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Peptide, protein

Pradipta Ranjan Rauta, Sarbani Ashe, Debasis Nayak, Bismita Nayak
Virulence-related outer membrane proteins (Omps) are expressed in bacteria (Gram-negative) such as V. cholerae and are vital to bacterial invasion in to eukaryotic cell and survival within macrophages that could be best candidate for development of vaccine against V. cholerae. Applying in silico approaches, the 3-D model of the Omp was developed using Swiss model server and validated byProSA and Procheck web server. The continuous stretch of amino acid sequences 26mer: RTRSNSGLLTWGDKQTITLEYGDPAL and 31mer: FFAGGDNNLRGYGYKSISPQDASGALTGAKY having B-cell binding sites were selected from sequence alignment after B cell epitopes prediction by BCPred and AAP prediction modules of BCPreds...
October 12, 2016: Computational Biology and Chemistry
Tiejun Chen, Hu Hou, Yan Fan, Shikai Wang, Qianru Chen, Leilei Si, Bafang Li
Chronic exposure to ultraviolet (UV) irradiation causes skin photoaging. This study was undertaken to identify the anti-photoaging mechanisms of gelatin hydrolysate (CH) derived from pacific cod skin. Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) and ELISA assays were used to investigate the effects of CH on matrix metalloproteinases (MMPs) and the signaling pathways after UV irradiation by using a mice skin photoaging model. The average molecular weight of CH was 1200Da, and 273/1000 residues were hydrophobic, Gly-Pro and Gly-Leu sequences and Arg at C-terminus appeared frequently in CH...
October 14, 2016: Journal of Photochemistry and Photobiology. B, Biology
Donatella Nardiello, Clelia Prattichizzo, Maria Teresa Rocchetti, Loreto Gesualdo, Diego Centonze
A dedicated proteomic approach based on nano-Liquid Chromatography coupled with tandem mass spectrometry in ion trap is proposed for the analysis of proteins trapped in sorbent resin cartridges used to remove inflammatory mediators from blood by coupled plasma filtration adsorption (CPFA). The final purpose of the proposed proteomic approach was to obtain a reference map of plasma proteins trapped in CPFA sorbents used for the extracorporeal blood purification of healthy pigs, with the potential impact to design new bio-filters able to control the inflammatory imbalance under pathological conditions, such as severe sepsis...
October 12, 2016: Journal of Pharmaceutical and Biomedical Analysis
Chongsheng He, Simone Sidoli, Robert Warneford-Thomson, Deirdre C Tatomer, Jeremy E Wilusz, Benjamin A Garcia, Roberto Bonasio
Interactions between noncoding RNAs and chromatin proteins play important roles in gene regulation, but the molecular details of most of these interactions are unknown. Using protein-RNA photocrosslinking and mass spectrometry on embryonic stem cell nuclei, we identified and mapped, at peptide resolution, the RNA-binding regions in ∼800 known and previously unknown RNA-binding proteins, many of which are transcriptional regulators and chromatin modifiers. In addition to known RNA-binding motifs, we detected several protein domains previously unknown to function in RNA recognition, as well as non-annotated and/or disordered regions, suggesting that many functional protein-RNA contacts remain unexplored...
October 20, 2016: Molecular Cell
Haibo Wang, Xiaokun Han, Eric Kunz, M Elizabeth Hartnett
Purpose: This study addresses the hypothesis that age-related stresses upregulate Thy-1 in choroidal endothelial cells (CECs) and contribute to CEC activation and migration, processes important in choroidal neovascularization (CNV). Methods: Measurements were made of Thy-1 protein (Western blot) in CECs and Thy-1 mRNA (real time quantitative PCR) in CECs treated with VEGF, CCL11, or PBS or in RPE/choroids from young or old donors or lasered or nonlasered mice. Immunolabeled Thy-1 in ocular sections was compared from young versus old human donor eyes or those with or without neovascular AMD or from lasered versus nonlasered mice...
October 1, 2016: Investigative Ophthalmology & Visual Science
Arne O Melleby, Mari E Strand, Andreas Romaine, Kate M Herum, Biljana Skrbic, Christen P Dahl, Ivar Sjaastad, Arnt E Fiane, Jorge Filmus, Geir Christensen, Ida G Lunde
Pressure overload is a frequent cause of heart failure. Heart failure affects millions of patients worldwide and is a major cause of morbidity and mortality. Cell surface proteoglycans are emerging as molecular players in cardiac remodeling, and increased knowledge about their regulation and function is needed for improved understanding of cardiac pathogenesis. Here we investigated glypicans (GPC1-6), a family of evolutionary conserved heparan sulfate proteoglycans anchored to the extracellular leaflet of the cell membrane, in experimental and clinical heart failure, and explored the function of glypican-6 in cardiac cells in vitro...
2016: PloS One
Qian Lu, Jihong Wang, Junshu Jiang, Shengnan Wang, Qilan Jia, Yue Wang, Weiping Li, Qin Zhou, Li Lv, Qingwei Li
BACKGROUND: The RGD-toxin protein Lj-RGD3 is a naturally occurring 118 amino acid peptide that can be obtained from the salivary gland of the Lampetra japonica fish. This unique peptide contains 3 RGD (Arg-Gly-Asp) motifs in its primary structure. Lj-RGD3 is available in recombinant form (rLj-RGD3) and can be produced in large quantities using DNA recombination techniques. The pharmacology of the three RGD motif-containing peptides has not been studied. This study investigated the protective effects of rLj-RGD3, a novel polypeptide, against ischemia/reperfusion-induced damage to the brain caused by middle cerebral artery occlusion (MCAO) in a rat stroke model...
2016: PloS One
I Caglar Tanrikulu, Audrey Forticaux, Song Jin, Ronald T Raines
Sticky-ended DNA duplexes can associate spontaneously into long double helices; however, such self-assembly is much less developed with proteins. Collagen is the most prevalent component of the extracellular matrix and a common clinical biomaterial. As for natural DNA, the ~10(3)-residue triple helices (~300 nm) of natural collagen are recalcitrant to chemical synthesis. Here we show how the self-assembly of short collagen-mimetic peptides (CMPs) can enable the fabrication of synthetic collagen triple helices that are nearly a micrometre in length...
November 2016: Nature Chemistry
Emanuele Mauri, Alessandro Sacchetti, Filippo Rossi
The use of polymers as biomaterials has provided significant advantages in therapeutic applications. In particular, the possibility to modify and functionalize polymer chains with compounds that are able to improve biocompatibility, mechanical properties, or cell viability allows the design of novel materials to meet new challenges in the biomedical field. With the polymer functionalization strategies, click chemistry is a powerful tool to improve cell-compatibility and drug delivery properties of polymeric devices...
October 7, 2016: Journal of Visualized Experiments: JoVE
Carlota Saldanha
Nitric oxide (NO) produced by endothelial cells interacts with erythrocyte through band 3 protein, being scavenged by haemoglobin. A signal transduction mechanism involving protein Gi and protein band 3 stimulates erythrocyte NO efflux when acetylcholine (ACh) binds to erythrocyte membrane acetylcholinesterase. Binding of normal plasma fibrinogen (Fib) levels, to erythrocyte membrane CD47 decreases the NO efflux. When high Fib concentration and ACh were present the efflux of NO from erythrocytes was normalized...
October 20, 2016: Clinical Hemorheology and Microcirculation
Gianluigi Franci, Federica Sarno, Angela Nebbioso, Lucia Altucci
Epigenetic modifications are functionally involved in gene expression regulation. In particular, histone posttranslational modifications play a crucial role in functional chromatin organization. Several drugs able to inhibit or stimulate some families of proteins involved in epigenetic histone regulation have been found, a number of which are FDA-approved for the treatment of cutaneous T-cell lymphoma or are in phase I/II/III clinical trials for solid tumors. Although some protein families, such as histone deacetylases and their inhibitors, are well characterized, our understanding of histone lysine demethylases is still incomplete...
October 21, 2016: Epigenetics: Official Journal of the DNA Methylation Society
Nathan A Bernhardt, Wenhui Xi, Wei Wang, Ulrich H E Hansmann
Recent experiments suggest that an amino acid sequence encodes not only the native fold of a protein but also other forms essential for its function, or important during folding or association. These various forms populate a multi-funnel folding and association landscape where mutations, changes in environment or interaction with other molecules switch between the encoded folds. We introduce replica-exchange-with- tunneling as a way to simulate efficiently switching between distinct folds of proteins and protein aggregates...
October 21, 2016: Journal of Chemical Theory and Computation
Najla Kharrat, Sabrine Belmabrouk, Rania Abdelhedi, Riadh Benmarzoug, Mourad Assidi, Mohammed H Al Qahtani, Ahmed Rebai
BACKGROUND: The identification of charge clusters (runs of charged residues) in proteins and their mapping within the protein structure sequence is an important step toward a comprehensive analysis of how these particular motifs mediate, via electrostatic interactions, various molecular processes such as protein sorting, translocation, docking, orientation and binding to DNA and to other proteins. Few algorithms that specifically identify these charge clusters have been designed and described in the literature...
October 17, 2016: BMC Genomics
Shaher Bano Mirza, Ramin Ekhteiari Salmas, M Qaiser Fatmi, Serdar Durdagi
The Klotho is known as lifespan enhancing protein involved in antagonizing the effect of Wnt proteins. Wnt proteins are stem cell regulators, and uninterrupted exposure of Wnt proteins to the cell can cause stem and progenitor cell senescence, which may lead to aging. Keeping in mind the importance of Klotho in Wnt signaling, in silico approaches have been applied to study the important interactions between Klotho and Wnt3 and Wnt3a (wingless-type mouse mammary tumor virus (MMTV) integration site family members 3 and 3a)...
October 21, 2016: Journal of Enzyme Inhibition and Medicinal Chemistry
Hongwei Yao, Myungwoon Lee, Shu Y Liao, Mei Hong
The fusion peptide (FP) and transmembrane domain (TMD) of viral fusion proteins play important roles during virus-cell membrane fusion, by inducing membrane curvature and transient dehydration. The structure of the water-soluble ectodomain of viral fusion proteins has been extensively studied crystallographically, but the structures of the FP and TMD bound to phospholipid membranes are not well understood. We recently investigated the conformations and lipid interactions of the separate FP and TMD peptides of the parainfluenza virus 5 (PIV5) fusion protein F using solid-state NMR...
October 21, 2016: Biochemistry
Bianka Swiderska, Sylwia Kedracka-Krok, Barbara Plytycz
The data described are related to the article "Lysenin family proteins in earthworm coelomocytes - comparative approach" (B. Swiderska, S. Kedracka-Krok, T. Panz, A.J. Morgan, A. Falniowski, P.Grzmil, B. Plytycz, 2016) [1]. Lysenin family proteins were identified based on unique peptides sequenced by tandem mass spectrometry coupled with liquid chromatography (LC-MS/MS) in lumbricid earthworms Eisenia andrei and E. fetida, the latter with or without the MUG-like fluorophore. Lysenin and lysenin-related protein 2 (LRP-2, fetidin) were identified in all 9 investigated specimens of Eisenia sp...
December 2016: Data in Brief
Ji-Hee Ha, Jung-Eun Kim, Yong-Sung Kim
The monospecific and bivalent characteristics of naturally occurring immunoglobulin G (IgG) antibodies depend on homodimerization of the fragment crystallizable (Fc) regions of two identical heavy chains (HCs) and the subsequent assembly of two identical light chains (LCs) via disulfide linkages between each HC and LC. Immunoglobulin Fc heterodimers have been engineered through modifications to the CH3 domain interface, with different mutations on each domain such that the engineered Fc fragments, carrying the CH3 variant pair, preferentially form heterodimers rather than homodimers...
2016: Frontiers in Immunology
Intidhar Bkhairia, Rabeb Ben Slama Ben Salem, Rim Nasri, Mourad Jridi, Sofiane Ghorbel, Moncef Nasri
Bioactive Liza aurata protein hydrolysates (LAPHs) were prepared by treatment with Trypsine (PH-TR), Esperase (PH-ES), enzyme preparations from Pseudomonas aeruginosa A2 (PH-A2), Bacillus subtilis A26 (PH-A26) and Liza aurata (PH-LA). Their functional properties and antioxidant activities were evaluated. The hydrolysates had degree of hydrolysis (DH) values ranging from 8.15 % to 13.05 %. Reverse-phase HPLC analyses of the LAPHs showed considerable variation in peptide composition. All hydrolysates had high protein content (83...
July 2016: Journal of Food Science and Technology
Ying Li, Xuemin Zheng, Min Gong, Jianning Zhang
The challenge of effectively delivering therapeutic agents to the brain has created an entire field of active research devoted to overcoming the blood brain barrier (BBB) and efficiently delivering drugs to the brain. Angiopep-2 can trigger transcytosis and traverse the BBB by recognizing low-density lipoprotein related protein-1 (LRP-1) expressed on the brain capillary endothelial cells. Here, we designed a novel strategy for the delivery of drugs to the brain. The novel drug delivery system was a combination of a receptor-targeting ligand, such as low-density lipoprotein related protein 1, and a cell-penetrating peptide (CPP)...
October 17, 2016: Oncotarget
Salvatore Santo Signorelli, Fiore Valerio, Castrogiovanni Davide, Gea Oliveri Conti, Fiore Maria, Morana Ignazio, Ferrante Margherita
Study on 295 consecutive medical patients to evaluate the potential of routine blood tests to identify the risk of deep vein thrombosis (DVT). The tests included in a DVT risk stratification model system were erythrocyte sedimentation rate, antithrombin III, C-reactive protein, D-dimer, and N-terminal pro-brain natriuretic peptide. The DVT risk stratification system was moderately prognostic (area under the curve: 0.838; 95% confidence interval: 0.771-0.904; P < .001), whereas its performance was as follows-sensitivity, 100%; specificity, 20%; positive predictive value, 21%; and negative predictive value, 100%...
October 20, 2016: Angiology
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