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Protein footprinting

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https://www.readbyqxmd.com/read/29471208/understanding-biopharmaceutical-production-at-single-nucleotide-resolution-using-ribosome-footprint-profiling
#1
REVIEW
Ioanna Tzani, Craig Monger, Paul Kelly, Niall Barron, Ronan M Kelly, Colin Clarke
Biopharmaceuticals such as monoclonal antibodies have revolutionised the treatment of a variety of diseases. The production of recombinant therapeutic proteins, however, remains expensive due to the manufacturing complexity of mammalian expression systems and the regulatory burden associated with administrating these medicines to patients in a safe and efficacious manner. In recent years, academic and industrial groups have begun to develop a greater understanding of the biology of host cell lines, such as Chinese hamster ovary (CHO) cells and utilise that information for process development and cell line engineering...
February 19, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29450991/mass-spectrometry-based-fast-photochemical-oxidation-of-proteins-fpop-for-higher-order-structure-characterization
#2
Ke Sherry Li, Liuqing Shi, Michael L Gross
Assessment of protein structure and interaction is crucial for understanding protein structure/function relationships. Compared to high-resolution structural tools, including X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-EM, and traditional low-resolution methods, such as circular dichroism, UV-vis, and florescence spectroscopy, mass spectrometry (MS)-based protein footprinting affords medium-to-high resolution (i.e., regional and residue-specific insights) by taking advantage of proteomics methods focused on the primary structure...
February 16, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29446497/specific-interaction-sites-determine-differential-adsorption-of-protein-structural-isomers-to-nanoparticle-surfaces
#3
Andrea Bortot, Serena Zanzoni, Mariapina D'Onofrio, Michael Assfalg
In biological milieus, nanoparticles (NPs) elicit bioactivity upon interaction with proteins. As a result of post-translational modification, proteins occur in a variety of alternative covalent forms, including structural isomers, which present unique molecular surfaces. We aimed at a detailed description of the recognition of protein isomeric species by NP surfaces. The transient adsorption of isomeric Ub dimers to NPs was investigated by solution NMR spectroscopy. Lys63-linked Ub2 and Lys48-linked Ub2 adsorbed to large anionic NPs with different affinity, while the binding strength was similar in the case of smaller particles...
February 15, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29444758/electron-transfer-process-in-microbial-electrochemical-technologies-the-role-of-cell-surface-exposed-conductive-proteins
#4
REVIEW
Nazua L Costa, Thomas A Clarke, Laura-Alina Philipp, Johannes Gescher, Ricardo O Louro, Catarina M Paquete
Electroactive microorganisms have attracted significant interest for the development of novel biotechnological systems of low ecological footprint. These can be used for the sustainable production of energy, bioremediation of metal-contaminated environments and production of added-value products. Currently, almost 100 microorganisms from the Bacterial and Archaeal domains are considered electroactive, given their ability to efficiently interact with electrodes in microbial electrochemical technologies. Cell-surface exposed conductive proteins are key players in the electron transfer between cells and electrodes...
January 31, 2018: Bioresource Technology
https://www.readbyqxmd.com/read/29433523/a-clinical-approach-to-new-onset-psychosis-associated-with-immune-dysregulation-the-concept-of-autoimmune-psychosis
#5
Souhel Najjar, Johann Steiner, Amanda Najjar, Karl Bechter
Growing data point to the overlap between psychosis and pathological processes associated with immunological dysregulation as well as inflammation. Notably, the recent discovery of antibodies against synaptic and neuronal cell membrane proteins such as anti-N-methyl-D-aspartate receptor provides more direct evidence of the etiological connection between autoimmunity and subsequent hazard of psychosis. Here, we advocate the use of term "autoimmune psychosis," as this term suggests that autoimmune disorders can masquerade as drug-resistant primary psychosis, and this subtype of psychosis has anatomical and immunological footprints in the brain, despite the frequent absence of structural abnormalities on conventional brain MRI...
February 13, 2018: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/29433444/a-novel-short-l-arginine-responsive-protein-coding-gene-laob-antiparallel-overlapping-to-a-cadc-like-transcriptional-regulator-in-escherichia-coli-o157-h7-sakai-originated-by-overprinting
#6
Sarah M Hücker, Sonja Vanderhaeghen, Isabel Abellan-Schneyder, Romy Wecko, Svenja Simon, Siegfried Scherer, Klaus Neuhaus
BACKGROUND: Due to the DNA triplet code, it is possible that the sequences of two or more protein-coding genes overlap to a large degree. However, such non-trivial overlaps are usually excluded by genome annotation pipelines and, thus, only a few overlapping gene pairs have been described in bacteria. In contrast, transcriptome and translatome sequencing reveals many signals originated from the antisense strand of annotated genes, of which we analyzed an example gene pair in more detail...
February 12, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29432487/structural-basis-of-mammalian-glycan-targeting-by-vibrio-cholerae-cytolysin-and-biofilm-proteins
#7
Swastik De, Katherine Kaus, Shada Sinclair, Brandon C Case, Rich Olson
Vibrio cholerae is an aquatic gram-negative microbe responsible for cholera, a pandemic disease causing life-threatening diarrheal outbreaks in populations with limited access to health care. Like most pathogenic bacteria, V. cholerae secretes virulence factors to assist colonization of human hosts, several of which bind carbohydrate receptors found on cell-surfaces. Understanding how pathogenic virulence proteins specifically target host cells is important for the development of treatment strategies to fight bacterial infections...
February 12, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29426832/genome-wide-tracking-of-dcas9-methyltransferase-footprints
#8
Christina Galonska, Jocelyn Charlton, Alexandra L Mattei, Julie Donaghey, Kendell Clement, Hongcang Gu, Arman W Mohammad, Elena K Stamenova, Davide Cacchiarelli, Sven Klages, Bernd Timmermann, Tobias Cantz, Hans R Schöler, Andreas Gnirke, Michael J Ziller, Alexander Meissner
In normal mammalian development cytosine methylation is essential and is directed to specific regions of the genome. Despite notable advances through mapping its genome-wide distribution, studying the direct contribution of DNA methylation to gene and genome regulation has been limited by the lack of tools for its precise manipulation. Thus, combining the targeting capability of the CRISPR-Cas9 system with an epigenetic modifier has attracted interest in the scientific community. In contrast to profiling the genome-wide cleavage of a nuclease competent Cas9, tracing the global activity of a dead Cas9 (dCas9) methyltransferase fusion protein is challenging within a highly methylated genome...
February 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29418028/stabilization-and-translation-of-synthetic-operon-derived-mrnas-in-chloroplasts-by-sequences-representing-ppr-protein-binding-sites
#9
Julia Legen, Stephanie Ruf, Xenia Kroop, Gongwei Wang, Alice Barkan, Ralph Bock, Christian Schmitz-Linneweber
The chloroplast is a prime target for genetic engineering in plants, offering various advantages over nuclear transformation. For example, chloroplasts allow the expression of polycistronic transcripts and thus to engineer complex metabolic pathways. Each cistron within such a longer transcript needs its own expression elements. Within the 5'-UTR, such expression elements are needed for stabilizing mRNAs and for translation of the downstream reading frame. One of the few effective expression elements used so far in transplastomic approaches is the intercistronic expression element (IEE)...
February 8, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29409278/involvement-of-foot-in-patients-with-spondyloarthritis-prevalence-and-clinical-features
#10
Hana Sahli, Asma Bachali, Raoudha Tekaya, Ines Mahmoud, Yassine Sedki, Olfa Saidane, Leila Abdelmoula
BACKGROUND: The purpose of this study was to evaluate the foot involvement in a group of patients with spondyloarthritis in regard to symptoms, type and frequency of deformities, location and radiological changes. METHODS: We conducted a cross sectional study including 60 patients with spondyloarthritis over a period of six months. Anamnesis, clinical examination, podoscopic examination, biological tests and X-rays of feet were done for each patient. RESULTS: Foot involvement was found in 31 patients (52%)...
November 10, 2017: Foot and Ankle Surgery: Official Journal of the European Society of Foot and Ankle Surgeons
https://www.readbyqxmd.com/read/29405007/production-and-chemoselective-modification-of-adeno-associated-virus-site-specifically-incorporating-an-unnatural-amino-acid-residue-into-its-capsid
#11
Rachel E Kelemen, Sarah B Erickson, Abhishek Chatterjee
The ability to modify the capsid proteins of human viruses is desirable both for installing probes to study their structure and function, and to attach retargeting agents to engineer viral infectivity. However, the installation of such capsid modifications currently faces two major challenges: (1) The complex and delicate capsid proteins often do not tolerate large modifications, and (2) capsid proteins are composed of the 20 canonical amino acids, precluding site-specific chemical modification of the virus...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29400454/biochemistry-of-peroxynitrite-and-protein-tyrosine-nitration
#12
Gerardo Ferrer-Sueta, Nicolás Campolo, Madia Trujillo, Silvina Bartesaghi, Sebastián Carballal, Natalia Romero, Beatriz Alvarez, Rafael Radi
Peroxynitrite is a short-lived and reactive biological oxidant formed from the diffusion-controlled reaction of the free radicals superoxide (O2•-) and nitric oxide (•NO). In this review, we first analyze the biochemical evidence for the formation of peroxynitrite in vivo and the reactions that lead to it. Then, we describe the principal reactions that peroxynitrite undergoes with biological targets and provide kinetic and mechanistic details. In these reactions, peroxynitrite has roles as (1) peroxide, (2) Lewis base, and (3) free radical generator...
February 5, 2018: Chemical Reviews
https://www.readbyqxmd.com/read/29394412/footprints-of-divergent-evolution-in-two-na-h-type-antiporter-gene-families-nhx-and-sos1-in-the-genus-populus
#13
Kuibin Meng, Yuxia Wu
Populus, a deciduous tree species of major economic and ecological value, grows across the range in which trees are distributed in the Northern Hemisphere. Patterns of DNA variation are often used to identify the evolutionary forces shaping the genotypes of distinctive species lineages. Sodium/hydrogen (Na+/H+) antiporter genes have been shown to play a central role in plant salt tolerance. Here, we analyzed DNA nucleotide polymorphisms in the Na+/H+ antiporter (NHX and SOS1) gene families across 30 different Populus species using several methods of phylogenetic analysis and functional verification...
January 31, 2018: Tree Physiology
https://www.readbyqxmd.com/read/29378358/chemical-footprinting-reveals-conformational-changes-following-activation-of-factor-xi
#14
Ingrid Stroo, J Arnoud Marquart, Kamran Bakhtiari, Tom Plug, Alexander B Meijer, Joost C M Meijers
Coagulation factor XI is activated by thrombin or factor XIIa resulting in a conformational change that converts the catalytic domain into its active form and exposing exosites for factor IX on the apple domains. Although crystal structures of the zymogen factor XI and the catalytic domain of the protease are available, the structure of the apple domains and hence the interactions with the catalytic domain in factor XIa are unknown. We now used chemical footprinting to identify lysine residue containing regions that undergo a conformational change following activation of factor XI...
February 2018: Thrombosis and Haemostasis
https://www.readbyqxmd.com/read/29370772/genome-wide-characterization-of-genetic-variants-and-putative-regions-under-selection-in-meat-and-egg-type-chicken-lines
#15
Clarissa Boschiero, Gabriel Costa Monteiro Moreira, Almas Ara Gheyas, Thaís Fernanda Godoy, Gustavo Gasparin, Pilar Drummond Sampaio Corrêa Mariani, Marcela Paduan, Aline Silva Mello Cesar, Mônica Corrêa Ledur, Luiz Lehmann Coutinho
BACKGROUND: Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection...
January 25, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29355258/analyzing-the-structure-of-macromolecules-in-their-native-cellular-environment-using-hydroxyl-radical-footprinting
#16
REVIEW
Emily E Chea, Lisa M Jones
Hydroxyl radical footprinting (HRF) has been successfully used to study the structure of both nucleic acids and proteins. The method utilizes hydroxyl radicals to oxidize solvent accessible sites in macromolecules. In recent years, the method has shown some utility for live cell analysis. In this review, we will survey the current state of the field for footprinting macromolecules in living cells. The field is relatively new, particularly for protein studies, with only a few publications on the development and application of HRF on live cells...
January 22, 2018: Analyst
https://www.readbyqxmd.com/read/29352085/the-expression-of-bacteriocin-production-and-self-resistance-in-lactobacillus-brevis-174a-is-mediated-by-two-regulatory-proteins
#17
Masafumi Noda, Rumi Miyauchi, Narandalai Danshiitsoodol, Yasuyuki Matoba, Takanori Kumagai, Masanori Sugiyama
We have previously shown that a lactic acid bacterium Lactobacillus (Lb.) brevis 174A isolated from a Citrus iyo fruit produces bacteriocin designated brevicin 174A, which is comprised of two antibacterial polypeptides (designated brevicin 174A-β and 174A-γ). We have also found a gene cluster, composed of eight open reading frames (ORFs), that contains genes for the biosynthesis of brevicin 174A, self-resistance to its own bacteriocin, and two transcriptional regulatory proteins.Some lactic acid bacterial strains have a system to start the production of bacteriocin at an adequate stage of the growth...
January 19, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29342409/development-and-characterization-of-an-allergoid-of-cat-dander-for-immunotherapy
#18
J P Sola, Y Pedreño, A Cerezo, M Peñalver-Mellado
BACKGROUND: Allergy to cats is a frequent cause of sensitization to indoor allergens and currently there are few alternatives to specific immunotherapy with cat native extracts. The objective is to develop and characterize a new allergoid to increase the tools available for use in clinical practice. METHODS: The allergoid cat dander extract (ACD) was developed from a native cat dander extract (NCD) by modification with glutaraldehyde, and the optimal process control was determined by SDS-PAGE, DOT BLOT and determination of free amine groups...
January 13, 2018: Allergologia et Immunopathologia
https://www.readbyqxmd.com/read/29341606/hogg1-removes-solution-accessible-8-oxog-lesions-from-globally-substituted-nucleosomes-except-at-the-dyad-region
#19
Katharina Bilotti, Mary E Tarantino, Sarah Delaney
Persistent DNA damage is responsible for mutagenesis, aging, and disease. Repair of the prototypic oxidatively damaged guanine lesion 8-oxo-7,8-dihydroguanine (8-oxoG) is initiated by oxoguanine glycosylase (hOGG1 in humans). In this work, we examine hOGG1 activity on DNA packaged as it is in chromatin, in a nucleosome core particle (NCP). We use synthetic methods to generate a population of NCPs with G to 8-oxoG substitutions and evaluate the global profile of hOGG1 repair in packaged DNA. For several turns of the helix, we observe that solution-accessible 8-oxoG are sites of activity for hOGG1...
January 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29334167/cross-linking-mass-spectrometry-for-studying-protein-structures-and-protein-protein-interactions-where-are-we-now-and-where-should-we-go-from-here
#20
Andrea Sinz
Structural mass spectrometry (MS) is gaining increasing importance in deriving valuable three-dimensional structural information on proteins and protein complexes and complements existing techniques, such as NMR spectroscopy and X-ray crystallography. Structural MS unites different MS-based techniques, i.e, hydrogen-deuterium exchange, native MS, ion-mobility MS, protein footprinting, and chemical cross-linking/MS, and allows fundamental questions in structural biology to be addressed. In this article, I will focus on the cross-linking/MS strategy...
January 15, 2018: Angewandte Chemie
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