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https://www.readbyqxmd.com/read/28811664/structure-based-cross-docking-analysis-of-antibody-antigen-interactions
#1
Krishna Praneeth Kilambi, Jeffrey J Gray
Antibody-antigen interactions are critical to our immune response, and understanding the structure-based biophysical determinants for their binding specificity and affinity is of fundamental importance. We present a computational structure-based cross-docking study to test the identification of native antibody-antigen interaction pairs among cognate and non-cognate complexes. We picked a dataset of 17 antibody-antigen complexes of which 11 have both bound and unbound structures available, and we generated a representative ensemble of cognate and non-cognate complexes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808001/two-transmembrane-dimers-of-the-bovine-papillomavirus-e5-oncoprotein-clamp-the-pdgf-%C3%AE-receptor-in-an-active-dimeric-conformation
#2
Alexander G Karabadzhak, Lisa M Petti, Francisco N Barrera, Anne P B Edwards, Andrés Moya-Rodríguez, Yury S Polikanov, J Alfredo Freites, Douglas J Tobias, Donald M Engelman, Daniel DiMaio
The dimeric 44-residue E5 protein of bovine papillomavirus is the smallest known naturally occurring oncoprotein. This transmembrane protein binds to the transmembrane domain (TMD) of the platelet-derived growth factor β receptor (PDGFβR), causing dimerization and activation of the receptor. Here, we use Rosetta membrane modeling and all-atom molecular dynamics simulations in a membrane environment to develop a chemically detailed model of the E5 protein/PDGFβR complex. In this model, an active dimer of the PDGFβR TMD is sandwiched between two dimers of the E5 protein...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28792967/aminophosphinates-against-helicobacter-pylori-ureolysis-biochemical-and-whole-cell-inhibition-characteristics
#3
Katarzyna Macegoniuk, Ewa Grela, Monika Biernat, Mateusz Psurski, Grażyna Gościniak, Anna Dziełak, Artur Mucha, Joanna Wietrzyk, Łukasz Berlicki, Agnieszka Grabowiecka
Urease is an important virulence factor from Helicobacter pylori that enables bacterial colonization of human gastric mucosa. Specific inhibition of urease activity can be regarded as a promising adjuvant strategy for eradication of this pathogen. A group of organophosphorus inhibitors of urease, namely, aminophosphinic acid and aminophosphonic acid derivatives, were evaluated in vitro against H. pylori urease. The kinetic characteristics of recombinant enzyme activity demonstrated a competitive reversible mode of inhibition with Ki values ranging from 0...
2017: PloS One
https://www.readbyqxmd.com/read/28791861/in-vivo-multienzyme-complex-coconstruction-of-n-acetylneuraminic-acid-lyase-and-n-acetylglucosamine-2-epimerase-for-biosynthesis-of-n-acetylneuraminic-acid
#4
Zhenfu Wang, Wei Zhuang, Jian Cheng, Wujin Sun, Jinglan Wu, Yong Chen, Hanjie Ying
Metabolic channeling enables efficient transfer of the intermediates by forming a multienzyme complex. To leverage the metabolic channeling for improved biosynthesis, we coexpressed N-acetylneuraminic acid lyase from C. glutamicum ATCC 13032 (CgNal) and N-acetylglucosamine-2-epimerase from Anabaena sp. CH1 (anAGE) in Escherichia coli and used the whole cell to synthesize N-acetylneuraminic acid (Neu5Ac) from N-acetylglucosamine (GlcNAc) and pyruvate. To get the multienzyme complex, polycistronic plasmid with high levels of CgNal and anAGE expression was constructed by tuning the orders of the genes...
August 18, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28774292/rosetta-broker-for-membrane-protein-structure-prediction-concentrative-nucleoside-transporter-3-and-corticotropin-releasing-factor-receptor-1-test-cases
#5
Dorota Latek
BACKGROUND: Membrane proteins are difficult targets for structure prediction due to the limited structural data deposited in Protein Data Bank. Most computational methods for membrane protein structure prediction are based on the comparative modeling. There are only few de novo methods targeting that distinct protein family. In this work an example of such de novo method was used to structurally and functionally characterize two representatives of distinct membrane proteins families of solute carrier transporters and G protein-coupled receptors...
August 3, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28763012/performance-of-a-rt-pcr-assay-in-comparison-to-fish-and-immunohistochemistry-for-the-detection-of-alk-in-non-small-cell-lung-cancer
#6
David R Hout, Brock L Schweitzer, Kasey Lawrence, Stephan W Morris, Tracy Tucker, Rosetta Mazzola, Rachel Skelton, Frank McMahon, John Handshoe, Mary Lesperance, Aly Karsan, David L Saltman
Patients with lung cancers harboring an activating anaplastic lymphoma kinase (ALK) rearrangement respond favorably to ALK inhibitor therapy. Fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) are validated and widely used screening tests for ALK rearrangements but both methods have limitations. The ALK RGQ RT-PCR Kit (RT-PCR) is a single tube quantitative real-time PCR assay for high throughput and automated interpretation of ALK expression. In this study, we performed a direct comparison of formalin-fixed paraffin-embedded (FFPE) lung cancer specimens using all three ALK detection methods...
August 1, 2017: Cancers
https://www.readbyqxmd.com/read/28725265/two-bifunctional-enzymes-from-the-marine-protist-thraustochytrium-roseum-biochemical-characterization-of-wax-ester-synthase-acyl-coa-diacylglycerol-acyltransferase-activity-catalyzing-wax-ester-and-triacylglycerol-synthesis
#7
Nannan Zhang, Zejing Mao, Ling Luo, Xia Wan, Fenghong Huang, Yangmin Gong
BACKGROUND: Triacylglycerols (TAGs) and wax esters (WEs) are important neutral lipids which serve as energy reservoir in some plants and microorganisms. In recent years, these biologically produced neutral lipids have been regarded as potential alternative energy sources for biofuel production because of the increased interest on developing renewable and environmentally benign alternatives for fossil fuels. In bacteria, the final step in TAG and WE biosynthetic pathway is catalyzed by wax ester synthase/acyl coenzyme A (acyl-CoA):diacylglycerol acyltransferase (WS/DGAT)...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28723607/production-of-recombinant-porin-from-y-pseudotuberculosis-in-a-water-soluble-form-for-pseudotuberculosis-diagnostics
#8
Vasily A Golotin, Olga Y Portnyagina, Natalia S Chopenko, Natalia Y Kim, Valery A Rasskazov, Olga D Novikova
OmpF porin from the outer membrane of Yersinia pseudotuberculosis was cloned into pET-40b(+) plasmid. Using E. coli Rosetta (DE3) strain, MX-medium, IPTG concentration of 0.2 mM and post-induction cultivation at 14 °C overnight allowed us to obtain a water-soluble form of the recombinant protein (rs-OmpF). Rs-OmpF was shown to have the ordered spatial structure at the levels of secondary and tertiary structure. Rs-OmpF was found to be effective as diagnostic antigen in ELISA for pseudotuberculosis diagnostics...
July 26, 2017: Biological Chemistry
https://www.readbyqxmd.com/read/28718923/using-homology-modeling-to-interrogate-binding-affinity-in-neutralization-of-ricin-toxin-by-a-family-of-single-domain-antibodies
#9
Andrea Bazzoli, David J Vance, Michael J Rudolph, Yinghui Rong, Siva Krishna Angalakurthi, Ronald T Toth, C Russell Middaugh, David B Volkin, David D Weis, John Karanicolas, Nicholas J Mantis
In this report we investigated, within a group of closely related single domain camelid antibodies (VH Hs), the relationship between binding affinity and neutralizing activity as it pertains to ricin, a fast-acting toxin and biothreat agent. The V1C7-like VH Hs (V1C7, V2B9, V2E8, and V5C1) are similar in amino acid sequence, but differ in their binding affinities and toxin-neutralizing activities. Using the X-ray crystal structure of V1C7 in complex with ricin's enzymatic subunit (RTA) as a template, Rosetta-based homology modeling coupled with energetic decomposition led us to predict that a single pairwise interaction between Arg29 on V5C1 and Glu67 on RTA was responsible for the difference in ricin toxin binding affinity between V1C7, a weak neutralizer, and V5C1, a moderate neutralizer...
July 18, 2017: Proteins
https://www.readbyqxmd.com/read/28682144/structural-modeling-of-human-cardiac-sodium-channel-pore-domain
#10
Xiaofeng Ji, Yi Xiao, Shiyong Liu
The pore domain of human voltage-dependent cardiac sodium channel Nav1.5 (hNav1.5) is the crucial binding targets for antiarrhythmic drugs and some local anesthetic drugs but its three-dimensional structure is still lacking. This has affected the detailed studies of the binding features and mechanism of these drugs. In this paper, we present a structural model for open-state pore domain of hNav1.5 built by using single template ROSETTA-membrane homology modeling with the crystal structure of NavMs. The assembled structural models are evaluated by rosettaMP energy and locations of binding sites...
July 6, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28675858/mentalization-in-adults-with-attention-deficit-hyperactivity-disorder-comparison-with-controls-and-patients-with-borderline-personality-disorder
#11
Nader Perroud, Deborah Badoud, Sébastien Weibel, Rosetta Nicastro, Roland Hasler, Anne-Lise Küng, Patrick Luyten, Peter Fonagy, Alexandre Dayer, Jean-Michel Aubry, Paco Prada, Martin Debbané
Emotion dysregulation and interpersonal hardships constitute core features of borderline personality disorder (BPD). Research has established the link between these core dysregulations and fluctuations in the capacity to appreciate the mental states that underlie behavior (mentalizing, operationalized as reflective functioning (RF)). As emotion dysregulation and interpersonal hardships also characterize adults with attention deficit hyperactivity disorder (ADHD), this study sought to examine the potential RF impairments affecting this population...
June 30, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28671122/rosetta-stone-for-amyloid-fibrils-the-key-role-of-ring-like-oligomers-in-amyloidogenesis
#12
Oxana V Galzitskaya, Olga M Selivanova
Deeper understanding of processes of protein misfolding, aggregation, formation of oligomers, protofibrils, and fibrils is crucial for the development of future medicine in treatment of amyloid-related diseases. While numerous reports illuminate the field, the above processes are extremely complex, as they depend on many varying parameters, such as the peptide concentration, temperature, pH, presence of metal ions, lipids, and organic solvents. Different mechanisms of amyloid fibril formation have been proposed, but the process of the oligomer-to-fibril transition is the least agreed upon...
2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28661426/rational-design-of-recombinant-papain-like-cysteine-protease-optimal-domain-structure-and-expression-conditions-for-wheat-derived-enzyme-triticain-%C3%AE
#13
Neonila V Gorokhovets, Vladimir A Makarov, Anastasiia I Petushkova, Olga S Prokopets, Mikhail A Rubtsov, Lyudmila V Savvateeva, Evgeni Yu Zernii, Andrey A Zamyatnin
Triticain-α is a papain-like cysteine protease from wheat (Triticumaestivum L.) that possesses activity towards toxic gluten-derived peptides, and was thus proposed as a novel therapeutic tool for celiac disease. We report an original approach employing rational design of domain architecture of Triticain-α and selection of the appropriate expression system for development of cheap and efficient protocol yielding active recombinant enzyme. The segregated catalytic domain of Triticain-α did not adopt native structure in bacteria, neither being expressed as a single protein nor upon conjugation or co-expression with extrinsic chaperones...
June 29, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28641560/functional-and-catalytic-characterization-of-the-detoxifying-enzyme-haloalkane-dehalogenase-from-rhizobium-leguminosarum
#14
Nikolaos Georgakis, Evangelia Chronopoulou, Maria Anna Gad, Dimitrios Skliros, Rodica Efrose, Emmanouil Flemetakis, Nikolaos E Labrou
Haloalkanes are acutely toxic to animals and humans and their toxic effects are mainly observed in the liver, kidneys and central nervous system. In the present work, the haloalkane dehalogenase from Rhizobium leguminosarum bv. trifolii (DrlA) was characterized. Reverse transcription polymerase chain reaction analysis and enzyme activity assays revealed that the DrlA gene expression in R. leguminosarum bv. trifolii is induced by 1,2-dibromoethane (1,2-DBE) during the early exponential phase. The gene of the enzyme was isolated, cloned and expressed in E...
June 20, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28630421/a-genome-wide-association-study-of-anorexia-nervosa-suggests-a-risk-locus-implicated-in-dysregulated-leptin-signaling
#15
Dong Li, Xiao Chang, John J Connolly, Lifeng Tian, Yichuan Liu, Elizabeth J Bhoj, Nora Robinson, Debra Abrams, Yun R Li, Jonathan P Bradfield, Cecilia E Kim, Jin Li, Fengxiang Wang, James Snyder, Maria Lemma, Cuiping Hou, Zhi Wei, Yiran Guo, Haijun Qiu, Frank D Mentch, Kelly A Thomas, Rosetta M Chiavacci, Roger Cone, Bingshan Li, Patrick A Sleiman, Hakon Hakonarson
We conducted a genome-wide association study (GWAS) of anorexia nervosa (AN) using a stringently defined phenotype. Analysis of phenotypic variability led to the identification of a specific genetic risk factor that approached genome-wide significance (rs929626 in EBF1 (Early B-Cell Factor 1); P = 2.04 × 10(-7); OR = 0.7; 95% confidence interval (CI) = 0.61-0.8) with independent replication (P = 0.04), suggesting a variant-mediated dysregulation of leptin signaling may play a role in AN...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28628127/rosettaes-a-sampling-strategy-enabling-automated-interpretation-of-difficult-cryo-em-maps
#16
Brandon Frenz, Alexandra C Walls, Edward H Egelman, David Veesler, Frank DiMaio
Accurate atomic modeling of macromolecular structures into cryo-electron microscopy (cryo-EM) maps is a major challenge, as the moderate resolution makes accurate placement of atoms difficult. We present Rosetta enumerative sampling (RosettaES), an automated tool that uses a fragment-based sampling strategy for de novo model completion of macromolecular structures from cryo-EM density maps at 3-5-Å resolution. On a benchmark set of nine proteins, RosettaES was able to identify near-native conformations in 85% of segments...
August 2017: Nature Methods
https://www.readbyqxmd.com/read/28616446/treatment-with-anti-fc%C3%AE%C2%B5ri%C3%AE-antibody-exacerbates-eae-and-t-cell-immunity-against-myelin
#17
Silvia Musio, Massimo Costanza, Pietro Luigi Poliani, Elena Fontana, Manuela Cominelli, Gabriella Abolafio, Lawrence Steinman, Rosetta Pedotti
OBJECTIVE: To investigate the effects of targeting the high-affinity receptor for immunoglobulin E (FcεRI), that plays a central role in allergic responses and is constitutively expressed on mast cells and basophils, in clinical disease and autoimmune T-cell response in experimental MS. METHODS: Experimental autoimmune encephalomyelitis (EAE) was induced in C57BL/6 mice by immunization with myelin oligodendrocyte glycoprotein 35-55. Anti-FcεRI α-chain antibody was administered intraperitoneally...
May 2017: Neurology® Neuroimmunology & Neuroinflammation
https://www.readbyqxmd.com/read/28604768/rosetta-msf-a-modular-framework-for-multi-state-computational-protein-design
#18
Patrick Löffler, Samuel Schmitz, Enrico Hupfeld, Reinhard Sterner, Rainer Merkl
Computational protein design (CPD) is a powerful technique to engineer existing proteins or to design novel ones that display desired properties. Rosetta is a software suite including algorithms for computational modeling and analysis of protein structures and offers many elaborate protocols created to solve highly specific tasks of protein engineering. Most of Rosetta's protocols optimize sequences based on a single conformation (i. e. design state). However, challenging CPD objectives like multi-specificity design or the concurrent consideration of positive and negative design goals demand the simultaneous assessment of multiple states...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28602734/molecular-characterization-and-gene-expression-of-cathepsin-l-in-nile-tilapia-oreochromis-niloticus
#19
Fu-Rui Liang, Yue-Hui Hong, Cong-Cong Ye, Hailin Deng, Jian-Ping Yuan, Yun-Fang Hao, Jiang-Hai Wang
Cathepsin L (CatL) has been widely known for its involvement in the innate immunity. However, it still remains poorly understand how CatL modulates the immune system of teleosts. Moreover, the CatL of Nile tilapia (NtCatL) has not been cloned or characterized. In this study, the gene encoding NtCatL was cloned, and was characterized by bioinformatics analysis, heterologous expression and protease activity assay. The coding sequence of NtCatL is 1017 bp in length and encodes 338 amino acid residues with a predicted molecular weight of 38...
August 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28601956/subjective-distress-associated-with-adult-adhd-evaluation-of-a-new-self-report
#20
Rosetta Nicastro, Martin Desseilles, Paco Prada, Sébastien Weibel, Nader Perroud, Marianne Gex-Fabry
The current study aims at documenting the psychometric properties of the Subjective Distress Associated with Adult ADHD-Self-Report (SDAAA-SR), a newly developed instrument for the assessment of psychological suffering in ADHD adults. The SDAAA-SR was administered to 247 students and 142 ADHD adults. Factor structure, internal consistency, test-retest reliability, convergent validity and discriminant validity were assessed. Sensitivity to change was examined in a subsample of 25 ADHD patients who participated in a 1-year therapy...
June 10, 2017: Attention Deficit and Hyperactivity Disorders
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