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https://www.readbyqxmd.com/read/28439563/mechanism-of-vps4-hexamer-function-revealed-by-cryo-em
#1
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
#2
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
#3
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/28437704/conserved-rna-polymerase-ii-initiation-complex-structure
#4
REVIEW
Merle Hantsche, Patrick Cramer
Recent cryo-electron microscopic studies have arrived at atomic models of the core transcription initiation complex comprising RNA polymerase (Pol) II and the basal transcription factors TBP, TFIIA, TFIIB, TFIIE, and TFIIF. A detailed comparison of two independently derived yeast and human core initiation complex structures reveals that they are virtually identical, demonstrating the conservation of the basic transcription machinery amongst eukaryotes. The additional factors TFIID, TFIIH, and Mediator have been located on the periphery of the core initiation complex, providing the topology of the entire initiation assembly, which comprises approximately 70 polypeptides with a molecular weight of ∼4 Megadalton...
April 21, 2017: Current Opinion in Structural Biology
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/28437170/psa-nadir-of-0-1-or-less-is-a-predictor-of-treatment-success-in-men-undergoing-salvage-whole-prostate-gland-cryoablation
#6
Yaw A Nyame, Ahmad Elshafei, Daniel Greene, Hans C Arora, Robert W Given, Kae Jack Tay, Thomas J Polascik, Ashley Ross, Vladimir Mouraviev, Franco Lugnani, J Stephen Jones
PURPOSE: To assess factors that affect prostate biopsy results following salvage whole gland cryoablation Patients and Methods: 174 patients underwent prostate biopsy following salvage whole gland cryoablation of the prostate in the Cryo OnLine Database registry. Wilcoxon rank-sum, χ2 tests, and logistic regression analysis were used to assess predictors of positive biopsy. PSA nadir was divided into a statistical tertile for comparisons between different nadir PSA cutpoints. RESULTS: 52/174 (29...
February 11, 2017: Journal of Endourology
https://www.readbyqxmd.com/read/28434999/smfret-experiments-of-the-rna-polymerase-ii-transcription-initiation-complex
#7
REVIEW
Nicole Malkusch, Thilo Dörfler, Julia Nagy, Tobias Eilert, Jens Michaelis
Single-molecule fluorescence and in particular single-molecule Förster Resonance Energy Transfer (smFRET(1)) is a powerful tool to provide real-time information on the dynamic architecture of large macromolecular structures such as eukaryotic transcription initiation complexes. In contrast to other structural biology methods, not only structural details, but dynamics transitions are revealed thus closing in on the underlying molecular mechanisms. Here, we describe a comprehensive quantitative biophysical toolbox which can be used for rigorous analysis of dynamic protein-nucleic acid complexes and is applied to the study of eukaryotic transcription initiation...
April 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28434130/characterization-of-extracellular-membrane-vesicles-of-an-antarctic-bacterium-shewanella-livingstonensis-ac10-and-their-enhanced-production-by-alteration-of-phospholipid-composition
#8
Fumiaki Yokoyama, Jun Kawamoto, Tomoya Imai, Tatsuo Kurihara
A cold-adapted bacterium, Shewanella livingstonensis Ac10, which produces eicosapentaenoic acid (EPA) as a component of its membrane phospholipids, is useful as a model to study the function of EPA and as a host for heterologous production of thermolabile proteins at low temperatures. In this study, we characterized extracellular membrane vesicles (EMVs) of this bacterium to examine the involvement of EPA in the biogenesis of EMVs and for the future application of EMVs to extracellular protein production. We found that this strain produced EMVs from the cell surface...
April 22, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28431243/cryo-em-structure-of-the-open-human-ether-%C3%A3-go-go-related-k-channel-herg
#9
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/28430448/structural-and-rheological-properties-of-temperature-responsive-amphiphilic-triblock-copolymers-in-aqueous-media
#10
Josefine Eilsø Nielsen, Kaizheng Zhu, Sverre Arne Sande, Lubomír Kováčik, Dušan Cmarko, Kenneth Dahl Knudsen, Bo Nyström
Thermoresponsive amphiphilic biodegradable block copolymers of the type poly(-caprolactone-co-lactide)-poly(ethylene glycol)-poly(-caprolactone-co-lactide) (PCLA-PEGm-PCLA) have great potential for various biomedical applications. In the present study, we have surveyed the effects of PEG-spacer length (m=1000 and 1500), temperature, and polymer concentration on the self-assembling process to form supramolecular structures in aqueous solutions of the PCLA-PEGm-PCLA copolymer. This copolymer has a lower critical solution temperature, and the cloud point depends on both concentration and PEG-length...
April 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28429009/aggregation-of-cyclic-polypeptoids-bearing-zwitterionic-end-groups-with-attractive-dipole-dipole-and-solvophobic-interactions-a-study-by-small-angle-neutron-scattering-and-molecular-dynamics-simulation
#11
Pu Du, Ang Li, Xin Li, Yueheng Zhang, Changwoo Do, Lilin He, Steven W Rick, Vijay T John, Revati Kumar, Donghui Zhang
Aggregation behavior of cyclic polypeptoids bearing zwitterionic end-groups in methanol has been studied using a combination of experimental and simulation techniques. The data from SANS and cryo-TEM indicate that the solution contains small clusters of these cyclic polypeptoids, ranging from a single polypeptoid chain to small oligomers, while the linear counterpart shows no cluster formation. Atomistic molecular dynamics simulations reveal that the driving force for this clustering behavior is due to the interplay between the effective repulsion due to the solvation of the dipoles formed by the charged end-groups in each polypeptoid chain and the attractive forces due to dipole-dipole interactions and the solvophobic effect...
April 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28428974/perspective-a-toolbox-for-protein-structure-determination-in-physiological-environment-through-oriented-2d-ordered-site-specific-immobilization
#12
M Altissimo, M Kiskinova, R Mincigrucci, L Vaccari, C Guarnaccia, C Masciovecchio
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based X-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize a number of proteins, and experimental conditions for structure determination that are incompatible with the physiological environment...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28424519/mechanism-of-chromatin-remodelling-revealed-by-the-snf2-nucleosome-structure
#13
Xiaoyu Liu, Meijing Li, Xian Xia, Xueming Li, Zhucheng Chen
Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron microscopy structure of chromatin remodeller Switch/sucrose non-fermentable (SWI2/SNF2) from Saccharomyces cerevisiae bound to the nucleosome. The structure shows that the two core domains of Snf2 are realigned upon nucleosome binding, suggesting activation of the enzyme. The core domains contact each other through two induced Brace helices, which are crucial for coupling ATP hydrolysis to chromatin remodelling...
April 19, 2017: Nature
https://www.readbyqxmd.com/read/28423895/supramolecularly-engineered-%C3%AF-amphiphile
#14
Priya Rajdev, Saptarshi Chakraborty, Marc Schmutz, Philippe J Mésini, Suhrit Ghosh
This article describes self-assembly of supramolecularly engineered naphthalene-diimide (NDI) derived amphiphiles NDI-1 and NDI-2. They have the same hydrophobic/ hydrophilic balance but merely differ by a single functional group, amide or ester, respectively. They exhibit distinct self-assembly in water; NDI-1 form hydrogel which upon aging forms crystals while NDI-2 forms micelle as revealed by in-depth structural analysis using cryo-TEM, DLS and SAXS studies. These results suggest H-bonding among the amide groups fully regulates the self-assembly by overruling the packing parameters...
April 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28423342/a-broadly-neutralizing-antibody-targets-the-dynamic-hiv-envelope-trimer-apex-via-a-long-rigidified-and-anionic-%C3%AE-hairpin-structure
#15
Jeong Hyun Lee, Raiees Andrabi, Ching-Yao Su, Anila Yasmeen, Jean-Philippe Julien, Leopold Kong, Nicholas C Wu, Ryan McBride, Devin Sok, Matthias Pauthner, Christopher A Cottrell, Travis Nieusma, Claudia Blattner, James C Paulson, Per Johan Klasse, Ian A Wilson, Dennis R Burton, Andrew B Ward
Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the surface HIV envelope (Env) trimer. Using cryo-electron microscopy, we solved the atomic structure of an apex bnAb, PGT145, in complex with Env. We showed that the long anionic HCDR3 of PGT145 penetrated between glycans at the trimer 3-fold axis, to contact peptide residues from all three Env protomers, and thus explains its highly trimer-specific nature...
April 18, 2017: Immunity
https://www.readbyqxmd.com/read/28421499/chapter-15-development-of-a-nationwide-network-for-ovarian-tissue-cryopreservation
#16
Jana Liebenthron, Markus Montag
Ovarian tissue cryopreservation is gaining much interest since the publication of the first live birth after retransplantation of frozen-thawed tissue in 2004 (Donnez et al., Lancet 364:1405-1410, 2004). In contrast to cryopreservation of gametes and embryos, ovarian tissue freezing is a complex requiring a proper approach in order to make this a viable option for fertility preservation of cancer patients. Due to the need in terms of laboratory space, equipment, personnel, and adequate logistics, an ovarian tissue cryobank is most economic if managed as a centralized service unit that interacts with numerous clinics covering the surgical part...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28421486/chapter-2-utility-of-animal-models-for-human-ovarian-tissue-cryopreservation
#17
Seul Ki Kim, Jung Ryeol Lee, S Samuel Kim
Success in cryopreservation of ovarian tissue (OT) in animal models has led to develop efficient cryo-technologies for human ovarian tissue. In this chapter, cryopreservation protocols developed for animal experiments are described.
2017: Methods in Molecular Biology
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
#18
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/28416636/p53-dynamically-directs-tfiid-assembly-on-target-gene-promoters
#19
R A Coleman, Z Qiao, S K Singh, C S Peng, M Cianfrocco, Z Zhang, A Piasecka, H Aldeborgh, G Basishvili, W L Liu
p53 is a central regulator that turns on vast gene networks to maintain cellular integrity upon various stimuli. p53 activates transcription initiation in part by aiding recruitment of TFIID to the promoter. However, the precise means by which p53 dynamically interacts with TFIID to facilitate assembly on target gene promoters remains elusive. To address this key question, we have undertaken an integrated approach involving single molecule fluorescence microscopy, single particle cryo-electron microscopy, and biochemistry...
April 17, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28413259/materials-genome-in-action-identifying-the-performance-limits-of-physical-hydrogen-storage
#20
Aaron W Thornton, Cory M Simon, Jihan Kim, Ohmin Kwon, Kathryn S Deeg, Kristina Konstas, Steven J Pas, Matthew R Hill, David A Winkler, Maciej Haranczyk, Berend Smit
The Materials Genome is in action: the molecular codes for millions of materials have been sequenced, predictive models have been developed, and now the challenge of hydrogen storage is targeted. Renewably generated hydrogen is an attractive transportation fuel with zero carbon emissions, but its storage remains a significant challenge. Nanoporous adsorbents have shown promising physical adsorption of hydrogen approaching targeted capacities, but the scope of studies has remained limited. Here the Nanoporous Materials Genome, containing over 850 000 materials, is analyzed with a variety of computational tools to explore the limits of hydrogen storage...
April 11, 2017: Chemistry of Materials: a Publication of the American Chemical Society
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