No abstract text is available yet for this article.
June 3, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28578909/editorial-overview-a-feast-of-structural-glycobiology
#15
EDITORIAL
Ute Krengel, Thilo Stehle
No abstract text is available yet for this article.
June 1, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28575754/mapping-modeling-and-characterization-of-protein-protein-interactions-on-a-proteomic-scale
#16
REVIEW
T M Cafarelli, A Desbuleux, Y Wang, S G Choi, D De Ridder, M Vidal
Proteins effect a number of biological functions, from cellular signaling, organization, mobility, and transport to catalyzing biochemical reactions and coordinating an immune response. These varied functions are often dependent upon macromolecular interactions, particularly with other proteins. Small-scale studies in the scientific literature report protein-protein interactions (PPIs), but slowly and with bias towards well-studied proteins. In an era where genomic sequence is readily available, deducing genotype-phenotype relationships requires an understanding of protein connectivity at proteome-scale...
May 30, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28558341/understanding-the-gpcr-biased-signaling-through-g-protein-and-arrestin-complex-structures
#17
REVIEW
X Edward Zhou, Karsten Melcher, H Eric Xu
G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and are important drug targets for many human diseases. The determination of the 3-D structure of GPCRs and their signaling complexes has promoted our understanding of GPCR biology and provided templates for structure-based drug discovery. In this review, we focus on the recent structure work on GPCR signaling complexes, the β2-adrenoreceptor-Gs and the rhodopsin-arrestin complexes in particular, and highlight the structural features of GPCR complexes involved in G protein- and arrestin-mediated signal transduction...
May 27, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28544984/histo-blood-group-antigens-as-mediators-of-infections
#18
REVIEW
Julie E Heggelund, Annabelle Varrot, Anne Imberty, Ute Krengel
The critical first step of a microbial infection is usually the attachment of pathogens to host cell glycans. Targets on host tissues are in particular the histo-blood group antigens (HBGAs), which are present in rich diversity in the mucus layer and on the underlying mucosa. Recent structural and functional studies have revealed significant new insight into the molecular mechanisms, explaining why individuals with certain blood groups are at increased risk of some infections. The most prominent example of blood-group-associated diseases is cholera, caused by infection with Vibrio cholerae...
May 22, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28528306/the-group-ii-intron-maturase-a-reverse-transcriptase-and-splicing-factor-go-hand-in-hand
#19
REVIEW
Chen Zhao, Anna Marie Pyle
The splicing of group II introns in vivo requires the assistance of a multifunctional intron encoded protein (IEP, or maturase). Each IEP is also a reverse-transcriptase enzyme that enables group II introns to behave as mobile genetic elements. During splicing or retro-transposition, each group II intron forms a tight, specific complex with its own encoded IEP, resulting in a highly reactive holoenzyme. This review focuses on the structural basis for IEP function, as revealed by recent crystal structures of an IEP reverse transcriptase domain and cryo-EM structures of an IEP-intron complex...
May 18, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28514705/a-topologically-diverse-family-of-fluoride-channels
#20
REVIEW
Christian B Macdonald, Randy B Stockbridge
Dual-topology proteins are likely evolutionary antecedents to a common motif in membrane protein structures, the inverted repeat. A family of fluoride channels, the Flucs, which protect microorganisms, fungi, and plants against cytoplasmic fluoride accumulation, has representatives of all topologies along this evolutionary trajectory, including dual-topology homodimers, antiparallel heterodimers, and, in eukaryotes, fused two-domain proteins with an inverted repeat motif. Recent high-resolution crystal structures of dual-topology homodimers, coupled with extensive functional information about both the homodimers and two-domain Flucs, provide a case study of the co-evolution of fold and function...
May 14, 2017: Current Opinion in Structural Biology
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