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Protein design

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https://www.readbyqxmd.com/read/28814063/icave-an-open-source-tool-for-visualizing-biomolecular-networks-in-3d-stereoscopic-3d-and-immersive-3d
#1
Vaja Liluashvili, Selim Kalayci, Eugene Fluder, Manda Wilson, Aaron Gabow, Zeynep H Gümüs
Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28813782/urea-cycle-pathway-targeted-therapeutic-action-of-naringin-against-ammonium-chloride-induced-hyperammonemic-rats
#2
Arumugam Ramakrishnan, Natesan Vijayakumar
Ammonia is a well-known neurotoxin that causes liver disease and urea cycle disorder. Excessive ammonia content in the blood leads to hyperammonemic condition and affects both excitatory and inhibitory neurotransmission including brain edema and coma. Naringin, a plant bioflavonoid present in various citrus fruits and mainly extracted from the grape fruit. This study was designed to assess the protective effect of naringin on ammonium chloride (NH4Cl) induced hyperammonemic rats. Experimental hyperammonemia was induced by intraperitoneal injections (i...
August 12, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28813678/therapeutic-antibodies-to-ganglioside-gd2-evolved-from-highly-selective-germline-antibodies
#3
Eric Sterner, Megan L Peach, Marc C Nicklaus, Jeffrey C Gildersleeve
Antibodies play a crucial role in host defense and are indispensable research tools, diagnostics, and therapeutics. Antibody generation involves binding of genomically encoded germline antibodies followed by somatic hypermutation and in vivo selection to obtain antibodies with high affinity and selectivity. Understanding this process is critical for developing monoclonal antibodies, designing effective vaccines, and understanding autoantibody formation. Prior studies have found that antibodies to haptens, peptides, and proteins evolve from polyspecific germline antibodies...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28813625/detection-of-first-line-drug-resistance-mutations-and-drug-protein-interaction-dynamics-from-tuberculosis-patients-in-south-india
#4
Somanna Ajjamada Nachappa, Sumana M Neelambike, Chokkanna Amruthavalli, Nallur B Ramachandra
Diagnosis of drug-resistant tuberculosis predominantly relies on culture-based drug susceptibility testing, which take weeks to produce a result and a more time-efficient alternative method is multiplex allele-specific PCR (MAS-PCR). Also, understanding the role of mutations in causing resistance helps better drug designing. AIMS: To evaluate the ability of MAS-PCR in the detection of drug resistance and to understand the mechanism of interaction of drugs with mutant proteins in Mycobacterium tuberculosis...
August 16, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28813101/forage-potential-of-native-ecotypes-of-paspalum-notatum-and-p-guenoarum
#5
Marcelo G Steiner, Miguel Dall'agnol, Carlos Nabinger, Simone M Scheffer-Basso, Roberto L Weiler, Carine Simioni, Maria Teresa Schifino-Wittmann, Éder A M DA Motta
The Paspalum genus includes several species that are important for livestock in Rio Grande do Sul, such as P. notatum and P. guenoarum, typical of native pastures of the Pampa biome. The aim of this study was to investigate forage production and chemical composition of four ecotypes of these species in relation to the cv. 'Pensacola' (P. notatum). Ecotypes of P. guenoarum (Azulão and Baio) and P. notatum (André da Rocha and Bagual) and the cv. 'Pensacola' were evaluated for two years, during which four cuts/year were made...
August 14, 2017: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/28812983/a-microfluidic-platform-for-modeling-metastatic-cancer-cell-matrix-invasion
#6
Laura Blaha, Chentian Zhang, Mario Cabodi, Joyce Y Wong
Invasion of the extracellular matrix is a critical step in the colonization of metastatic tumors. The invasion process is thought to be driven by both chemokine signaling and interactions between invading cancer cells and physical components of the metastatic niche, including endothelial cells that line capillary walls and serve as a barrier to both diffusion and invasion of the underlying tissue. Transwell chambers, a tool for generating artificial chemokine gradients to induce cell migration, have facilitated recent work to investigate the chemokine contributions to matrix invasion...
August 16, 2017: Biofabrication
https://www.readbyqxmd.com/read/28812882/aberrantly-large-single-channel-conductance-of-polyhistidine-arm-containing-protein-nanopores
#7
Avinash Kumar Thakur, Motahareh Ghahari Larimi, Kristin Gooden, Liviu Movileanu
There have been only a few studies reporting on the impact of polyhistidine affinity tags on the structure, function, and dynamics of proteins. Because of their relatively short size, they are often assumed to have little or no effect on the conformation and activity of a protein. Here, using membrane protein design and single-molecule electrophysiology, we determined that the presence of a hexahistidine arm at the N-terminus of a truncated FhuA-based protein nanopore, leaving the C-terminus untagged, produces an unusual increase in the unitary conductance up to ~8 nS in 1 M KCl...
August 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28812535/associating-mutations-causing-cystinuria-with-disease-severity-with-the-aim-of-providing-precision-medicine
#8
Henry J Martell, Kathie A Wong, Juan F Martin, Ziyan Kassam, Kay Thomas, Mark N Wass
BACKGROUND: Cystinuria is an inherited disease that results in the formation of cystine stones in the kidney, which can have serious health complications. Two genes (SLC7A9 and SLC3A1) that form an amino acid transporter are known to be responsible for the disease. Variants that cause the disease disrupt amino acid transport across the cell membrane, leading to the build-up of relatively insoluble cystine, resulting in formation of stones. Assessing the effects of each mutation is critical in order to provide tailored treatment options for patients...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28812431/oral-administration-of-curcumin-attenuates-visceral-hyperalgesia-through-inhibiting-phosphorylation-of-trpv1-in-rat-model-of-ulcerative-colitis
#9
Mei Yang, Juan Wang, Chunxue Yang, Hongxiu Han, Weifang Rong, Guohua Zhang
Background Curcumin has been reported to have anti-inflammatory and anti-nociceptive effects. The present study was designed to explore the potential therapeutic effects of curcumin on visceral hyperalgesia and inflammation in a rat model of ulcerative colitis. We observed the effects of orally administered curcumin on the disease activity index, histological change in colon, colorectal distension-induced abdominal withdrawal reflex, the expression of transient receptor potential vanilloid 1 (TRPV1) and phosphorylated TRPV1 in dextran sulfate sodium-induced colitis rats...
January 2017: Molecular Pain
https://www.readbyqxmd.com/read/28812395/current-research-on-circular-rnas-associated-with-colorectal-cancer
#10
Penghui Wang, Xiaodong He
Representing a novel type of endogenous noncoding RNAs, circular RNAs (circRNAs) have recently gained much attention for their involvement in multiple biological processes. CircRNAs are ubiquitously expressed in eukaryotic cells and modulate gene expression by acting as sponges of microRNAs (miRNAs) or other proteins, such as RNA-binding proteins (RBPs). Due to their unique structure, circRNAs are more stable than linear RNAs. Expression profiles of circRNAs are associated with clinicopathological characteristics of colorectal cancer patients, such as differentiation, TNM classification and distant metastasis...
August 16, 2017: Scandinavian Journal of Gastroenterology
https://www.readbyqxmd.com/read/28812358/bioinspired-active-stealth-magneto-nanomicelles-for-theranostics-combining-efficient-mri-and-enhanced-drug-delivery
#11
Kai-Long Zhang, Jie Zhou, Hong Zhou, Ying Wu, Rui Liu, Li-Li Wang, Wei-Wen Lin, Guoming Huang, Huang-Hao Yang
The mononuclear phagocyte system (MPS), with key roles in recognition and clearance of foreign particles, is a major constraint to nanoparticle-based delivery systems. The desire to improve the delivery efficiency has prompted the search for stealthy long-circulating nanoplatforms. Herein, we design an antiphagocytic delivery system with "active" stealth behavior for cancer theranostics combining efficient MRI and enhanced drug delivery. We modify self-peptide, a synthetic peptide for active immunomodulation, to biodegradable poly (lactide-glycolide)-poly (ethylene glycol) (PLGA-PEG), then utilize the self-assembly properties of PLGA-PEG to form nanomicelles that encapsulating iron oxide (IO) nanoparticles and anticancer drug paclitaxel (PTX)...
August 16, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28812348/inhibition-of-heterogeneous-ice-nucleation-by-bioinspired-coatings-of-polyampholytes
#12
Zhiyuan He, Liuchun Zheng, Zhenqi Liu, Shenglin Jin, Chuncheng Li, Jianjun Wang
Controlling of heterogeneous ice nucleation (HIN) on foreign surfaces is of great importance for anti-ice nucleation material design. In this work, we studied the HIN behaviors on various ion-modified poly(butylene succinate) (PBS) surfaces via chain-extension reaction. Inspired by antifreeze proteins (AFPs), the PBS-based polyampholytes, containing both negative and positive charge groups on a single chain, show excellent performance of ice nucleation inhibition and freezing delay. Unlike the extremely high price and low availability of AFPs, these PBS-based polyampholytes can be commercially synthesized under mild reaction conditions...
August 16, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28812082/a-broader-view-on-ion-heating-in-traveling-wave-devices-using-fragmentation-of-csi-clusters-and-extent-of-h%C3%AB-migration-as-molecular-thermometers
#13
Frederik Lermyte, Frank Sobott
Electron transfer dissociation (ETD) is becoming increasingly important in mass spectrometry-based analysis of peptides and proteins. Supplemental collisional activation of undissociated electron transfer products can significantly increase fragmentation yield and sequence coverage, but hydrogen rearrangements - specifically, transfer of a hydrogen radical from a c to a z fragment - lead to distorted isotope distributions and increased potential for signal overlap. Concomitant collisional activation during the ion/ion reaction significantly reduces these rearrangements, but, in ion traps, also leads to lower reaction rates and reduced overlap of anion and cation clouds...
August 16, 2017: Analyst
https://www.readbyqxmd.com/read/28811833/nsitematch-prediction-of-binding-sites-of-nucleotides-by-identifying-the-structure-similarity-of-local-surface-patches
#14
Jie Sun, Ke Chen
Nucleotides play a central role in life-form metabolism, by interacting with proteins and mediating the function of proteins. It is estimated that nucleotides constitute about 15% of the biologically relevant ligands included in PDB. Prediction of binding sites of nucleotides is useful in understanding the function of proteins and can facilitate the in silico design of drugs. In this study, we propose a nucleotide-binding site predictor, namely, NSiteMatch. The NSiteMatch algorithm integrates three different strategies: geometrical analysis, energy calculation, and template comparison...
2017: Computational and Mathematical Methods in Medicine
https://www.readbyqxmd.com/read/28811600/exploring-leishmania-secretory-proteins-to-design-b-and-t-cell-multi-epitope-subunit-vaccine-using-immunoinformatics-approach
#15
Nazia Khatoon, Rajan Kumar Pandey, Vijay Kumar Prajapati
Visceral leishmaniasis (VL) is a fatal form of leishmaniasis which affects 70 countries, worldwide. Increasing drug resistance, HIV co-infection, and poor health system require operative vaccination strategy to control the VL transmission dynamics. Therefore, a holistic approach is needed to generate T and B memory cells to mediate long-term immunity against VL infection. Consequently, immunoinformatics approach was applied to design Leishmania secretory protein based multi-epitope subunit vaccine construct consisting of B and T cell epitopes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811599/histone-deacetylase-6-hdac6-is-an-essential-factor-for-oocyte-maturation-and-asymmetric-division-in-mice
#16
Dongjie Zhou, Yun-Jung Choi, Jin-Hoi Kim
Tubastatin A (Tub-A), a highly selective histone deacetylase 6 (HDAC6) inhibitor, has been widely used as a cytotoxic anticancer agent, or for the treatment of patients with asthma. However, the potential toxicity of Tub-A on oocyte maturation and asymmetric division is still unclear. Therefore, the present study was designed to examine the effect and potential regulatory role of Tub-A on the meiotic maturation of oocytes. We observed that Tub-A treatment induced an increased level of the acetylation of α-tubulin, and a failure of spindle migration and actin cap formation...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811551/nano-metamaterials-for-ultrasensitive-terahertz-biosensing
#17
Dong-Kyu Lee, Ji-Hun Kang, Junghoon Kwon, Jun-Seok Lee, Seok Lee, Deok Ha Woo, Jae Hun Kim, Chang-Seon Song, Q-Han Park, Minah Seo
As a candidate for a rapid detection of biomaterials, terahertz (THz) spectroscopy system can be considered with some advantage in non-destructive, label-free, and non-contact manner. Because protein-ligand binding energy is in the THz range, especially, most important conformational information in molecular interactions can be captured by THz electromagnetic wave. Based on the THz time-domain spectroscopy system, THz nano-metamaterial sensing chips were prepared for great enhancing of detection sensitivity...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811266/expression-and-purification-of-a-difficult-sarcomeric-protein-telethonin
#18
Huanbo Tan, Wencheng Su, Pengju Wang, Wenyu Zhang, Michael Sattler, Peijian Zou
Telethonin anchors the N-terminal region of titin in the Z-disk of the sarcomere by binding to two immunoglobulin-like (Ig) domains (Z1 and Z2) of titin (Z1Z2). Thereby telethonin plays an important role in myofibril assembly and in muscle development and functional regulation. The expression and purification of recombinant telethonin is very challenging. In previous studies, recombinant telethonin expressed from E. coli was refolded in the presence of Z1Z2. Here, we report various strategies to establish a reliable and efficient protocol for the preparation of telethonin and titin Z1Z2 protein...
August 12, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28811207/anion-%C3%AF-interactions-in-active-centers-of-superoxide-dismutases
#19
Vesna R Ribić, Srđan Đ Stojanović, Mario V Zlatović
We investigated 1060 possible anion-π interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-π interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-π interactions. Anion-π interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-π interactions using ab initio calculations...
August 12, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28811027/design-of-carbohydrate-electron-transfer-peptides-for-human-histocytic-lymphoma-cell-sensing
#20
Kazuharu Sugawara, Toshihiko Kadoya, Hideki Kuramitz, Yoshihiro Mihara
A carbohydrate/electro-transfer peptide probe was fabricated to perform cell sensing. The probe consisted of a cello-oligosaccharide that was created by the conjugation of an electron-transfer peptide (Y5C) and a carbohydrate via a Schiff base. An oxidation wave due to a phenolic hydroxyl group was obtained by scanning with a glassy carbon electrode. This cell-sensing system was based on a competitive reaction between carbohydrates on a cell surface and the probe as each reacted to a protein that recognized the carbohydrate...
August 29, 2017: Analytica Chimica Acta
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