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https://www.readbyqxmd.com/read/28817608/data-driven-coarse-graining-of-large-biomolecular-structures
#1
Yi-Ling Chen, Michael Habeck
Advances in experimental and computational techniques allow us to study the structure and dynamics of large biomolecular assemblies at increasingly higher resolution. However, with increasing structural detail it can be challenging to unravel the mechanism underlying the function of molecular machines. One reason is that atomistic simulations become computationally prohibitive. Moreover it is difficult to rationalize the functional mechanism of systems composed of tens of thousands to millions of atoms by following each atom's movements...
2017: PloS One
https://www.readbyqxmd.com/read/28816310/role-of-intrinsic-hydrogen-bonds-in-the-assembly-of-perylene-imide-derivatives-in-solution-and-at-the-liquid-solid-interface
#2
Zongxia Guo, Kun Wang, Ping Yu, Shengyue Zhang, Kai Sun, Zhibo Li
The impact of hydrogen bond formation on the supramolecular assembly of two perylene imide derivatives (PMAMI and PDINH) was systematically investigated in solution and at the liquid-solid interface. PDINH has intrinsic hydrogen bond sites, but this is not the case for PMAMI. The solution assembly was explored by morphological methods (SEM, AFM, TEM and cryo-TEM) and spectral characterization (UV-vis, FL, XRD, and FTIR spectra). The surface assembly at the liquid-solid interface was detected by scanning tunneling microscopy (STM)...
August 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28815272/gold-nanoparticle-based-localized-surface-plasmon-immunosensor-for-staphylococcal-enterotoxin-a-sea-detection
#3
Maroua Ben Haddada, David Hu, Michèle Salmain, Lu Zhang, Chen Peng, Yi Wang, Bo Liedberg, Souhir Boujday
We describe the engineering of stable gold nanoparticle (AuNP) bioconjugates for the detection of staphylococcal enterotoxin A (SEA) using localized surface plasmon resonance (LSPR). Two types of AuNP bioconjugates were prepared by covalently attaching anti-SEA antibody (Ab) or SEA to AuNPs. This was achieved by reacting Traut's reagent with lysine residues of both proteins to generate thiol groups that bind to gold atoms on the AuNP surface. These bioconjugates were characterized in-depth by absorption spectroscopy, cryo-transmission electron microscopy, dynamic light scattering, and zeta potential measurements...
August 16, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28813641/aim2-inflammasome-activation-and-regulation-a-structural-perspective
#4
Bing Wang, Qian Yin
Absent in melanoma 2 (AIM2) inflammasome is a multi-protein platform that recognizes aberrant cytoplasmic dsDNA and induces cytokine maturation, release and pyroptosis. It is composed of AIM2, apoptosis-associated speck-like protein containing a CARD (ASC), and caspase-1. Recent X-ray crystallographic and high resolution cryo-electron microscopic (cryo-EM) studies have revealed a series of structures in AIM2 inflammasome activation and regulation. One prominent feature common in multiple steps is the assembly of high-order structures, especially helical filaments nucleated by upstream molecules, rather than stoichiometric complexes...
August 13, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28811642/octahedron-iron-oxide-nanocrystals-prohibited-clostridium-difficile-spore-germination-and-attenuated-local-and-systemic-inflammation
#5
Wei-Ting Lee, Ya-Na Wu, Yi-Hsuan Chen, Shang-Rung Wu, Tsai-Miao Shih, Tsung-Ju Li, Li-Xing Yang, Chen-Sheng Yeh, Pei-Jane Tsai, Dar-Bin Shieh
Clinical management of Clostridium difficile infection is still far from satisfactory as bacterial spores are resistant to many chemical agents and physical treatments. Certain types of nanoparticles have been demonstrated to exhibit anti-microbial efficacy even in multi-drug resistance bacteria. However, most of these studies failed to show biocompatibility to the mammalian host cells and no study has revealed in vivo efficacy in C. difficile infection animal models. The spores treated with 500 µg/mL Fe3-δO4 nanoparticles for 20 minutes, 64% of the spores were inhibited from transforming into vegetative cells, which was close to the results of the sodium hypochlorite-treated positive control...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811473/plant-made-polio-type-3-stabilized-vlps-a-candidate-synthetic-polio-vaccine
#6
Johanna Marsian, Helen Fox, Mohammad W Bahar, Abhay Kotecha, Elizabeth E Fry, David I Stuart, Andrew J Macadam, David J Rowlands, George P Lomonossoff
Poliovirus (PV) is the causative agent of poliomyelitis, a crippling human disease known since antiquity. PV occurs in two distinct antigenic forms, D and C, of which only the D form elicits a robust neutralizing response. Developing a synthetically produced stabilized virus-like particle (sVLP)-based vaccine with D antigenicity, without the drawbacks of current vaccines, will be a major step towards the final eradication of poliovirus. Such a sVLP would retain the native antigenic conformation and the repetitive structure of the original virus particle, but lack infectious genomic material...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28810122/crystal-face-distributions-and-surface-site-densities-of-two-synthetic-goethites-implications-for-adsorption-capacities-as-a-function-of-particle-size
#7
Kenneth J T Livi, Mario Villalobos, Rowan K Leary, Maria Varela, Jon Barnard, Milton Villacís-García, Rodolfo Zanella, Anna Goodridge, Paul A Midgley
Two synthetic goethites of varying crystal sizes distributions were analyzed by BET, conventional TEM, cryo-TEM, atomic resolution STEM and HRTEM, and electron tomography in order to determine the effects of crystal size, shape, and atomic scale surface roughness on their adsorption capacities. The two samples were determined by BET to have very different site densities based on CrVI adsorption experiments. Model specific surfaces areas generated from TEM observations showed that, based on size and shape, there should be little difference in their adsorption capacities...
August 15, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28809539/polymersomes-with-endosomal-ph-induced-vesicle-to-micelle-morphology-transition-and-a-potential-application-for-controlled-doxorubicin-delivery
#8
Turgay Yildirim, Anja Traeger, Pelin Sungur, Stephanie Hoeppener, Carolin Kellner, Ilknur Yildirim, David Pretzel, Stephanie Schubert, Ulrich S Schubert
A series of pH responsive block copolymers were synthesized via the reversible addition-fragmentation chain transfer (RAFT) polymerization of 3,4-dihydro-2H-pyran (DHP) protected 2-hydroxyethyl methacrylate (HEMA) (2-((tetrahydro-2H-pyran-2-yl)oxy)ethyl methacrylate (THP-HEMA)) and 2-(dimethylamino) ethyl methacrylate (DMAEMA) using p(THP-HEMA) as a macro chain transfer agent (mCTA). The degree of polymerization (DP) of the p(THP-HEMA) block was fixed to 35, whereas the DP of the p(DMAEMA) block was systematically varied from 21 to 50...
August 15, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28809395/cryo-em-structures-of-the-80s-ribosomes-from-human-parasites-trichomonas-vaginalis-and-toxoplasma-gondii
#9
Zhifei Li, Qiang Guo, Lvqin Zheng, Yongsheng Ji, Yi-Ting Xie, De-Hua Lai, Zhao-Rong Lun, Xun Suo, Ning Gao
As an indispensable molecular machine universal in all living organisms, the ribosome has been selected by evolution to be the natural target of many antibiotics and small-molecule inhibitors. High-resolution structures of pathogen ribosomes are crucial for understanding the general and unique aspects of translation control in disease-causing microbes. With cryo-electron microscopy technique, we have determined structures of the cytosolic ribosomes from two human parasites, Trichomonas vaginalis and Toxoplasma gondii, at resolution of 3...
August 15, 2017: Cell Research
https://www.readbyqxmd.com/read/28808031/changes-in-aggregation-states-of-light-harvesting-complexes-as-a-mechanism-for-modulating-energy-transfer-in-desert-crust-cyanobacteria
#10
Leeat Bar Eyal, Reza Ranjbar Choubeh, Eyal Cohen, Ido Eisenberg, Carmen Tamburu, Márta Dorogi, Renata Ünnep, Marie-Sousai Appavou, Reinat Nevo, Uri Raviv, Ziv Reich, Győző Garab, Herbert van Amerongen, Yossi Paltiel, Nir Keren
In this paper we propose an energy dissipation mechanism that is completely reliant on changes in the aggregation state of the phycobilisome light-harvesting antenna components. All photosynthetic organisms regulate the efficiency of excitation energy transfer (EET) to fit light energy supply to biochemical demands. Not many do this to the extent required of desert crust cyanobacteria. Following predawn dew deposition, they harvest light energy with maximum efficiency until desiccating in the early morning hours...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28803776/mechanism-of-enzyme-repair-by-the-aaa-chaperone-rubisco-activase
#11
Javaid Y Bhat, Goran Miličić, Gabriel Thieulin-Pardo, Andreas Bracher, Andrew Maxwell, Susanne Ciniawsky, Oliver Mueller-Cajar, John R Engen, F Ulrich Hartl, Petra Wendler, Manajit Hayer-Hartl
How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco...
July 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28802041/cryo-em-structure-of-the-tom-core-complex-from-neurospora-crassa
#12
Thomas Bausewein, Deryck J Mills, Julian D Langer, Beate Nitschke, Stephan Nussberger, Werner Kühlbrandt
The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The complex is a 148 kDa symmetrical dimer of ten membrane protein subunits that create a shallow funnel on the cytoplasmic membrane surface. In the core of the dimer, the β-barrels of the Tom40 pore form two identical preprotein conduits. Each Tom40 pore is surrounded by the transmembrane segments of the α-helical subunits Tom5, Tom6, and Tom7...
August 10, 2017: Cell
https://www.readbyqxmd.com/read/28801059/editorial-overview-cryo-electron-microscopy-exciting-advances-in-cryoem-herald-a-new-era-in-structural-biology
#13
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/28799758/ph-sensitive-interactions-between-cellulose-nanocrystals-and-dopc-liposomes
#14
Yotam Navon, Harisoa Radavidson, Jean-Luc Putaux, Bruno Jean, Laurent Heux
The interaction of DOPC vesicles with cellulose nanocrystals (CNCs) have been investigated using several complementary techniques. Dynamic light scattering, zeta-potential, cryo-transmission electron microscopy and isothermal titration calorimetry (ITC) analyses confirmed the formation of pH-dependent CNC-liposome complexes. ITC was used to characterize the thermodynamic properties of this interaction. Positive values of enthalpy were found at pH lower than 5 where the charge sign of the constituents was opposite...
August 11, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28798962/structural-pathway-of-regulated-substrate-transfer-and-threading-through-an-hsp100-disaggregase
#15
Célia Deville, Marta Carroni, Kamila B Franke, Maya Topf, Bernd Bukau, Axel Mogk, Helen R Saibil
Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including Escherichia coli ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through the central pore of tandem adenosine triphosphatase (ATPase) rings. To visualize protein disaggregation, we determined cryo-electron microscopy structures of inactive and substrate-bound ClpB in the presence of adenosine 5'-O-(3-thiotriphosphate), revealing closed AAA+ rings with a pronounced seam...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28796492/structural-and-morphological-description-of-sn-snox-core-shell-nanoparticles-synthesized-and-isolated-from-ionic-liquid
#16
Nadia Soulmi, Damien Dambournet, Cécile Rizzi, Juliette Sirieix-Plénet, Mathieu Duttine, Alain Wattiaux, Jolanta Swiatowska, Olaf J Borkiewicz, Henri Groult, Laurent Gaillon
The potential application of high capacity Sn-based electrode materials for energy storage, particularly in rechargeable batteries, has led to extensive research activities. In this scope, the development of an innovative synthesis route allowing to downsize particles to the nanoscale is of particular interest owing to the ability of such nanomaterial to better accommodate volume changes upon electrochemical reactions. Here, we report on the use of room temperature ionic liquid (i.e., [EMIm(+)][TFSI(-)]) as solvent, template, and stabilizer for Sn-based nanoparticles...
August 10, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28795863/a-new-era-of-studying-p53-mediated-transcription-activation
#17
Wei-Li Liu, Robert A Coleman, Sameer K Singh
To prevent tumorigenesis, p53 stimulates transcription by facilitating the recruitment of the transcription machinery on target gene promoters. Cryo-Electron Microscopy studies on p53-bound RNA Polymerase II (Pol II) reveal that p53 structurally regulates Pol II to affect its DNA binding and elongation, providing new insights into p53-mediated transcriptional regulation.
August 10, 2017: Transcription
https://www.readbyqxmd.com/read/28795512/single-particle-cryo-em-improved-ab-initio-3d-reconstruction-with-simple-prime
#18
Cyril F Reboul, Michael Eager, Dominika Elmlund, Hans Elmlund
Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. We developed the SIMPLE open-source image-processing suite for analysing cryo-EM images of single-particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single-particle projections in 3D. Here we extend our previous work on PRIME and introduce new stochastic optimisation algorithms that improve the robustness of the approach...
August 10, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28794948/glucosomes-glycosylated-vesicle-in-vesicle-aggregates-in-water-from-ph-responsive-microbial-glycolipid
#19
Niki Baccile, Patrick Le Griel, Sylvain Prévost, Bernd Everaert, Inge N A Van Bogaert, Sophie Roelants, Wim Soetaert
Vesicle-in-vesicle self-assembled containers, or vesosomes, are promising alternatives to liposomes because of their possible hierarchical encapsulation and high stability. We report herein the first example of sugar-based vesicles-in-vesicles, which we baptize glucosomes. These were prepared by using a natural microbial glycolipid (branched C22 sophorolipid) extracted from the culture medium of the yeast Pseudohyphozyma bogoriensis. Glucosomes spontaneously formed in water between pH 6 and pH 4 at room temperature, without the requirement of any additive...
August 2017: ChemistryOpen
https://www.readbyqxmd.com/read/28794042/palmitoylation-contributes-to-membrane-curvature-in-influenza-a-virus-assembly-and-hemagglutinin-mediated-membrane-fusion
#20
Petr Chlanda, Elena Mekhedov, Hang Waters, Alexander Sodt, Cindi Schwartz, Vinod Nair, Paul S Blank, Joshua Zimmerberg
The highly conserved cytoplasmic tail of influenza virus glycoprotein hemagglutinin (HA) contains three cysteines, post-translationally modified by covalently bound fatty acids. While viral HA acylation is crucial in virus replication, its physico-chemical role is unknown. We used virus-like particles (VLP) to study the effect of acylation on morphology, protein incorporation, lipid composition, and membrane fusion. De-acylation interrupted HA-M1 interactions since de-acylated mutant HA fail to incorporate an M1 layer within spheroidal VLP, and filamentous particles incorporated increased numbers of neuraminidase (NA)...
August 9, 2017: Journal of Virology
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