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https://www.readbyqxmd.com/read/27936519/a-computational-approach-for-studying-antibody-antigen-interactions-without-prior-structural-information-the-anti-testosterone-binding-antibody-as-a-case-study
#1
Artturi Koivuniemi, Kristiina Takkinen, Tarja Nevanen
Given the increasing exploitation of antibodies in different contexts such as molecular diagnostics and therapeutics, it would be beneficial to unravel the atomistic level properties of antibody-antigen complexes with the help of computational modeling. Thus, here we have studied the feasibility of computational tools to gather atomic scale information regarding the antibody-antigen complexes solely starting from an amino acid sequence. First, we constructed a homology model for the anti-testosterone binding antibody based on the knowledge based classification of complementary determining regions (CDRs) and implicit solvent molecular dynamics simulations...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936518/computational-investigation-of-proton-transfer-pka-shifts-and-ph-optimum-of-protein-dna-and-protein-rna-complexes
#2
Yunhui Peng, Emil Alexov
Protein-nucleic acid interactions play a crucial role in many biological processes. This work investigates the changes of pKa values and protonation states of ionizable groups (including nucleic acid bases) that may occur at protein-nucleic acid binding. Taking advantage of the recently developed pKa calculation tool DelphiPka, we utilize the large protein-nucleic acid interaction database (NPIDB database) to model pKa shifts caused by binding. It has been found that the protein's interfacial basic residues experience favorable electrostatic interactions while the protein acidic residues undergo proton uptake to reduce the energy cost upon the binding...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936517/-novel-biomarkers-for-the-assessment-of-pediatric-systemic-lupus-erythematosus-nephritis
#3
Artemis Koutsonikoli, Maria Trachana, Evangelia Farmaki, Vasiliki Tzimouli, Polyxeni Pratsidou-Gertsi, Nikoleta Printza, Alexandros Garyphallos, Vasiliki Galanopoulou, Florence Kanakoudi-Tsakalidou, Fotios Papachristou
OBJECTIVES: The discovery of serum biomarkers specific for pediatric Lupus Nephritis (pLN) will facilitate the non-invasive diagnosis, follow-up and more appropriate use of treatment. The aim of this study was to explore the role of serum High-Mobility-Group-Box-1 (HMGB1) protein, antibodies against nucleosomes (anti-NCS), complement factor C1q (anti-C1q) and glomerular basement membrane (anti-GBM) in pLN. METHODS: Serum samples of 42 patients with pediatric Systemic Lupus Erythematosus (pSLE) (22 with pLN and 20 without renal involvement), fifteen patients with other autoimmune nephritis (AN) and 26 healthy controls (HCs) were examined using ELISA...
December 9, 2016: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/27936516/neuroprotection-of-hypoxic-postconditioning-against-global-cerebral-ischemia-through-influencing-posttranslational-regulations-of-heat-shock-protein-27-in-adult-rats
#4
Lixuan Zhan, Liu Liu, Kongping Li, Baoxing Wu, Dandan Liu, Donghai Liang, Haixia Wen, Yanmei Wang, Weiwen Sun, Weiping Liao, En Xu
We previously reported that hypoxic postconditioning (HPC) ameliorated hippocampal neuronal death induced by transient global cerebral ischemia (tGCI) in adult rats. However, the mechanism of HPC-induced neuroprotection is still elusive. Notably, heat shock protein 27 (Hsp27) has recently emerged as a potent neuroprotectant in cerebral ischemia. Although its robust protective effect on stroke has been recognized, the mechanism of Hsp27-mediated neuroprotection is largely unknown. Here, we investigated the potential molecular mechanism by which HPC modulates the posttranslational regulations of Hsp27 after tGCI...
December 9, 2016: Brain Pathology
https://www.readbyqxmd.com/read/27936514/comparing-acquired-angioedema-with-hereditary-angioedema-type-i-ii-findings-from-the-icatibant-outcome-survey
#5
Hilary J Longhurst, Andrea Zanichelli, Teresa Caballero, Laurence Bouillet, Werner Aberer, Marcus Maurer, Olivier Fain, Vincent Fabien, Irmgard Andresen
Icatibant is approved for hereditary angioedema with C1 inhibitor deficiency type I/II (C1-INH-HAE type I/II) and has shown promise in treatment of angioedema due to acquired C1 inhibitor deficiency (C1-INH-AAE). Data from the Icatibant Outcome Survey was analyzed to evaluate effectiveness of icatibant in the treatment of patients with C1-INH-AAE and compare disease characteristics with those with C1-INH-HAE type I/II. Key medical history (including prior occurrence of attacks) was recorded upon IOS enrollment...
December 9, 2016: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/27936513/probing-the-structural-dynamics-of-the-crispr-cas9-rna-guided-dna-cleavage-system-by-coarse-grained-modeling
#6
Wenjun Zheng
In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936512/genome-editing-of-the-disease-susceptibility-gene-cslob1-in-citrus-confers-resistance-to-citrus-canker
#7
Hongge Jia, Yunzen Zhang, Vladimir Orbovic, Jin Xu, Frank White, Jeffrey Jones, Nian Wang
Citrus is a highly valued tree crop worldwide, while, at the same time, citrus production faces many biotic challenges, including bacterial canker and Huanglongbing (HLB). Breeding for disease resistant varieties is the most efficient and sustainable approach to control plant diseases. Traditional breeding of citrus varieties is challenging due to multiple limitations, including polyploidy, polyembryony, extended juvenility, and long crossing cycles. Targeted genome editing technology has the potential to shorten varietal development for some traits, including disease resistance...
December 9, 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27936510/systematic-evaluation-of-cs-rosetta-for-membrane-protein-structure-prediction-with-sparse-noe-restraints
#8
Katrin Reichel, Olivier Fisette, Tatjana Braun, Olivier F Lange, Gerhard Hummer, Lars V Schäfer
We critically test and validate the CS-Rosetta methodology for de novo structure prediction of α-helical membrane proteins (MPs) from NMR data, such as chemical shifts and NOE distance restraints. By systematically reducing the number and type of NOE restraints, we focus on determining the regime in which MP structures can be reliably predicted and pinpoint the boundaries of the approach. Five MPs of known structure were used as test systems, phototaxis sensory rhodopsin II (pSRII), a subdomain of pSRII, disul_de binding protein B (DsbB), microsomal prostaglandin E2 synthase-1 (mPGES-1), and translocator protein (TSPO)...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936500/sodium-co-limits-and-catalyzes-macronutrients-in-a-prairie-food-web
#9
Michael Kaspari, Karl A Roeder, Brittany Benson, Michael D Weiser, Nathan Sanders
Nitrogen and phosphorus frequently limit terrestrial plant production, but have a mixed record in regulating the abundance of terrestrial invertebrates. We contrasted four ways that Na could interact with an NP fertilizer to shape the plants and invertebrates of an inland prairie. We applied NP and Na to m(2) plots in a factorial design. Aboveground invertebrate abundance was independently co-limited by NaCl and NP, but with +NP plots supporting more individuals. We suggest the disparity arises because NP enhanced plant height by 35% (1SD) over controls, providing both food and habitat while NaCl provides only food...
December 9, 2016: Ecology
https://www.readbyqxmd.com/read/27936499/the-anatomy-of-mammalian-sweet-taste-receptors
#10
Jean-Baptiste Chéron, Jérôme Golebiowski, Serge Antonczak, Sébastien Fiorucci
All sweet-tasting compounds are detected by a single G-protein coupled receptor (GPCR), the heterodimer T1R2-T1R3, for which no experimental structure is available. The sweet taste receptor is a class C GPCR, and the recently published crystallographic structures of metabotropic glutamate receptor (mGluR) 1 and 5 provide a significant step forward for understanding structure-function relationships within this family. In this article, we recapitulate more than six hundred single point site-directed mutations and available structural data to obtain a critical alignment of the sweet taste receptor sequences with respect to other class C GPCRs...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936498/invasive-exotic-shrub-modifies-a-classic-animal-habitat-relationship-and-alters-patterns-of-vertebrate-seed-predation
#11
Peter W Guiden, John L Orrock
Recent evidence suggests that invasive exotic plants can provide novel habitats that alter animal behavior. However, it remains unclear whether classic animal-habitat associations that influence the spatial distribution of plant-animal interactions, such as small mammal use of downed woody debris, persist in invaded habitats. We removed an invasive exotic shrub (buckthorn, Rhamnus cathartica) from 7 of 15 plots in Wisconsin. In each plot, we deployed 200 tagged Quercus rubra seeds in November 2014. After five months, tags were recovered to track spatial patterns of small mammal seed predation...
December 9, 2016: Ecology
https://www.readbyqxmd.com/read/27936497/pro-inflammatory-cytokine-ifn%C3%AE-and-microbiome-derived-metabolites-dictate-epigenetic-switch-between-foxp3-isoforms-in-celiac-disease-regulation-of-foxp3-isoforms-in-celiac-disease
#12
Gloria Serena, Shu Yan, Stephanie Camhi, Shilpi Patel, Rosiane S Lima, Anna Sapone, Maureen M Leonard, Rupa Mukherjee, Barbara J Nath, Karen M Lammers, Alessio Fasano
Celiac disease (CD) is an autoimmune enteropathy triggered by gluten and characterized by a strong Th1/Th17 immune response in the small intestine. Treg cells are CD4(+) CD25(++) FOXP3(+) cells that regulate the immune response. Conversely to its counterpart, FOXP3 full length (FL), the alternatively spliced isoform FOXP3 Δ2 cannot properly down-regulate Th17 driven immune response. Since the active state of CD has been associated with impairments in Treg cell function, we aimed at determining whether imbalances between FOXP3 isoforms may be associated with the disease...
December 9, 2016: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/27936496/simultaneous-stimulation-of-the-sbpase-fbp-aldolase-and-the-photorespiratory-gdc-h-protein-increases-co2-assimilation-vegetative-biomass-and-seed-yield-in-arabidopsis
#13
Andrew J Simkin, Patricia E Lopez-Calcagno, Philip A Davey, Lauren R Headland, Tracy Lawson, Stefan Timm, Hermann Bauwe, Christine A Raines
In this paper we have altered the levels of three different enzymes involved in the Calvin Benson cycle and photorespiratory pathway. We have generated transgenic Arabidopsis plants with altered combinations of sedoheptulose 1,7-bisphosphatase (SBPase), fructose 1,6-bisphophate aldolase (FBPA) and the glycine decarboxylase H-protein (GDC-H) gene identified as targets to improve photosynthesis based on previous studies. Here, we show that increasing the levels of the three corresponding proteins, either independently or in combination, significantly increases the quantum efficiency of PSII...
December 9, 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27936495/t-bet-overexpression-regulates-ahr-mediated-th-17-differentiation-through-an-ifn%C3%AE-independent-pathway
#14
Masahiro Yokosawa, Yuya Kondo, Masahiro Tahara, Mana Iizuka-Koga, Seiji Segawa, Shunta Kaneko, Hiroto Tsuboi, Keigyou Yoh, Satoru Takahash, Isao Matsumoto, Takayuki Sumida
Various transcription factors are also known to enhance or suppress Th-17 differentiation. We previously showed that the development of collagen-induced arthritis was suppressed in T-bet transgenic (T-bet Tg) mice and T-bet seemed to suppress Th-17 differentiation through an IFNγ-independent pathway, although the precise mechanism remains to be clarified. The present study was designed to further investigate the mechanisms involved in the regulation of Th-17 differentiation by T-bet overexpression, and we found the new relation between T-bet and aryl hydrocarbon receptor (AHR)...
December 9, 2016: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/27936494/five-new-c19-diterpenoid-alkaloids-from-delphinium-tianshanicum-w-t-wang
#15
By Ji-Fa Zhang, Lian-Hai Shan, Feng Gao, Shuai Huang, Xian-Li Zhou
Five new diterpenoid alkaloids tianshanitine A-E (1-5), along with ten known compounds (6-15), were isolated from the ethanolic extracts of the whole plant of Delphinium tianshanicum W. T. Wang. Their structures were determined based on extensive spectroscopic analyses, including 1D, 2D NMR, HRESIMS, and the structure of tianshanitine C (3) was confirmed by X-ray diffraction analysis. Tianshanitine A (1) is the first example of natural diterpenoid alkaloid containing a benzoyl group at C-1 position. Tianshanitine B (2) is a rare natural diterpenoid alkaloid including a hydroxyl group at C-16 position...
December 9, 2016: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/27936493/new-additions-to-the-cluspro-server-motivated-by-capri
#16
Sandor Vajda, Christine Yueh, Dmitri Beglov, Tanggis Bohnuud, Scott E Mottarella, Bing Xia, David R Hall, Dima Kozakov
The heavily used protein-protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for Small Angle X-ray Scattering (SAXS) data in docking; (2) considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936492/lncrna-a-versatile-regulator-of-the-nf-%C3%AE%C2%BAb-signaling-circuit
#17
REVIEW
Xiaohua Mao, Zhenyi Su, Adnan K Mookhtiar
The Nuclear Factor-κB (NF-κB) family of transcription factors play an essential role for the regulation of inflammatory responses, immune function and malignant transformation. Aberrant activity of this signaling pathway may lead to inflammation, autoimmune diseases and oncogenesis. Over the last two decades great progress has been made in the understanding of NF-κB activation and how the response is counteracted for maintaining tissue homeostasis. Therapeutic targeting of this pathway has largely remained ineffective due to the widespread role of this vital pathway and the lack of specificity of the therapies currently available...
December 9, 2016: Immunology
https://www.readbyqxmd.com/read/27936491/intrinsic-%C3%AE-helix-propensities-compact-hydrodynamic-radii-in-intrinsically-disordered-proteins
#18
Lance R English, Erin C Tilton, Benjamin J Ricard, Steven T Whitten
Proteins that lack tertiary stability under normal conditions, known as intrinsically disordered, exhibit a wide range of biological activities. Molecular descriptions for the biology of intrinsically disordered proteins (IDPs) consequently rely on disordered structural models, which in turn require experiments that assess the origins to structural features observed. For example, while hydrodynamic size is mostly insensitive to sequence composition in chemically denatured proteins, IDPs show strong sequence-specific effects in the hydrodynamic radius (Rh ) when measured under normal conditions...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936490/combining-ancestral-sequence-reconstruction-with-protein-design-to-identify-an-interface-hotspot-in-a-key-metabolic-enzyme-complex
#19
Alexandra Holinski, Kristina Heyn, Rainer Merkl, Reinhard Sterner
It is important to identify hotspot residues that determine protein-protein interactions in interfaces of macromolecular complexes. We have applied a combination of ancestral sequence reconstruction and protein design to identify hotspots within imidazole glycerol phosphate synthase (ImGPS). ImGPS is a key metabolic enzyme complex, which links histidine and de novo purine biosynthesis and consists of the cyclase subunit HisF and the glutaminase subunit HisH. Initial fluorescence titration experiments showed that HisH from Zymomonas mobilis (zmHisH) binds with high affinity to the reconstructed HisF from the last universal common ancestor (LUCA-HisF) but not to HisF from Pyrobaculum arsenaticum (paHisF), which differ by 103 residues...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936488/ro52-trim21-deficient-expression-and-function-in-different-subsets-of-peripheral-blood-mononuclear-cells-is-associated-with-a-pro-inflammatory-cytokine-response-in-patients-with-idiopathic-inflammatory-myopathies
#20
D Gómez-Martín, A S Galindo-Feria, A Barrera-Vargas, J Merayo-Chalico, G Juárez-Vega, J Torres-Ruiz, J Alcocer-Varela
The presence of anti-Ro52/Trim21 autoantibodies has been associated with a distinctive clinical profile and has gained value as a prognostic marker in idiopathic inflammatory myopathies (IIM). The aim of the present work was to analyze Ro52/Trim21 expression in different subsets of peripheral blood mononuclear cells (PBMCs) of patients with IIM, as well as the ubiquitination profile and its association with pro-inflammatory cytokine production. We included 18 patients with recent onset IIM and 18 age and gender-matched healthy donors...
December 9, 2016: Clinical and Experimental Immunology
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