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Structural Proteomics

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https://read.qxmd.com/read/30901150/combining-rapid-data-independent-acquisition-and-crispr-gene-deletion-for-studying-potential-protein-functions-a-case-of-hmgn1
#1
Martin Mehnert, Wenxue Li, Chongde Wu, Barbora Salovska, Yansheng Liu
CRISPR-Cas gene editing holds substantial promise in many biomedical disciplines and basic research. Due to the important functional implications of non-histone chromosomal protein HMG-14 (HMGN1) in regulating chromatin structure and tumor immunity, we performed gene knockout of HMGN1 by CRISPR in cancer cells and studied the following proteomic regulation events. In particular, we utilized DIA mass spectrometry (DIA-MS) and reproducibly measured more than 6200 proteins (protein- FDR 1%) and more than 82,000 peptide precursors in the single MS shots of two hours...
March 22, 2019: Proteomics
https://read.qxmd.com/read/30897459/divergent-proteomics-response-of-apostichopus-japonicus-suffering-from-skin-ulceration-syndrome-and-pathogen-infection
#2
Zhimeng Lv, Ming Guo, Chenghua Li, Yina Shao, Xuelin Zhao, Weiwei Zhang
Skin ulceration syndrome (SUS) of sea cucumber is a common and serious disease that affects the stable development of Apostichopus japonicus in the culture industry. The part of sea cucumber that suffers from major injury and is directly observed is the body wall, in which protein variations should be the most direct evidence of the disease. To understand the response mechanisms of A. japonicus in SUS progression, we investigated protein changes in the body wall of diseased A. japonicus induced by Vibrio splendidus and individuals with natural diseases by isobaric tags for relative and absolute quantification (iTRAQ)...
March 13, 2019: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://read.qxmd.com/read/30896804/identification-of-red-blood-cell-membrane-defects-in-a-patient-with-hereditary-spherocytosis-using-next%C3%A2-generation-sequencing-technology-and-matrix%C3%A2-assisted-laser-desorption-ionization-time%C3%A2-of%C3%A2-flight-mass-spectrometry
#3
Leyla Türker Şener, Melih Aktan, Gürcan Albeniz, Aziz Şener, Duran Üstek, Işıl Albeniz
Hereditary spherocytosis (HS) is characterized by the morphological transformation of erythrocytes into a spherical shape due to a hereditary defect in cell membrane proteins (ghosts) associated with disruption of erythrocyte skeletal structures. Contrary to the literature, pores were detected in the erythrocytes of a patient with HS. The aim of the present study was to determine the affected proteins and genes that were responsible for the pores. Ghost isolation was performed to determine the proteins responsible for the pores observed on the erythrocytes of the patient...
March 14, 2019: Molecular Medicine Reports
https://read.qxmd.com/read/30896308/disorder-in-milk-proteins-adipophilin-and-tip47-important-constituents-of-the-milk-fat-globule-membrane
#4
Elrashdy M Redwan, Saleh A Alkarim, Amr A El-Hanafy, Yasser M Saad, Hussein A Almehdar, Vladimir N Uversky
Milk fat globules (MFGs), which are secreted by the epithelial cells of the lactating mammary glands, account for the most of the nutritional value of milk. They are enveloped by the milk fat globule membrane (MFGM), a complex structure consisting of three phospholipid membrane monolayers and containing various lipids. Depending on the origin of milk, specific proteins accounts for 5-70% of the MFGM mass. Proteome of MFGMs includes hundreds of proteins, with nine major components being adipophilin, butyrophilin, cluster of differentiation 36, fatty acid binding protein, lactadherin, mucin 1, mucin 15, tail-interacting protein 47 (TIP47), and xanthine oxidoreductase...
March 21, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30893800/the-dual-prey-inactivation-strategy-of-spiders-in-depth-venomic-analysis-of-cupiennius-salei
#5
Lucia Kuhn-Nentwig, Nicolas Langenegger, Manfred Heller, Dominique Koua, Wolfgang Nentwig
Most knowledge of spider venom concerns neurotoxins acting on ion channels, whereas proteins and their significance for the envenomation process are neglected. The here presented comprehensive analysis of the venom gland transcriptome and proteome of Cupiennius salei focusses on proteins and cysteine-containing peptides and offers new insight into the structure and function of spider venom, here described as the dual prey-inactivation strategy. After venom injection, many enzymes and proteins, dominated by α-amylase, angiotensin-converting enzyme, and cysteine-rich secretory proteins, interact with main metabolic pathways, leading to a major disturbance of the cellular homeostasis...
March 19, 2019: Toxins
https://read.qxmd.com/read/30891955/an-integrative-approach-using-systems-biology-mutational-analysis-with-molecular-dynamics-simulation-to-challenge-the-functionality-of-a-target-protein
#6
Nikita Bora, Anupam Nath Jha
Visceral leishmaniasis affects millions of people worldwide in areas where Leishmania donovani is endemic. The protozoan species serves a greater threat as it has gradually evolved drug resistance whereby requiring newer approaches to treat the infection. State-of-art techniques are mostly directed toward finding better targets extracted from the available proteome data. In light of recent computational advancements, we ascertain and validate one such target, adenylosuccinate lyase (ADSL) by implementation of in-silico methods which led to the identification of critical amino acid residues that affects its functional attributes...
March 20, 2019: Chemical Biology & Drug Design
https://read.qxmd.com/read/30891015/mixotrophic-growth-under-micro-oxic-conditions-in-the-purple-sulfur-bacterium-thiodictyon-syntrophicum
#7
Samuel M Luedin, Nicola Storelli, Francesco Danza, Samuele Roman, Matthias Wittwer, Joël F Pothier, Mauro Tonolla
The microbial ecosystem of the meromictic Lake Cadagno (Ticino, Swiss Alps) has been studied intensively in order to understand structure and functioning of the anoxygenic phototrophic sulfur bacteria community living in the chemocline. It has been found that the purple sulfur bacterium " Thiodictyon syntrophicum " strain Cad16T , belonging to the Chromatiaceae, fixes around 26% of all bulk inorganic carbon in the chemocline, both during day and night. With this study, we elucidated for the first time the mode of carbon fixation of str...
2019: Frontiers in Microbiology
https://read.qxmd.com/read/30889472/the-multiple-origins-of-proteins-present-in-tupanvirus-particles
#8
REVIEW
Paulo Victor de Miranda Boratto, Ana Cláudia Dos Santos Pereira Andrade, Rodrigo Araújo Lima Rodrigues, Bernard La Scola, Jônatas Santos Abrahão
In the last few decades, the isolation of amoebae-infecting giant viruses has challenged established principles related to the definition of virus, their evolution, and their particle structures represented by a variety of shapes and sizes. Tupanviruses are one of the most recently described amoebae-infecting viruses and exhibit a peculiar morphology with a cylindrical tail attached to the capsid. Proteomic analysis of purified viral particles revealed that virions are composed of over one hundred proteins with different functions...
March 16, 2019: Current Opinion in Virology
https://read.qxmd.com/read/30889197/development-of-high-performance-two-dimensional-gel-electrophoresis-for-human-hair-shaft-proteome
#9
Sing Ying Wong, Onn Haji Hashim, Nobuhiro Hayashi
The primary components of human hair shaft-keratin and keratin-associated proteins (KAPs), together with their cross-linked networks-are the underlying reason for its rigid structure. It is therefore requisite to overcome the obstacle of hair insolubility and establish a reliable protocol for the proteome analysis of this accessible specimen. The present study employed an alkaline-based method for the efficient isolation of hair proteins and subsequently examined them using gel-based proteomics. The introduction of two proteomic protocols, namely the conventional and modified protocol, have resulted in the detection of more than 400 protein spots on the two-dimensional gel electrophoresis (2DE)...
2019: PloS One
https://read.qxmd.com/read/30887086/testing-empirical-support-for-evolutionary-models-that-root-the-tree-of-life
#10
Derek Caetano-Anollés, Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anollés
Trees of life (ToLs) can only be rooted with direct methods that seek optimization of character state information in ingroup taxa. This involves optimizing phylogenetic tree, model and data in an exercise of reciprocal illumination. Rooted ToLs have been built from a census of protein structural domains in proteomes using two kinds of models. Fully-reversible models use standard-ordered (additive) characters and Wagner parsimony to generate unrooted trees of proteomes that are then rooted with Weston's generality criterion...
March 18, 2019: Journal of Molecular Evolution
https://read.qxmd.com/read/30886688/the-skin-regeneration-potential-of-a-pro-angiogenic-secretome-from-human-skin-derived-multipotent-stromal-cells
#11
Anny Waloski Robert, Felipe Azevedo Gomes, Michele Patricia Rode, Maiara Marques da Silva, Maria Beatriz da Rocha Veleirinho, Marcelo Maraschin, Leila Hayashi, Giordano Wosgrau Calloni, Marco Augusto Stimamiglio
Multipotent stromal cells stimulate skin regeneration after acute or chronic injuries. However, many stem cell therapy protocols are limited by the elevated number of cells required and poor cell survival after transplantation. Considering that the beneficial effects of multipotent stromal cells on wound healing are typically mediated by paracrine mechanisms, we examined whether the conditioned medium from skin-derived multipotent stromal cells would be beneficial for restoring the skin structure of mice after wounding...
January 2019: Journal of Tissue Engineering
https://read.qxmd.com/read/30886625/transcriptomic-and-proteomic-analysis-of-shaan2a-cytoplasmic-male-sterility-and-its-maintainer-line-in-brassica-napus
#12
Luyun Ning, Hao Wang, Dianrong Li, Zhiwei Lin, Yonghong Li, Weiguo Zhao, Hongbo Chao, Liyun Miao, Maoteng Li
Cytoplasmic male sterility (CMS) lines are widely used for hybrid production in Brassica napus . The Shaan2A CMS system is one of the most important in China and has been used for decades; however, the male sterility mechanism underlying Shaan2A CMS remains unknown. Here, we performed transcriptomic and proteomic analysis, combined with additional morphological observation, in the Shaan2A CMS. Sporogenous cells, endothecium, middle layer, and tapetum could not be clearly distinguished in Shaan2A anthers. Furthermore, Shaan2A anther chloroplasts contained fewer starch grains than those in Shaan2B (a near-isogenic line of Shaan2A), and the lamella structure of chloroplasts in Shaan2A anther wall cells was obviously aberrant...
2019: Frontiers in Plant Science
https://read.qxmd.com/read/30886158/prevention-of-respiratory-syncytial-virus-infection-with-probiotic-lactic-acid-bacterium-lactobacillus-gasseri-sbt2055
#13
Kei Eguchi, Naoki Fujitani, Hisako Nakagawa, Tadaaki Miyazaki
Lactobacillus gasseri SBT2055 (LG2055) is a probiotic lactic acid bacterium with multifunctional effects, including the prevention of influenza A virus infection in mice, reduction of adipocyte size in mice, and increased lifespan in C. elegans. We investigated whether LG2055 exhibits antiviral activity against respiratory syncytial virus (RSV), a global pathogen for which a preventive strategy is required. Following oral administration of LG2055 in mice, the RSV titre in the lung was significantly decreased, while body weight was not decreased after virus infection...
March 18, 2019: Scientific Reports
https://read.qxmd.com/read/30886054/the-synaptomic-theory-of-behavior-and-brain-disease
#14
Seth G N Grant
The purpose of this article is to outline a new molecular and synaptic theory of behavior called the "synaptomic theory," named because it is centered on the synaptome-the complement of synapses in the brain. Synaptomic theory posits that synapses are structures of high molecular complexity and vast diversity that are observable in maps of the brain and that these synaptome maps are fundamental to behavior. Synaptome maps are a means of writing or storing information that can be retrieved by the patterns of activity that stimulate synapses...
March 18, 2019: Cold Spring Harbor Symposia on Quantitative Biology
https://read.qxmd.com/read/30879067/heterogeneous-clinical-phenotypes-and-cerebral-malformations-reflected-by-rotatin-cellular-dynamics
#15
Laura V Vandervore, Rachel Schot, Esmee Kasteleijn, Renske Oegema, Katrien Stouffs, Alexander Gheldof, Martyna M Grochowska, Marianne L T van der Sterre, Leontine M A van Unen, Martina Wilke, Peter Elfferich, Peter J van der Spek, Daphne Heijsman, Anna Grandone, Jeroen A A Demmers, Dick H W Dekkers, Johan A Slotman, Gert-Jan Kremers, Gerben J Schaaf, Roy G Masius, Anton J van Essen, Patrick Rump, Arie van Haeringen, Els Peeters, Umut Altunoglu, Tugba Kalayci, Raymond A Poot, William B Dobyns, Nadia Bahi-Buisson, Frans W Verheijen, Anna C Jansen, Grazia M S Mancini
Recessive mutations in RTTN, encoding the protein rotatin, were originally identified as cause of polymicrogyria, a cortical malformation. With time, a wide variety of other brain malformations has been ascribed to RTTN mutations, including primary microcephaly. Rotatin is a centrosomal protein possibly involved in centriolar elongation and ciliogenesis. However, the function of rotatin in brain development is largely unknown and the molecular disease mechanism underlying cortical malformations has not yet been elucidated...
March 16, 2019: Brain: a Journal of Neurology
https://read.qxmd.com/read/30877506/identification-of-naphthalene-carboxylase-subunits-of-the-sulfate-reducing-culture-n47
#16
J S Koelschbach, H Mouttaki, J Merl-Pham, M E Arnold, R U Meckenstock
Expanding industrialization and the associated usage and production of mineral oil products has caused a worldwide spread of polycyclic aromatic hydrocarbons. These pollutants accumulate and persist under anoxic conditions but little is known about the biochemical reactions catalyzing their anaerobic degradation. Recently, carboxylation of naphthalene was demonstrated for the sulfate-reducing culture N47. Proteogenomic studies on N47 allowed the identification of a gene cluster with products suggested to be involved in the initial reaction of naphthalene degradation...
March 15, 2019: Biodegradation
https://read.qxmd.com/read/30877253/unifying-structural-signature-of-eukaryotic-%C3%AE-helical-host-defense-peptides
#17
Nannette Y Yount, David C Weaver, Ernest Y Lee, Michelle W Lee, Huiyuan Wang, Liana C Chan, Gerard C L Wong, Michael R Yeaman
Diversity of α-helical host defense peptides (αHDPs) contributes to immunity against a broad spectrum of pathogens via multiple functions. Thus, resolving common structure-function relationships among αHDPs is inherently difficult, even for artificial-intelligence-based methods that seek multifactorial trends rather than foundational principles. Here, bioinformatic and pattern recognition methods were applied to identify a unifying signature of eukaryotic αHDPs derived from amino acid sequence, biochemical, and three-dimensional properties of known αHDPs...
March 15, 2019: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/30876926/thrombospondin-2-regulates-extracellular-matrix-production-lox-levels-and-cross-linking-via-downregulation-of-mir-29
#18
N E Calabro, A Barrett, A Chamorro-Jorganes, S Tam, N J Kristofik, Hao Xing, Ayomipose M Loye, W C Sessa, K Hansen, T R Kyriakides
Collagen fibrillogenesis and crosslinking have long been implicated in extracellular matrix (ECM)-dependent processes such as fibrosis and scarring. However, the extent to which matricellular proteins influence ECM protein production and fibrillar collagen crosslinking has yet to be determined. Here we show that thrombospondin 2 (TSP2), an anti-angiogenic matricellular protein, is an important modulator of ECM homeostasis. Specifically, through a fractionated quantitative proteomics approach, we show that loss of TSP2 leads to a unique ECM phenotype characterized by a significant decrease in fibrillar collagen, matricellular, and structural ECM protein production in the skin of TSP2 KO mice...
March 12, 2019: Matrix Biology: Journal of the International Society for Matrix Biology
https://read.qxmd.com/read/30872567/systems-biology-approaches-to-investigating-the-roles-of-extracellular-vesicles-in-human-diseases
#19
REVIEW
András Gézsi, Árpád Kovács, Tamás Visnovitz, Edit I Buzás
Extracellular vesicles (EVs) are membrane-enclosed structures secreted by cells. In the past decade, EVs have attracted substantial attention as carriers of complex intercellular information. They have been implicated in a wide variety of biological processes in health and disease. They are also considered to hold promise for future diagnostics and therapy. EVs are characterized by a previously underappreciated heterogeneity. The heterogeneity and molecular complexity of EVs necessitates high-throughput analytical platforms for detailed analysis...
March 15, 2019: Experimental & Molecular Medicine
https://read.qxmd.com/read/30870787/protein-disulfide-isomerase-plasma-levels-in-healthy-humans-reveal-proteomic-signatures-involved-in-contrasting-endothelial-phenotypes
#20
Percíllia Victória Santos de Oliveira, Sheila Garcia-Rosa, Ana Teresa Azevedo Sachetto, Ana Iochabel Soares Moretti, Victor Debbas, Tiphany Coralie De Bessa, Nathalia Tenguan Silva, Alexandre da Costa Pereira, Daniel Martins-de-Souza, Marcelo Larami Santoro, Francisco Rafael Martins Laurindo
Redox-related plasma proteins are candidate reporters of protein signatures associated with endothelial structure/function. Thiol-proteins from protein disulfide isomerase (PDI) family are unexplored in this context. Here, we investigate the occurrence and physiological significance of a circulating pool of PDI in healthy humans. We validated an assay for detecting PDI in plasma of healthy individuals. Our results indicate high inter-individual (median = 330 pg/mL) but low intra-individual variability over time and repeated measurements...
February 19, 2019: Redox Biology
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