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Acta Crystallographica. Section D, Structural Biology

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https://www.readbyqxmd.com/read/28580916/cryo-electron-microscopy-of-chromatin-biology
#1
Marcus D Wilson, Alessandro Costa
The basic unit of chromatin, the nucleosome core particle (NCP), controls how DNA in eukaryotic cells is compacted, replicated and read. Since its discovery, biochemists have sought to understand how this protein-DNA complex can help to control so many diverse tasks. Recent electron-microscopy (EM) studies on NCP-containing assemblies have helped to describe important chromatin transactions at a molecular level. With the implementation of recent technical advances in single-particle EM, our understanding of how nucleosomes are recognized and read looks to take a leap forward...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580915/the-potential-use-of-single-particle-electron-microscopy-as-a-tool-for-structure-based-inhibitor-design
#2
S Rawson, M J McPhillie, R M Johnson, C W G Fishwick, S P Muench
Recent developments in electron microscopy (EM) have led to a step change in our ability to solve the structures of previously intractable systems, especially membrane proteins and large protein complexes. This has provided new opportunities in the field of structure-based drug design, with a number of high-profile publications resolving the binding sites of small molecules and peptide inhibitors. There are a number of advantages of EM over the more traditional X-ray crystallographic approach, such as resolving different conformational states and permitting the dynamics of a system to be better resolved when not constrained by a crystal lattice...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580914/high-resolution-cryo-em-proteasome-structures-in-drug-development
#3
Edward P Morris, Paula C A da Fonseca
With the recent advances in biological structural electron microscopy (EM), protein structures can now be obtained by cryo-EM and single-particle analysis at resolutions that used to be achievable only by crystallographic or NMR methods. We have explored their application to study protein-ligand interactions using the human 20S proteasome, a well established target for cancer therapy that is also being investigated as a target for an increasing range of other medical conditions. The map of a ligand-bound human 20S proteasome served as a proof of principle that cryo-EM is emerging as a realistic approach for more general structural studies of protein-ligand interactions, with the potential benefits of extending such studies to complexes that are unfavourable to other methods and allowing structure determination under conditions that are closer to physiological, preserving ligand specificity towards closely related binding sites...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580913/the-ribosome-and-its-role-in-protein-folding-looking-through-a-magnifying-glass
#4
Abid Javed, John Christodoulou, Lisa D Cabrita, Elena V Orlova
Protein folding, a process that underpins cellular activity, begins co-translationally on the ribosome. During translation, a newly synthesized polypeptide chain enters the ribosomal exit tunnel and actively interacts with the ribosome elements - the r-proteins and rRNA that line the tunnel - prior to emerging into the cellular milieu. While understanding of the structure and function of the ribosome has advanced significantly, little is known about the process of folding of the emerging nascent chain (NC)...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580912/trends-in-the-electron-microscopy-data-bank-emdb
#5
Ardan Patwardhan
Recent technological advances, such as the introduction of the direct electron detector, have transformed the field of cryo-EM and the landscape of molecular and cellular structural biology. This study analyses these trends from the vantage point of the Electron Microscopy Data Bank (EMDB), the public archive for three-dimensional EM reconstructions. Over 1000 entries were released in 2016, representing almost a quarter of the total number of entries (4431). Structures at better than 6 Å resolution now represent one of the fastest-growing categories, while the share of annually released tomography-related structures is approaching 20%...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580911/a-pipeline-approach-to-single-particle-processing-in-relion
#6
Rafael Fernandez-Leiro, Sjors H W Scheres
The formal concept of a workflow to single-particle analysis of cryo-electron microscopy (cryo-EM) images in the RELION program is described. In this approach, the structure-determination process is considered as a graph, where intermediate results in the form of images or metadata are the vertices, and different functionalities of the program are the edges. The new implementation automatically logs all user actions, facilitates file management and disk cleaning, and allows convenient browsing of the history of a project...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580910/electron-bio-imaging-centre-ebic-the-uk-national-research-facility-for-biological-electron-microscopy
#7
Daniel K Clare, C Alistair Siebert, Corey Hecksel, Christoph Hagen, Valerie Mordhorst, Michael Grange, Alun W Ashton, Martin A Walsh, Kay Grünewald, Helen R Saibil, David I Stuart, Peijun Zhang
The recent resolution revolution in cryo-EM has led to a massive increase in demand for both time on high-end cryo-electron microscopes and access to cryo-electron microscopy expertise. In anticipation of this demand, eBIC was set up at Diamond Light Source in collaboration with Birkbeck College London and the University of Oxford, and funded by the Wellcome Trust, the UK Medical Research Council (MRC) and the Biotechnology and Biological Sciences Research Council (BBSRC) to provide access to high-end equipment through peer review...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580909/the-dynamo-package-for-tomography-and-subtomogram-averaging-components-for-matlab-gpu-computing-and-ec2-amazon-web-services
#8
Daniel Castaño-Díez
Dynamo is a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580908/recent-developments-in-the-ccp-em-software-suite
#9
Tom Burnley, Colin M Palmer, Martyn Winn
As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessible via a user-friendly graphical user interface as well as a command-line interface suitable for scripting...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580907/introducing-the-proceedings-of-the-ccp-em-spring-symposium
#10
Tom Burnley
No abstract text is available yet for this article.
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28471369/pepsi-saxs-an-adaptive-method-for-rapid-and-accurate-computation-of-small-angle-x-ray-scattering-profiles
#11
Sergei Grudinin, Maria Garkavenko, Andrei Kazennov
A new method called Pepsi-SAXS is presented that calculates small-angle X-ray scattering profiles from atomistic models. The method is based on the multipole expansion scheme and is significantly faster compared with other tested methods. In particular, using the Nyquist-Shannon-Kotelnikov sampling theorem, the multipole expansion order is adapted to the size of the model and the resolution of the experimental data. It is argued that by using the adaptive expansion order, this method has the same quadratic dependence on the number of atoms in the model as the Debye-based approach, but with a much smaller prefactor in the computational complexity...
May 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28471368/the-first-plant-acyl-coa-binding-protein-structures-the-close-homologues-osacbp1-and-osacbp2-from-rice
#12
Ze Hua Guo, Wallace H Y Chan, Geoffrey K W Kong, Quan Hao, Mee Len Chye
Acyl-CoA-binding proteins (ACBPs) are a family of proteins that facilitate the binding of long-chain acyl-CoA esters at a conserved acyl-CoA-binding domain. ACBPs act to form intracellular acyl-CoA pools, transport acyl-CoA esters and regulate lipid metabolism. In the model plant Arabidopsis thaliana, a family of six ACBPs has been demonstrated to function in stress and development. Six ACBPs (OsACBPs) have also been identified in Oryza sativa (rice), but they are not as well characterized as those in Arabidopsis thaliana...
May 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28471367/crystal-structure-of-the-novel-amino-acid-racemase-isoleucine-2-epimerase-from-lactobacillus-buchneri
#13
Junji Hayashi, Yuta Mutaguchi, Yume Minemura, Noriko Nakagawa, Kazunari Yoneda, Taketo Ohmori, Toshihisa Ohshima, Haruhiko Sakuraba
Crystal structures of Lactobacillus buchneri isoleucine 2-epimerase, a novel branched-chain amino-acid racemase, were determined for the enzyme in the apo form, in complex with pyridoxal 5'-phosphate (PLP), in complex with N-(5'-phosphopyridoxyl)-L-isoleucine (PLP-L-Ile) and in complex with N-(5'-phosphopyridoxyl)-D-allo-isoleucine (PLP-D-allo-Ile) at resolutions of 2.77, 1.94, 2.65 and 2.12 Å, respectively. The enzyme assembled as a tetramer, with each subunit being composed of N-terminal, C-terminal and large PLP-binding domains...
May 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28471366/structure-of-the-family-b-dna-polymerase-from-the-hyperthermophilic-archaeon-pyrobaculum-calidifontis
#14
Jingxu Guo, Wenling Zhang, Alun R Coker, Steve P Wood, Jonathan B Cooper, Shazeel Ahmad, Syed Ali, Naeem Rashid, Muhummad Akhtar
The family B DNA polymerase from Pyrobaculum calidifontis (Pc-polymerase) consists of 783 amino acids and is magnesium-ion dependent. It has an optimal pH of 8.5, an optimal temperature of 75°C and a half-life of 4.5 h at 95°C, giving it greater thermostability than the widely used Taq DNA polymerase. The enzyme is also capable of PCR-amplifying larger DNA fragments of up to 7.5 kb in length. It was shown to have functional, error-correcting 3'-5' exonuclease activity, as do the related high-fidelity DNA polymerases from Pyrococcus furiosus, Thermococcus kodakarensis KOD1 and Thermococcus gorgonarius, which have extensive commercial applications...
May 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28471365/structural-features-of-ns3-of-dengue-virus-serotypes-2-and-4-in-solution-and-insight-into-rna-binding-and-the-inhibitory-role-of-quercetin
#15
Ankita Pan, Wuan Geok Saw, Malathy Sony Subramanian Manimekalai, Ardina Grüber, Shin Joon, Tsutomu Matsui, Thomas M Weiss, Gerhard Grüber
Dengue virus (DENV), which has four serotypes (DENV-1 to DENV-4), is the causative agent of the viral infection dengue. DENV nonstructural protein 3 (NS3) comprises a serine protease domain and an RNA helicase domain which has nucleotide triphosphatase activities that are essential for RNA replication and viral assembly. Here, solution X-ray scattering was used to provide insight into the overall structure and flexibility of the entire NS3 and its recombinant helicase and protease domains for Dengue virus serotypes 2 and 4 in solution...
May 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28471364/structural-study-of-the-x-ray-induced-enzymatic-reduction-of-molecular-oxygen-to-water-by-steccherinum-murashkinskyi-laccase-insights-into-the-reaction-mechanism
#16
K M Polyakov, S Gavryushov, S Ivanova, T V Fedorova, O A Glazunova, A N Popov, O V Koroleva
The laccase from Steccherinum murashkinskyi is a member of the large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates, accompanied by the reduction of dioxygen to water. The reducing properties of X-ray radiation and the high quality of the laccase crystals allow the study of the catalytic reduction of dioxygen to water directly in a crystal. A series of diffraction data sets with increasing absorbed radiation dose were collected from a single crystal of Steccherinum murashkinskyi laccase at 1...
May 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375150/responses-to-atomic-resolution-a-badly-abused-term-in-structural-biology
#17
Wah Chiu, James Holton, Paul Langan, Nicholas K Sauter, Ilme Schlichting, Tom Terwilliger, Jennifer L Martin, Randy J Read, Soichi Wakatsuki
No abstract text is available yet for this article.
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375149/-atomic-resolution-a-badly-abused-term-in-structural-biology
#18
Alexander Wlodawer, Zbigniew Dauter
No abstract text is available yet for this article.
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375148/low-dose-fixed-target-serial-synchrotron-crystallography
#19
Robin L Owen, Danny Axford, Darren A Sherrell, Anling Kuo, Oliver P Ernst, Eike C Schulz, R J Dwayne Miller, Henrike M Mueller-Werkmeister
The development of serial crystallography has been driven by the sample requirements imposed by X-ray free-electron lasers. Serial techniques are now being exploited at synchrotrons. Using a fixed-target approach to high-throughput serial sampling, it is demonstrated that high-quality data can be collected from myoglobin crystals, allowing room-temperature, low-dose structure determination. The combination of fixed-target arrays and a fast, accurate translation system allows high-throughput serial data collection at high hit rates and with low sample consumption...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375147/crystal-structures-of-hsp104-n-terminal-domains-from-saccharomyces-cerevisiae-and-candida-albicans-suggest-the-mechanism-for-the-function-of-hsp104-in-dissolving-prions
#20
Peng Wang, Jingzhi Li, Clarissa Weaver, Aaron Lucius, Bingdong Sha
Hsp104 is a yeast member of the Hsp100 family which functions as a molecular chaperone to disaggregate misfolded polypeptides. To understand the mechanism by which the Hsp104 N-terminal domain (NTD) interacts with its peptide substrates, crystal structures of the Hsp104 NTDs from Saccharomyces cerevisiae (ScHsp104NTD) and Candida albicans (CaHsp104NTD) have been determined at high resolution. The structures of ScHsp104NTD and CaHsp104NTD reveal that the yeast Hsp104 NTD may utilize a conserved putative peptide-binding groove to interact with misfolded polypeptides...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
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