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Non-structural protein 1

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https://www.readbyqxmd.com/read/27936128/crystal-structure-of-the-streptomyces-coelicolor-sortase-e1-transpeptidase-provides-insight-into-the-binding-mode-of-the-novel-class-e-sorting-signal
#1
Michele D Kattke, Albert H Chan, Andrew Duong, Danielle L Sexton, Michael R Sawaya, Duilio Cascio, Marie A Elliot, Robert T Clubb
Many species of Gram-positive bacteria use sortase transpeptidases to covalently affix proteins to their cell wall or to assemble pili. Sortase-displayed proteins perform critical and diverse functions for cell survival, including cell adhesion, nutrient acquisition, and morphological development, among others. Based on their amino acid sequences, there are at least six types of sortases (class A to F enzymes); however, class E enzymes have not been extensively studied. Class E sortases are used by soil and freshwater-dwelling Actinobacteria to display proteins that contain a non-canonical LAXTG sorting signal, which differs from 90% of known sorting signals by substitution of alanine for proline...
2016: PloS One
https://www.readbyqxmd.com/read/27934230/autoxidation-of-reduced-horse-heart-cytochrome-c-catalyzed-by-cardiolipin-containing-membranes
#2
Lee Serpas, Bridget Milorey, Leah A Pandiscia, Anthony W Addison, Reinhard Schweitzer-Stenner
Visible circular dichroism, absorption, and fluorescence spectroscopy were used to probe the binding of horse heart ferrocytochrome c to anionic cardiolipin (CL) head groups on the surface of 1,1',2,2'-tetraoleoyl cardiolipin (TOCL)/1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) (20%:80%) liposomes in an aerobic environment. We found that ferrocytochrome c undergoes a conformational transition upon binding that leads to complete oxidation of the protein at intermediate and high CL concentrations. At low lipid concentrations, the protein maintains a structure that is only slightly different from its native one, whereas an ensemble of misligated predominantly hexacoordinated low-spin states become increasingly populated at high lipid concentrations...
December 8, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/27933225/rational-design-of-dual-active-sites-in-a-single-protein-scaffold-a-case-study-of-heme-protein-in-myoglobin
#3
Xiao-Gang Shu, Ji-Hu Su, Ke-Jie Du, Yong You, Shu-Qin Gao, Ge-Bo Wen, Xiangshi Tan, Ying-Wu Lin
Rational protein design has been proven to be a powerful tool for creating functional artificial proteins. Although many artificial metalloproteins with a single active site have been successfully created, those with dual active sites in a single protein scaffold are still relatively rare. In this study, we rationally designed dual active sites in a single heme protein scaffold, myoglobin (Mb), by retaining the native heme site and creating a copper-binding site remotely through a single mutation of Arg118 to His or Met...
June 2016: ChemistryOpen
https://www.readbyqxmd.com/read/27930654/whole-organism-developmental-expression-profiling-identifies-rab-28-as-a-novel-ciliary-gtpase-associated-with-the-bbsome-and-intraflagellar-transport
#4
Victor L Jensen, Stephen Carter, Anna A W M Sanders, Chunmei Li, Julie Kennedy, Tiffany A Timbers, Jerry Cai, Noemie Scheidel, Breandán N Kennedy, Ryan D Morin, Michel R Leroux, Oliver E Blacque
Primary cilia are specialised sensory and developmental signalling devices extending from the surface of most eukaryotic cells. Defects in these organelles cause inherited human disorders (ciliopathies) such as retinitis pigmentosa and Bardet-Biedl syndrome (BBS), frequently affecting many physiological and developmental processes across multiple organs. Cilium formation, maintenance and function depend on intracellular transport systems such as intraflagellar transport (IFT), which is driven by kinesin-2 and IFT-dynein motors and regulated by the Bardet-Biedl syndrome (BBS) cargo-adaptor protein complex, or BBSome...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27929054/in-silico-identification-of-snp-diversity-in-cultivated-and-wild-tomato-species-insight-from-molecular-simulations
#5
Archana Bhardwaj, Yogeshwar Vikram Dhar, Mehar Hasan Asif, Sumit K Bag
Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27926736/structure-of-cc-chemokine-receptor-2-with-orthosteric-and-allosteric-antagonists
#6
Yi Zheng, Ling Qin, Natalia V Ortiz Zacarías, Henk de Vries, Gye Won Han, Martin Gustavsson, Marta Dabros, Chunxia Zhao, Robert J Cherney, Percy Carter, Dean Stamos, Ruben Abagyan, Vadim Cherezov, Raymond C Stevens, Adriaan P IJzerman, Laura H Heitman, Andrew Tebben, Irina Kufareva, Tracy M Handel
CC chemokine receptor 2 (CCR2) is one of 19 members of the chemokine receptor subfamily of human class A G-protein-coupled receptors. CCR2 is expressed on monocytes, immature dendritic cells, and T-cell subpopulations, and mediates their migration towards endogenous CC chemokine ligands such as CCL2 (ref. 1). CCR2 and its ligands are implicated in numerous inflammatory and neurodegenerative diseases including atherosclerosis, multiple sclerosis, asthma, neuropathic pain, and diabetic nephropathy, as well as cancer...
December 7, 2016: Nature
https://www.readbyqxmd.com/read/27923202/structure-based-optimization-of-salt-bridge-network-across-the-complex-interface-of-ptpn4-pdz-domain-with-its-peptide-ligands-in-neuroglioma
#7
Xian Xiao, Qiang-Hua He, Li-Yan Yu, Song-Qing Wang, Yang Li, Hua Yang, Ai-Hua Zhang, Xiao-Hong Ma, Yu-Jie Peng, Bing Chen
The PTP non-receptor type 4 (PTPN4) is an important regulator protein in learning, spatial memory and cerebellar synaptic plasticity; targeting the PDZ domain of PTPN4 has become as attractive therapeutic strategy for human neuroglioma. Here, we systematically examined the complex crystal structures of PTPN4 PDZ domain with its known peptide ligands; a number of charged amino acid residues were identified in these ligands and in the peptide-binding pocket of PDZ domain, which can constitute a complicated salt-bridge network across the complex interface...
November 30, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27918527/induction-and-suppression-of-antiviral-rna-interference-by-influenza-a-virus-in-mammalian-cells
#8
Yang Li, Megha Basavappa, Jinfeng Lu, Shuwei Dong, D Alexander Cronkite, John T Prior, Hans-Christian Reinecker, Paul Hertzog, Yanhong Han, Wan-Xiang Li, Sihem Cheloufi, Fedor V Karginov, Shou-Wei Ding, Kate L Jeffrey
Influenza A virus (IAV) causes annual epidemics and occasional pandemics, and is one of the best-characterized human RNA viral pathogens(1). However, a physiologically relevant role for the RNA interference (RNAi) suppressor activity of the IAV non-structural protein 1 (NS1), reported over a decade ago(2), remains unknown(3). Plant and insect viruses have evolved diverse virulence proteins to suppress RNAi as their hosts produce virus-derived small interfering RNAs (siRNAs) that direct specific antiviral defence(4-7) by an RNAi mechanism dependent on the slicing activity of Argonaute proteins (AGOs)(8,9)...
December 5, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27917832/1-45%C3%A2-%C3%A3-resolution-structure-of-srpn18-from-the-malaria-vector-anopheles-gambiae
#9
David A Meekins, Xin Zhang, Kevin P Battaile, Scott Lovell, Kristin Michel
Serine protease inhibitors (serpins) in insects function within development, wound healing and immunity. The genome of the African malaria vector, Anopheles gambiae, encodes 23 distinct serpin proteins, several of which are implicated in disease-relevant physiological responses. A. gambiae serpin 18 (SRPN18) was previously categorized as non-inhibitory based on the sequence of its reactive-center loop (RCL), a region responsible for targeting and initiating protease inhibition. The crystal structure of A. gambiae SRPN18 was determined to a resolution of 1...
December 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27917827/the-n14-anti-afamin-antibody-fab-a-rare-vl1-cdr-glycosylation-crystallographic-re-sequencing-molecular-plasticity-and-conservative-versus-enthusiastic-modelling
#10
Andreas Naschberger, Barbara G Fürnrohr, Tihana Lenac Rovis, Suzana Malic, Klaus Scheffzek, Hans Dieplinger, Bernhard Rupp
The monoclonal antibody N14 is used as a detection antibody in ELISA kits for the human glycoprotein afamin, a member of the albumin family, which has recently gained interest in the capture and stabilization of Wnt signalling proteins, and for its role in metabolic syndrome and papillary thyroid carcinoma. As a rare occurrence, the N14 Fab is N-glycosylated at Asn26L at the onset of the VL1 antigen-binding loop, with the α-1-6 core fucosylated complex glycan facing out of the L1 complementarity-determining region...
December 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27914953/both-secreted-and-the-cellular-levels-of-bdnf-attenuated-due-to-tau-hyperphosphorylation-in-primary-cultures-of-cortical-neurons
#11
İrem Lütfiye Atasoy, Erdinç Dursun, Duygu Gezen Ak, Derya Metin Armağan, Melek Öztürk, Selma Yılmazer
Intracellular aggregation of hyperphosphorylated tau in neurofibrillary tangles (NFTs) is a major neuropathological hallmark of taupathies such as Alzheimer's disease. Okadaic acid (OKA) is a potent inhibitor of PP2A, leading to abnormal tau phosphorylation. Brain-derived neurotrophic factor (BDNF) is a neurotrophin that is selectively downregulated in AD. In this study, we investigated the effects of OKA induced tau hyperphosphorylation on secreted and cellular levels of BDNF in primary cortical neurons that were treated with 25nM OKA...
November 30, 2016: Journal of Chemical Neuroanatomy
https://www.readbyqxmd.com/read/27914808/influenza-a-virus-ns1-protein-induced-a20-contributes-to-viral-replication-by-suppressing-interferon-induced-antiviral-response
#12
Wenjing Feng, Xiaoning Sun, Ning Shi, Maolin Zhang, Zhenhong Guan, Ming Duan
The innate immune response provides the first line of defense against viruses and other pathogens by responding to specific microbial molecules. A20 is a cytoplasmic ubiquitin-editing protein that negatively regulates the retinoic acid-inducible gene I (RIG-I)-mediated activation of interferon regulatory factors (IRF) 3. Here, we found that influenza A virus (IAV) non-structural protein (NS) 1 dramatically induced the protein level of A20 in A549 cells whose expression levels were positively associated with the viral virulence...
December 1, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27914608/evaluation-of-size-exclusion-chromatography-columns-packed-with-sub-3%C3%AE-m-particles-for-the-analysis-of-biopharmaceutical-proteins
#13
Alexandre Goyon, Alain Beck, Olivier Colas, Koen Sandra, Davy Guillarme, Szabolcs Fekete
The aim of this study was to evaluate the practical possibilities and limitations of several recently introduced size exclusion chromatographic (SEC) columns of 150×4.6mm, sub-3μm (Agilent AdvanceBioSEC 2.7μm, Tosoh TSKgel UP-SW3000 2.0μm, Phenomenex Yarra SEC X-150 1.8μm and Waters Acquity BEH200 1.7μm) for the separation of biopharmaceutical proteins. For this purpose, some model proteins were tested, as well as several commercial therapeutic monoclonal antibodies (mAbs) and antibody-drug-conjugates (ADCs)...
November 27, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/27911710/eml-proteins-in-microtubule-regulation-and-human-disease
#14
REVIEW
Andrew M Fry, Laura O'Regan, Jessica Montgomery, Rozita Adib, Richard Bayliss
The EMLs are a conserved family of microtubule-associated proteins (MAPs). The founding member was discovered in sea urchins as a 77-kDa polypeptide that co-purified with microtubules. This protein, termed EMAP for echinoderm MAP, was the major non-tubulin component present in purified microtubule preparations made from unfertilized sea urchin eggs [J. Cell Sci. (1993) 104: , 445-450; J. Cell Sci. (1987) 87: (Pt 1), 71-84]. Orthologues of EMAP were subsequently identified in other echinoderms, such as starfish and sand dollar, and then in more distant eukaryotes, including flies, worms and vertebrates, where the name of ELP or EML (both for EMAP-like protein) has been adopted [BMC Dev...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27911399/tools-to-study-the-role-of-architectural-protein-hmgb1-in-the-processing-of-helix-distorting-site-specific-dna-interstrand-crosslinks
#15
Anirban Mukherjee, Karen M Vasquez
High mobility group box 1 (HMGB1) protein is a non-histone architectural protein that is involved in regulating many important functions in the genome, such as transcription, DNA replication, and DNA repair. HMGB1 binds to structurally distorted DNA with higher affinity than to canonical B-DNA. For example, we found that HMGB1 binds to DNA interstrand crosslinks (ICLs), which covalently link the two strands of the DNA, cause distortion of the helix, and if left unrepaired can cause cell death. Due to their cytotoxic potential, several ICL-inducing agents are currently used as chemotherapeutic agents in the clinic...
November 10, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27910948/improved-in-cell-structure-determination-of-proteins-at-near-physiological-concentration
#16
Teppei Ikeya, Tomomi Hanashima, Saori Hosoya, Manato Shimazaki, Shiro Ikeda, Masaki Mishima, Peter Güntert, Yutaka Ito
Investigating three-dimensional (3D) structures of proteins in living cells by in-cell nuclear magnetic resonance (NMR) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. In-cell NMR provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cells. However, so far only a single de novo 3D protein structure could be determined based on data derived only from in-cell NMR...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27903271/differential-humoral-and-cellular-immunity-induced-by-vaccination-using-plasmid-dna-and-protein-recombinant-expressing-the-ns3-protein-of-dengue-virus-type-3
#17
M L Hurtado-Melgoza, A Ramos-Ligonio, L M Álvarez-Rodríguez, T Meza-Menchaca, A López-Monteon
BACKGROUND: The dengue non-structural 3 (NS3) is a multifunctional protein, containing a serine-protease domain, located at the N-terminal portion, and helicase, NTPase and RTPase domains present in the C-terminal region. This protein is considered the main target for CD4+ and CD8+ T cell responses during dengue infection, which may be involved in protection. However, few studies have been undertaken evaluating the use of this protein as a protective antigen against dengue, as well as other flavivirus...
December 1, 2016: Journal of Biomedical Science
https://www.readbyqxmd.com/read/27902320/in-silico-analysis-of-surface-structure-variation-of-pcv2-capsid-resulted-from-loops-mutation-of-its-capsid-protein-cap
#18
Naidong Wang, Yang Zhan, Aibing Wang, Lijie Zhang, Reza Khayat, Yi Yang
Outbreaks of porcine circovirus (PCV) type 2 (PCV2) associated diseases (PCVADs) have caused substantial economic losses worldwide in the last 20 y. The PCV capsid protein (Cap) is the sole structural protein and main antigenic determinant of this virus. In this study, not only were phylogenetic trees constructed, but variation of surface structure of the PCV capsid were analyzed in the course of evolution. Unique surface patterns of the icosahedral 5-fold axes of the PCV2 capsid were identified and characterized, all of which were absent in PCV type 1 (PCV1)...
October 18, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27901020/structural-decoding-of-netrin-4-reveals-a-regulatory-function-towards-mature-basement-membranes
#19
Raphael Reuten, Trushar R Patel, Matthew McDougall, Nicolas Rama, Denise Nikodemus, Benjamin Gibert, Jean-Guy Delcros, Carina Prein, Markus Meier, Stéphanie Metzger, Zhigang Zhou, Jennifer Kaltenberg, Karen K McKee, Tobias Bald, Thomas Tüting, Paola Zigrino, Valentin Djonov, Wilhelm Bloch, Hauke Clausen-Schaumann, Ernst Poschl, Peter D Yurchenco, Martin Ehrbar, Patrick Mehlen, Jörg Stetefeld, Manuel Koch
Netrins, a family of laminin-related molecules, have been proposed to act as guidance cues either during nervous system development or the establishment of the vascular system. This was clearly demonstrated for netrin-1 via its interaction with the receptors DCC and UNC5s. However, mainly based on shared homologies with netrin-1, netrin-4 was also proposed to play a role in neuronal outgrowth and developmental/pathological angiogenesis via interactions with netrin-1 receptors. Here, we present the high-resolution structure of netrin-4, which shows unique features in comparison with netrin-1, and show that it does not bind directly to any of the known netrin-1 receptors...
November 30, 2016: Nature Communications
https://www.readbyqxmd.com/read/27900730/understanding-the-interactions-of-high-mobility-group-of-protein-domain-b1-with-dna-adducts-generated-by-platinum-anticancer-molecules-using-in-silico-approaches
#20
Gauri Misra, Shipra Gupta, Neetu Jabalia
Platinum coordination compounds having cis geometry are frequently prescribed for various types of cancers. Protein dysregulation is one of the major factors contributing towards cancer metastasis. Head and neck squamous cell carcinoma (HNSCC) is one of the cancers where platinum-based compounds are used either alone or in combination with radiation as therapy. The underlying interactions of these compounds with both DNA and proteins are crucial for the drug response. The compounds forms DNA adducts which are recognized by conserved, non-chromosomal high-mobility group box 1 (HMGB1) proteins...
November 30, 2016: Interdisciplinary Sciences, Computational Life Sciences
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