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https://www.readbyqxmd.com/read/28446752/near-atomic-structure-of-japanese-encephalitis-virus-reveals-critical-determinants-of-virulence-and-stability
#1
Xiangxi Wang, Shi-Hua Li, Ling Zhu, Qing-Gong Nian, Shuai Yuan, Qiang Gao, Zhongyu Hu, Qing Ye, Xiao-Feng Li, Dong-Yang Xie, Neil Shaw, Junzhi Wang, Thomas S Walter, Juha T Huiskonen, Elizabeth E Fry, Cheng-Feng Qin, David I Stuart, Zihe Rao
Although several different flaviviruses may cause encephalitis, Japanese encephalitis virus is the most significant, being responsible for thousands of deaths each year in Asia. The structural and molecular basis of this encephalitis is not fully understood. Here, we report the cryo-electron microscopy structure of mature Japanese encephalitis virus at near-atomic resolution, which reveals an unusual "hole" on the surface, surrounded by five encephalitic-specific motifs implicated in receptor binding. Glu138 of E, which is highly conserved in encephalitic flaviviruses, maps onto one of these motifs and is essential for binding to neuroblastoma cells, with the E138K mutation abrogating the neurovirulence and neuroinvasiveness of Japanese encephalitis virus in mice...
April 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28439563/mechanism-of-vps4-hexamer-function-revealed-by-cryo-em
#2
Min Su, Emily Z Guo, Xinqiang Ding, Yan Li, Jeffrey T Tarrasch, Charles L Brooks, Zhaohui Xu, Georgios Skiniotis
Vps4 is a member of AAA(+) ATPase (adenosine triphosphatase associated with diverse cellular activities) that operates as an oligomer to disassemble ESCRT-III (endosomal sorting complex required for transport III) filaments, thereby catalyzing the final step in multiple ESCRT-dependent membrane remodeling events. We used electron cryo-microscopy to visualize oligomers of a hydrolysis-deficient Vps4 (vacuolar protein sorting-associated protein 4) mutant in the presence of adenosine 5'-triphosphate (ATP). We show that Vps4 subunits assemble into an asymmetric hexameric ring following an approximate helical path that sequentially stacks substrate-binding loops along the central pore...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28438387/structural-insights-into-the-mechanism-of-group-ii-intron-splicing
#3
REVIEW
Chen Zhao, Anna Marie Pyle
While the major architectural features and active-site components of group II introns have been known for almost a decade, information on the individual stages of splicing has been lacking. Recent advances in crystallography and cryo-electron microscopy (cryo-EM) have provided major new insights into the structure of intact lariat introns. Conformational changes that mediate the steps of splicing and retrotransposition are being elucidated, revealing the dynamic, highly coordinated motions that are required for group II intron activity...
April 21, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28437792/phase-plate-cryo-em-structure-of-a-class-b-gpcr-g-protein-complex
#4
Yi-Lynn Liang, Maryam Khoshouei, Mazdak Radjainia, Yan Zhang, Alisa Glukhova, Jeffrey Tarrasch, David M Thal, Sebastian G B Furness, George Christopoulos, Thomas Coudrat, Radostin Danev, Wolfgang Baumeister, Laurence J Miller, Arthur Christopoulos, Brian K Kobilka, Denise Wootten, Georgios Skiniotis, Patrick M Sexton
Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, such as osteoporosis, diabetes and obesity. Here we report the structure of a full-length class B receptor, the calcitonin receptor, in complex with peptide ligand and heterotrimeric Gαsβγ protein determined by Volta phase-plate single-particle cryo-electron microscopy. The peptide agonist engages the receptor by binding to an extended hydrophobic pocket facilitated by the large outward movement of the extracellular ends of transmembrane helices 6 and 7...
April 24, 2017: Nature
https://www.readbyqxmd.com/read/28437479/conformational-dynamics-of-bacterial-trigger-factor-in-apo-and-ribosome-bound-states
#5
Mehmet Tarik Can, Zeynep Kurkcuoglu, Gokce Ezeroglu, Arzu Uyar, Ozge Kurkcuoglu, Pemra Doruker
The chaperone trigger factor (TF) binds to the ribosome exit tunnel and helps cotranslational folding of nascent chains (NC) in bacterial cells and chloroplasts. In this study, we aim to investigate the functional dynamics of fully-atomistic apo TF and its complex with 50S. As TF accomodates a high percentage of charged residues on its surface, the effect of ionic strength on TF dynamics is assessed here by performing five independent molecular dynamics (MD) simulations (total of 1.3 micro-second duration) at 29 mM and 150 mM ionic strengths...
2017: PloS One
https://www.readbyqxmd.com/read/28431243/cryo-em-structure-of-the-open-human-ether-%C3%A3-go-go-related-k-channel-herg
#6
Weiwei Wang, Roderick MacKinnon
The human ether-à-go-go-related potassium channel (hERG, Kv11.1) is a voltage-dependent channel known for its role in repolarizing the cardiac action potential. hERG alteration by mutation or pharmacological inhibition produces Long QT syndrome and the lethal cardiac arrhythmia torsade de pointes. We have determined the molecular structure of hERG to 3.8 Å using cryo-electron microscopy. In this structure, the voltage sensors adopt a depolarized conformation, and the pore is open. The central cavity has an atypically small central volume surrounded by four deep hydrophobic pockets, which may explain hERG's unusual sensitivity to many drugs...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28419915/enhanced-imaging-of-lipid-rich-nanoparticles-embedded-in-methylcellulose-films-for-transmission-electron-microscopy-using-mixtures-of-heavy-metals
#7
Jalal Asadi, Sophie Ferguson, Hussain Raja, Christian Hacker, Phedra Marius, Richard Ward, Christos Pliotas, James Naismith, John Lucocq
Synthetic and naturally occurring lipid-rich nanoparticles are of wide ranging importance in biomedicine. They include liposomes, bicelles, nanodiscs, exosomes and virus particles. The quantitative study of these particles requires methods for high-resolution visualization of the whole population. One powerful imaging method is cryo-EM of vitrified samples, but this is technically demanding, requires specialized equipment, provides low contrast and does not reveal all particles present in a population. Another approach is classical negative stain-EM, which is more accessible but is difficult to standardize for larger lipidic structures, which are prone to artifacts of structure collapse and contrast variability...
April 10, 2017: Micron: the International Research and Review Journal for Microscopy
https://www.readbyqxmd.com/read/28396444/the-cryo-em-structure-of-yjeq-bound-to-the-30s-subunit-suggests-a-fidelity-checkpoint-function-for-this-protein-in-ribosome-assembly
#8
Aida Razi, Alba Guarné, Joaquin Ortega
Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechanisms of YjeQ in the context of the mature subunit, we determined the cryo-EM structure of the fully assembled 30S subunit in complex with YjeQ at 5.8-Å resolution. We found that binding of YjeQ stabilizes helix 44 into a conformation similar to that adopted by the subunit during proofreading...
April 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28393837/cryo-em-structures-of-mers-cov-and-sars-cov-spike-glycoproteins-reveal-the-dynamic-receptor-binding-domains
#9
Yuan Yuan, Duanfang Cao, Yanfang Zhang, Jun Ma, Jianxun Qi, Qihui Wang, Guangwen Lu, Ying Wu, Jinghua Yan, Yi Shi, Xinzheng Zhang, George F Gao
The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD)...
April 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28390173/structure-of-a-aaa-unfoldase-in-the-process-of-unfolding-substrate
#10
Zev A Ripstein, Rui Huang, Rafal Augustyniak, Lewis E Kay, John L Rubinstein
AAA+ unfoldases are thought to unfold substrate through the central pore of their hexameric structures, but how this process occurs is not known. VAT, the Thermoplasma acidophilum homologue of eukaryotic CDC48/p97, works in conjunction with the proteasome to degrade misfolded or damaged proteins. We show that in the presence of ATP, VAT with its regulatory N-terminal domains removed unfolds other VAT complexes as substrate. We captured images of this transient process by electron cryomicroscopy (cryo-EM) to reveal the structure of the substrate-bound intermediate...
April 8, 2017: ELife
https://www.readbyqxmd.com/read/28382301/bayesian-modeling-of-biomolecular-assemblies-with-cryo-em-maps
#11
Michael Habeck
A growing array of experimental techniques allows us to characterize the three-dimensional structure of large biological assemblies at increasingly higher resolution. In addition to X-ray crystallography and nuclear magnetic resonance in solution, new structure determination methods such cryo-electron microscopy (cryo-EM), crosslinking/mass spectrometry and solid-state NMR have emerged. Often it is not sufficient to use a single experimental method, but complementary data need to be collected by using multiple techniques...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28380338/understanding-card-tricks-in-apoptosomes
#12
Li Wang, Qi Qiao, Hao Wu
While earlier studies of Apaf-1 holo-apoptosome architecture revealed the spectacular heptameric wheel-like structure formed by Apaf-1, the central CARD disk responsible for caspase-9 recruitment remained incompletely resolved. In a recent issue of Structure, Su et al. (2017) describe a crystal structure of the complex between Apaf-1 CARD and caspase-9 CARD. Together with two recent cryo-EM structures, this work brings us closer to a full view of the holo-apoptosome.
April 4, 2017: Structure
https://www.readbyqxmd.com/read/28379137/structural-basis-of-protein-translocation-by-the-vps4-vta1-aaa-atpase
#13
Nicole Monroe, Han Han, Peter S Shen, Wesley I Sundquist, Christopher P Hill
Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM structure of the active Vps4 hexamer with its cofactor Vta1, ADP•BeFx, and an ESCRT-III substrate peptide. Four Vps4 subunits form a helix whose interfaces are consistent with ATP-binding, is stabilized by Vta1, and binds the substrate peptide. The fifth subunit approximately continues this helix but appears to be dissociating...
April 5, 2017: ELife
https://www.readbyqxmd.com/read/28373698/the-structures-of-a-naturally-empty-cowpea-mosaic-virus-particle-and-its-genome-containing-counterpart-by-cryo-electron-microscopy
#14
Emma L Hesketh, Yulia Meshcheriakova, Rebecca F Thompson, George P Lomonossoff, Neil A Ranson
Cowpea mosaic virus (CPMV) is a picorna-like plant virus. As well as an intrinsic interest in CPMV as a plant pathogen, CPMV is of major interest in biotechnology applications such as nanotechnology. Here, we report high resolution cryo electron microscopy (cryo-EM) maps of wild type CPMV containing RNA-2, and of naturally-formed empty CPMV capsids. The resolution of these structures is sufficient to visualise large amino acids. We have refined an atomic model for each map and identified an essential amino acid involved in genome encapsidation...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28370077/flexible-fitting-to-cryo-em-density-map-using-ensemble-molecular-dynamics-simulations
#15
Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, Florence Tama
Flexible fitting is a computational algorithm to derive a new conformational model that conforms to low-resolution experimental data by transforming a known structure. A common application is against data from cryo-electron microscopy to obtain conformational models in new functional states. The conventional flexible fitting algorithms cannot derive correct structures in some cases due to the complexity of conformational transitions. In this study, we show the importance of conformational ensemble in the refinement process by performing multiple fittings trials using a variety of different force constants...
April 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28368809/a-two-phase-improved-correlation-method-for-automatic-particle-selection-in-cryo-em
#16
Fa Zhang, Yu Chen, Fei Ren, Xuan Wang, Zhiyong Liu, Xiaohua Wan
Particle selection from cryo-electron microscopy (Cryo-EM) images is very important for high-resolution reconstruction of macromolecular structure. The methods of particle selection can be roughly grouped into two classes, template-matching methods and feature-based methods. In general, template-matching methods usually generate better results than feature-based methods. However, the accuracy of template-matching methods is restricted by the noise and low contrast of Cryo-EM images. Moreover, the processing speed of template-matching methods, restricted by the random orientation of particles, further limits their practical applications...
March 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28368393/structure-of-the-40s-abce1-post-splitting-complex-in-ribosome-recycling-and-translation-initiation
#17
André Heuer, Milan Gerovac, Christian Schmidt, Simon Trowitzsch, Anne Preis, Peter Kötter, Otto Berninghausen, Thomas Becker, Roland Beckmann, Robert Tampé
The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the underlying splitting mechanism remains enigmatic. Here, we present a cryo-EM structure of the yeast 40S-ABCE1 post-splitting complex at 3.9-Å resolution. Compared to the pre-splitting state, we observe repositioning of ABCE1's iron-sulfur cluster domain, which rotates 150° into a binding pocket on the 40S subunit. This repositioning explains a newly observed anti-association activity of ABCE1...
April 3, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28359961/natural-and-artificial-protein-cages-design-structure-and-therapeutic-applications
#18
REVIEW
Jonathan Gardiner Heddle, Soumyananda Chakraborti, Kenji Iwasaki
Advanced electron microscopy techniques have been used to solve many viral capsid structures. The resulting detailed structural knowledge contributes to understanding of the mechanisms of self-assembly, maturation pathways and virion-host cell interactions. It also acts as inspiration for design and production of capsid-like artificial protein cages. Both natural and artificial cages have potential uses in medicine including as vaccines and in drug delivery. For vaccines, virus-like particles formed only from outer virion shells, lacking genetic material, offer the simplest basis for development, while encapsulation of target molecules inside protein cages is potentially more challenging...
March 27, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28352916/a-threonine-turnstile-defines-a-dynamic-amphiphilic-binding-motif-in-the-aaa-atpase-p97-allosteric-binding-site
#19
James C Burnett, Chaemin Lim, Brian D Peyser, Lalith P Samankumara, Marina Kovaliov, Raffaele Colombo, Stacie L Bulfer, Matthew G LaPorte, Ann R Hermone, Connor F McGrath, Michelle R Arkin, Rick Gussio, Donna M Huryn, Peter Wipf
The turnstile motion of two neighboring threonines sets up a dynamic side chain interplay that can accommodate both polar and apolar ligands in a small molecule allosteric protein binding site. A computational model based on SAR data and both X-ray and cryo-EM structures of the AAA ATPase p97 was used to analyze the effects of paired threonines at the inhibitor site. Specifically, the Thr side chain hydroxyl groups form a hydrogen bonding network that readily accommodates small, highly polar ligand substituents...
March 29, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28351611/structural-insights-of-whamm-s-interaction-with-microtubules-by-cryo-em
#20
Tianyang Liu, Anbang Dai, Yong Cao, Rui Zhang, Meng-Qiu Dong, Hong-Wei Wang
WASP homolog associated with actin, membranes, and microtubules (WHAMM) is a vertebrate protein functioning in membrane tubulation for intracellular membrane trafficking and specific organelle formation. Composed of multiple domains, WHAMM can bind to membrane and microtubule (MT) and promote actin polymerization nucleation. Previous work revealed that WHAMM's activity to promote actin nucleation is repressed upon binding to MTs. Here, we discovered that WHAMM interacts with αβ-tubulin through a small peptide motif within its MT-binding domain...
March 25, 2017: Journal of Molecular Biology
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