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Journal of Structural Biology

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https://www.readbyqxmd.com/read/29908248/detection-of-single-alpha-helices-in-large-protein-sequence-sets-using-hardware-acceleration
#1
Ákos Kovács, Dániel Dudola, László Nyitray, Gábor Tóth, Zoltán Nagy, Zoltán Gáspári
Single alpha-helices (SAHs) are increasingly recognized as important structural and functional elements of proteins. Comprehensive identification of SAH segments in large protein datasets was largely hindered by the slow speed of the most restrictive prediction tool for their identification, FT_CHARGE on common hardware. We have previously implemented an FPGA-based version of this tool allowing fast analysis of a large number of sequences. Using this implementation, we have set up of a semi-automated pipeline capable of analyzing full UniProt releases in reasonable time and compiling monthly updates of a comprehensive database of SAH segments...
June 13, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29908247/psf-correction-in-soft-x-ray-tomography
#2
Axel Ekman, Venera Weinhardt, Jian-Hua Chen, Gerry McDermott, Mark A Le Gros, Carolyn Larabell
In this manuscript, we introduce a linear approximation of the forward model of soft x-ray tomography (SXT), such that the reconstruction is solvable by standard iterative schemes. This linear model takes into account the three-dimensional point spread function (PSF) of the optical system, which consequently enhances the reconstruction data. The feasibility of the model is demonstrated on both simulated and experimental data, based on theoretically estimated and experimentally measured PSFs.
June 13, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29906506/high-resolution-crystal-structure-of-substrate-free-human-neprilysin
#3
Stephen Moss, Vasanta Subramanian, K Ravi Acharya
Neprilysin is a transmembrane M13 zinc metalloprotease responsible for the degradation of several biologically active peptides including insulin, enkephalin, substance P, bradykinin, endothelin-1, neurotensin and amyloid-β. The protein has received attention for its role in modulating blood pressure responses with its inhibition producing an antihypertensive response. To date, several inhibitor bound crystal structures of the human neprilysin extracellular domain have been determined, but, a structure free of bound inhibitor or substrate has yet to be reported...
June 12, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29902523/analytical-symmetry-detection-in-protein-assemblies-ii-dihedral-and-cubic-symmetries
#4
Guillaume Pagès, Sergei Grudinin
Protein assemblies are often symmetric, as this organization has many advantages compared to individual proteins. Complex protein structures thus very often possess high-order symmetries. Detection and analysis of these symmetries has been a challenging problem and no efficient algorithms have been developed so far. This paper presents the extension of our cyclic symmetry detection method for higher-order symmetries with multiple symmetry axes. These include dihedral and cubic, i.e., tetrahedral, octahedral, and icosahedral, groups...
June 11, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29886194/structural-and-biochemical-characterization-of-spoiiiaf-a-component-of-a-sporulation-essential-channel-in-bacillus-subtilis
#5
N Zeytuni, K A Flanagan, L J Worrall, S C Massoni, A H Camp, N C J Strynadka
Environmental stress factors initiate the developmental process of sporulation in some Gram-positive bacteria including Bacillus subtilis. Upon sporulation initiation the bacterial cell undergoes a series of morphological transformations that result in the creation of a single dormant spore. Early in sporulation, an asymmetric cell division produces a larger mother cell and smaller forespore. Next, the mother cell septal membrane engulfs the forespore, and an essential channel, the so-called feeding-tube apparatus, is formed...
June 7, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29885491/identification-of-a-novel-tetrameric-structure-for-human-apolipoprotein-d
#6
Claudia S Kielkopf, Jason K K Low, Yee-Foong Mok, Surabhi Bhatia, Tony Palasovski, Aaron J Oakley, Andrew E Whitten, Brett Garner, Simon H J Brown
Apolipoprotein-D is a 25 kDa glycosylated member of the lipocalin family that folds into an eight-stranded β-barrel with a single adjacent α-helix. Apolipoprotein-D specifically binds a range of small hydrophobic ligands such as progesterone and arachidonic acid and has an antioxidant function that is in part due to the reduction of peroxidised lipids by methionine-93. Therefore, apolipoprotein-D plays multiple roles throughout the body and is protective in Alzheimer's disease, where apolipoprotein-D overexpression reduces the amyloid-β burden in Alzheimer's disease mouse models...
June 6, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29879487/solid-state-nmr-analysis-of-the-sodium-pump-krokinobacter-rhodopsin-2-and-its-h30a-mutant
#7
Jagdeep Kaur, Clara Nassrin Kriebel, Peter Eberhardt, Orawan Jakdetchai, Alexander J Leeder, Ingrid Weber, Lynda J Brown, Richard C D Brown, Johanna Becker-Baldus, Christian Bamann, Josef Wachtveitl, Clemens Glaubitz
Krokinobacter eikastus rhodopsin 2 (KR2) is a pentameric, light-driven ion pump, which selectively transports sodium or protons. The mechanism of ion selectivity and transfer is unknown. By using conventional as well as dynamic nuclear polarization (DNP)-enhanced solid-state NMR, we were able to analyse the retinal polyene chain between positions C10 and C15 as well as the Schiff base nitrogen in the KR2 resting state. In addition, 50% of the KR2 13 C and 15 N resonances could be assigned by multidimensional high-field solid-state NMR experiments...
June 4, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29879486/reductive-power-of-the-archaea-right-handed-coiled-coil-nanotube-rhcc-nt-and-incorporation-of-mercury-clusters-inside-protein-cages
#8
Matthew McDougall, Kevin McEleney, Olga Francisco, Benchmen Trieu, Kelly Efehi Ogbomo, Gregg Tomy, Jörg Stetefeld
Coiled coils are well described as powerful oligomerization motifs and exhibit a large diversity of functions, including gene regulation, cell division, membrane fusion and drug extrusion. The archaea S-layer originated right-handed coiled coil -RHCC-NT- is characterized by extreme stability and is free of cysteine and histidine moieties. In the current study, we have followed a multidisciplinary approach to investigate the capacity of RHCC-NT to bind a variety of ionic complex metal ions. At the outside of the RHCC-NT, one mercury ion forms an electrostatic interaction with the S-methyl moiety of the single methionine residue present in each coil...
June 4, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29864529/cryoem-cloud-tools-a-software-platform-to-deploy-and-manage-cryo-em-jobs-in-the-cloud
#9
Michael A Cianfrocco, Indrajit Lahiri, Frank DiMaio, Andres E Leschziner
Access to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have developed tools that will submit cryo-EM analysis routines and atomic model building jobs directly to Amazon Web Services (AWS) from a local computer or laptop. These new software tools ("cryoem-cloud-tools") have incorporated optimal data movement, security, and cost-saving strategies, giving novice users access to complex cryo-EM data processing pipelines...
June 1, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29859330/biochemical-characterization-of-the-skeletal-matrix-of-the-massive-coral-porites-australiensis-the-saccharide-moieties-and-their-localization
#10
Takeshi Takeuchi, Laurent Plasseraud, Isabelle Ziegler-Devin, Nicolas Brosse, Chuya Shinzato, Noriyuki Satoh, Frédéric Marin
To construct calcium carbonate skeletons of sophisticated architecture, scleractinian corals secrete an extracellular skeletal organic matrix (SOM) from aboral ectodermal cells. The SOM, which is composed of proteins, saccharides, and lipids, performs functions critical for skeleton formation. Even though polysaccharides constitute the major component of the SOM, its contribution to coral skeleton formation is poorly understood. To this end, we analyzed the SOM of the massive colonial coral, Porites australiensis, the skeleton of which has drawn great research interest because it records environmental conditions throughout the life of the colony...
May 30, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29859329/spectral-comparisons-of-mammalian-cells-and-intact-organelles-by-solid-state-nmr
#11
Sabrina H Werby, Lynette Cegelski
Whole-cell protein profiling, spatial localization, and quantification of activities such as gene transcription and protein translation are possible with modern biochemical and biophysical techniques. Yet, addressing questions of overall compositional changes within a cell - capturing the relative amounts of protein and ribosomal RNA levels and lipid content simultaneously - would require numerous extractions and purifications with caveats due to isolation yields and detection methods. A holistic view of cellular composition would aid in the study of cellular composition and function...
May 30, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29859328/plasmin-driven-fibrinolysis-in-a-quasi-two-dimensional-nanoscale-fibrin-matrix
#12
Tímea Feller, Jolán Hársfalvi, Csilla Csányi, Balázs Kiss, Miklós Kellermayer
Fibrin plays a fundamentally important role during hemostasis. To withstand the shear forces of blood flow and prevent embolisation, fibrin monomers form a three-dimensional polymer network that serves as an elastic scaffold for the blood clot. The complex spatial hierarchy of the fibrin meshwork, however, severely complicates the exploration of structural features, mechanical properties and molecular changes associated with the individual fibers of the clot. Here we developed a quasi-two-dimensional nanoscale fibrin matrix that enables the investigation of fibrin properties by topographical analysis using atomic force microscopy...
May 30, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29857134/the-protofilament-architecture-of-a-de-novo-designed-coiled-coil-based-amyloidogenic-peptide
#13
Mônica Santos de Freitas, Raheleh Rezaei Araghi, Enrico Brandenburg, Jork Leiterer, Franziska Emmerling, Kristin Folmert, Ulla I M Gerling-Driessen, Benjamin Bardiaux, Christoph Böttcher, Kevin Pagel, Anne Diehl, Hans V Berlepsch, Hartmut Oschkinat, Beate Koksch
Amyloid fibrils are polymers formed by proteins under specific conditions and in many cases they are related to pathogenesis, such as Parkinson's and Alzheimer's diseases. Their hallmark is the presence of a β-sheet structure. High resolution structural data on these systems as well as information gathered from multiple complementary analytical techniques is needed, from both a fundamental and a pharmaceutical perspective. Here, a previously reported de novo designed, pH-switchable coiled coil-based peptide that undergoes structural transitions resulting in fibril formation under physiological conditions has been exhaustively characterized by transmission electron microscopy (TEM), cryo-TEM, atomic force microscopy (AFM), wide-angle X-ray scattering (WAXS) and solid-state NMR (ssNMR)...
May 29, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29852221/mechanical-variations-in-proteins-with-large-scale-motions-highlight-the-formation-of-structural-locks
#14
Sophie Sacquin-Mora
Protein function depends just as much on flexibility as on structure, and in numerous cases, a protein's biological activity involves transitions that will impact both its conformation and its mechanical properties. Here, we use a coarse-grain approach to investigate the impact of structural changes on protein flexibility. More particularly, we focus our study on proteins presenting large-scale motions. We show how calculating directional force constants within residue pairs, and investigating their variation upon protein closure, can lead to the detection of a limited set of residues that form a structural lock in the protein's closed conformation...
May 28, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29852220/know-your-detergents-a-case-study-on-detergent-background-in-negative-stain-electron-microscopy
#15
Theresa Gewering, Dovile Januliene, Anne B Ries, Arne Moeller
Electron cryo-microscopy (cryo-EM) of purified macromolecular complexes is now providing 3D-structures at near-atomic resolution (Kühlbrandt, 2014).Cryo-EM can tolerate heterogeneous specimens, however, high-resolution efforts demand highly optimized samples. Therefore, significant pre-screening and evaluation is essential before a final dataset can be obtained. While cryo-EM is comparably slow and requires access to expensive high-end electron microscopes, room temperature negative stain EM is fast, inexpensive and provides immediate feedback...
May 28, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29775653/atomic-structure-of-a-rationally-engineered-gene-delivery-vector-aav2-5
#16
Matthew Burg, Claire Rosebrough, Lauren M Drouin, Antonette Bennett, Mario Mietzsch, Paul Chipman, Robert McKenna, Duncan Sousa, Mark Potter, Barry Byrne, R Jude Samulski, Mavis Agbandje-McKenna
AAV2.5 represents the first structure-guided in-silico designed Adeno-associated virus (AAV) gene delivery vector. This engineered vector combined the receptor attachment properties of AAV serotype 2 (AAV2) with the muscle tropic properties of AAV1, and exhibited an antibody escape phenotype because of a modified antigenic epitope. To confirm the design, the structure of the vector was determined to a resolution of 2.78 Å using cryo-electron microscopy and image reconstruction. The structure of the major viral protein (VP), VP3, was ordered from residue 219 to 736, as reported for other AAV structures, and the five AAV2...
May 15, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29763735/effects-of-flexibility-of-the-%C3%AE-2-chain-of-type-i-collagen-on-collagenase-cleavage
#17
Arya Mekkat, Erik Poppleton, Bo An, Robert Visse, Hideaki Nagase, David L Kaplan, Barbara Brodsky, Yu-Shan Lin
Cleavage of collagen by collagenases such as matrix metalloproteinase 1 (MMP-1) is a key step in development, tissue remodeling, and tumor proliferation. The abundant heterotrimeric type I collagen composed of two α1(I) chains and one α2(I) chain is efficiently cleaved by MMP-1 at a unique site in the triple helix, a process which may be initiated by local unfolding within the peptide chains. Atypical homotrimers of the α1(I) chain, found in embryonic and cancer tissues, are very resistant to MMP cleavage...
May 12, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29758270/collagen-gly-missense-mutations-effect-of-residue-identity-on-collagen-structure-and-integrin-binding
#18
Yimin Qiu, Arya Mekkat, Hongtao Yu, Sezin Yigit, Samir Hamaia, Richard W Farndale, David L Kaplan, Yu-Shan Lin, Barbara Brodsky
Gly missense mutations in type I collagen, which replace a conserved Gly in the repeating (Gly-Xaa-Yaa)n sequence with a larger residue, are known to cause Osteogenesis Imperfecta (OI). The clinical consequences of such mutations range from mild to lethal, with more serious clinical severity associated with larger Gly replacement residues. Here, we investigate the influence of the identity of the residue replacing Gly within and adjacent to the integrin binding 502 GFPGER507 sequence on triple-helix structure, stability and integrin binding using a recombinant bacterial collagen system...
May 11, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29738832/topology-of-interaction-between-titin-and-myosin-thick-filaments
#19
Miklós Kellermayer, Dominik Sziklai, Zsombor Papp, Brennan Decker, Eszter Lakatos, Zsolt Mártonfalvi
Titin is a giant protein spanning between the Z- and M-lines of the sarcomere. In the A-band titin is associated with the myosin thick filament. It has been speculated that titin may serve as a blueprint for thick-filament formation due to the super-repeat structure of its A-band domains. Accordingly, titin might provide a template that determines the length and structural periodicity of the thick filament. Here we tested the titin ruler hypothesis by mixing titin and myosin at in situ stoichiometric ratios (300 myosins per 12 titins) in buffers of different ionic strength (KCl concentration range 100-300 mM)...
May 5, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29729323/structure-of-the-dna-binding-domain-of-human-myelin-gene-regulatory-factor-reveals-its-potential-protein-dna-recognition-mode
#20
Baohua Chen, Yun Zhu, Sheng Ye, Rongguang Zhang
Myelin-gene regulatory factor (MYRF) is a membrane-bound transcription factors, which is responsible for the differentiation of oligodendrocytes and myelination of central nervous system. Followed by a self-cleavage by the intramolecular chaperone auto-processing (ICA) domain, DNA-binding domain (DBD) of MYRF is released from the endoplasmic reticulum (ER) and translocated to the nucleus to regulate gene expression. In present work, we have solved the crystal structure of the human MYRF-DBD to 1.85-Å resolution...
May 2, 2018: Journal of Structural Biology
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