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https://www.readbyqxmd.com/read/28940798/protein-structure-prediction-using-rosetta-in-casp12
#1
Sergey Ovchinnikov, Hahnbeom Park, David Kim, Frank DiMaio, David Baker
We describe several notable aspects of our structure predictions using Rosetta in CASP12 in the free modeling (FM) and refinement (TR) categories. First, we had previously generated (and published) models for most large protein families lacking experimentally determined structures using Rosetta guided by co-evolution based contact predictions, and for several targets these models proved better starting points for comparative modeling than any known crystal structure-our model database thus starts to fulfill one of the goals of the original protein structure initiative...
September 22, 2017: Proteins
https://www.readbyqxmd.com/read/28934318/identification-of-lag3-high-affinity-aptamers-by-ht-selex-and-conserved-motif-accumulation-cma
#2
Mario Martínez Soldevilla, Sandra Hervas, Helena Villanueva, Teresa Lozano, Obdulia Rabal, Julen Oyarzabal, Juan José Lasarte, Maurizio Bendandi, Susana Inoges, Ascensión López-Díaz de Cerio, Fernando Pastor
LAG3 receptor belongs to a family of immune-checkpoints expressed in T lymphocytes and other cells of the immune system. It plays an important role as a rheostat of the immune response. Focus on this receptor as a potential therapeutic target in cancer immunotherapy has been underscored after the success of other immune-checkpoint blockade strategies in clinical trials. LAG3 showcases the interest in the field of autoimmunity as several studies show that LAG3-targeting antibodies can also be used for the treatment of autoimmune diseases...
2017: PloS One
https://www.readbyqxmd.com/read/28927835/evaluation-of-rice-tetraticopeptide-domain-containing-thioredoxin-as-a-novel-solubility-enhancing-fusion-tag-in-escherichia-coli
#3
Wenjun Xiao, Li Jiang, Weiyu Wang, Ruyue Wang, Jun Fan
Fusion of solubility-enhancing tag is frequently used for improving soluble production of target protein in Escherichia coli. The Arabidopsis tetraticopeptide domain-containing thioredoxin (TDX) has been documented to exhibit functions of disulfide reductase, foldase chaperone, and holdase chaperone. Here, we identified that fusion of rice TDX with the smaller size increased soluble expression levels of three fluorescent proteins with different fluorophores in the E. coli strain BL21(DE3) or the Rosetta (DE3) strain with coexpression of six rare tRNAs, but decreased conformational quality of certain fluorescent proteins, as comparison with the His6-tagged ones...
September 15, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28923896/experimental-and-theoretical-approaches-to-investigate-the-immunogenicity-of-taenia-solium-derived-ke7-antigen
#4
Raúl J Bobes, José Navarrete-Perea, Adrián Ochoa-Leyva, Víctor Hugo Anaya, Marisela Hernández, Jacquelynne Cervantes-Torres, Karel Estrada, Filiberto Sánchez-Lopez, Xavier Soberón, Gabriela Rosas, Cáris Maroni Nunes, Martín García-Varela, Rogerio Rafael Sotelo-Mundo, Alonso Alexis López-Zavala, Goar Gevorkian, Gonzalo Acero, Juan P Laclette, Gladis Fragoso, Edda Sciutto
Taenia solium cysticercosis, a parasitic disease that affects human health in various regions of the world, is preventable by vaccination. Both the 97-amino-acid-long KETc7 peptide and its carboxyl-terminal, 18-amino-acid-long sequence (GK-1) are found in Taenia crassiceps Both peptides, with proven protective capacity against cysticercosis, are part of the highly conserved, cestode-native, 264-amino-acid long protein KE7. KE7 belongs to a ubiquitously distributed family of proteins associated to membrane processes and may participate in several vital cell pathways...
September 18, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28922368/a-tree-of-life-based-on-ninety-eight-expressed-genes-conserved-across-diverse-eukaryotic-species
#5
Pawan Kumar Jayaswal, Vivek Dogra, Asheesh Shanker, Tilak Raj Sharma, Nagendra Kumar Singh
Rapid advances in DNA sequencing technologies have resulted in the accumulation of large data sets in the public domain, facilitating comparative studies to provide novel insights into the evolution of life. Phylogenetic studies across the eukaryotic taxa have been reported but on the basis of a limited number of genes. Here we present a genome-wide analysis across different plant, fungal, protist, and animal species, with reference to the 36,002 expressed genes of the rice genome. Our analysis revealed 9831 genes unique to rice and 98 genes conserved across all 49 eukaryotic species analysed...
2017: PloS One
https://www.readbyqxmd.com/read/28885157/conformational-space-sampling-method-using-multi-subpopulation-differential-evolution-for-de-novo-protein-structure-prediction
#6
Xiao-Hu Hao, Gui-Jun Zhang, Xiao-Gen Zhou
Protein structure prediction can be considered as a multimodal optimization problem for sampling the protein conformational space associated with an extremely complex energy landscape. To address this problem, a conformational space sampling method using multi-subpopulation differential evolution, MDE, is proposed. MDE first devotes to generate given numbers of concerned modal under the ultrafast shape recognition based modal identification protocol, which regards each individual as one modal at beginning. Then, differential evolution is used for keeping the preserved modal survival in the evolution process...
September 5, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28867285/mating-in-the-closest-living-relatives-of-animals-is-induced-by-a-bacterial-chondroitinase
#7
Arielle Woznica, Joseph P Gerdt, Ryan E Hulett, Jon Clardy, Nicole King
We serendipitously discovered that the marine bacterium Vibrio fischeri induces sexual reproduction in one of the closest living relatives of animals, the choanoflagellate Salpingoeca rosetta. Although bacteria influence everything from nutrition and metabolism to cell biology and development in eukaryotes, bacterial regulation of eukaryotic mating was unexpected. Here, we show that a single V. fischeri protein, the previously uncharacterized EroS, fully recapitulates the aphrodisiac-like activity of live V...
September 7, 2017: Cell
https://www.readbyqxmd.com/read/28861634/novel-one-pot-atp-regeneration-system-based-on-three-enzyme-cascade-for-industrial-ctp-production
#8
Junzhi Wang, Cheng Zheng, Tianyi Zhang, Yingmiao Liu, Zhuopei Cheng, Dong Liu, Hanjie Ying, Huanqing Niu
OBJECTIVES: To develop a new one-pot polyphosphate kinase (PPK) system with low cost and high efficiency for ATP regeneration in industrial CTP production. RESULTS: We developed a new one-pot PPK system by applying a three-enzyme cascade (CMK, NDK and PPK) with an in vitro polyP-based ATP regeneration system. The PPK was selected from twenty sources, and was made solvable by fusion expressing with soluble protein and constructing polycistronic plasmids, or co-expressing with molecular chaperones GroES/EL...
August 31, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/28843817/a-novel-resistance-gene-lnu-h-confers-resistance-to-lincosamides-inriemerella-anatipestiferch-2
#9
Hong-Yan Luo, Ma-Feng Liu, Ming-Shu Wang, Xin-Xin Zhao, Ren-Yong Jia, Shun Chen, Kun-Feng Sun, Qiao Yang, Ying Wu, Xiao-Yue Chen, Francis Biville, Yuan-Feng Zou, Bo Jing, An-Chun Cheng, De-Kang Zhu
The Gram-negative bacteria Riemerella anatipestifer CH-2 is resistant to lincosamide (the MIC value of lincomycin is 128 µg/ml). The G148_1775 gene of R. anatipestifer CH-2, designated lnu(H), encodes a 260-amino-acid protein with ≤ 41% identity to other reported lincosamide nucleotidyltransferases. The E. coli Rosetta (DE3) containing pBAD24-lnu(H) plasmid showed 4- and 2-fold increases in lincomycin and clindamycin MICs, respectively. A kinetic assay of the purified Lnu(H) enzyme for lincomycin and clindamycin showed that the protein could inactive lincosamides...
August 23, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/28827102/shuffle%C3%A2-t7-strain-is-capable-of-producing-high-amount-of-recombinant-human-fibroblast-growth-factor-1-rhfgf-1-with-proper-physicochemical-and-biological-properties
#10
Marzieh Nasiri, Jalal Babaie, Samira Amiri, Ebrahim Azimi, Shiva Shamshiri, Vahid Khalaj, Majid Golkar, Pezhman Fard-Esfahani
BACKGROUND: Human fibroblast growth factor-1 (FGF-1) has powerful mitogenic activities in a variety of cell types and plays significant roles in many physiological processes e.g. angiogenesis and wound healing. There is increasing demand for large scale production of recombinant human FGF-1 (rhFGF-1), in order to investigate the potential medical use. In the present study, we explored SHuffle™ T7 strain for production of rhFGF-1. METHODS: A synthetic gene encoding Met-140 amino acid form of human FGF-1 was utilized for expression of the protein in three different E...
August 18, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28826489/acidic-c-terminal-domains-autoregulate-the-rna-chaperone-hfq
#11
Andrew Santiago-Frangos, Jeliazko R Jeliazkov, Jeffrey J Gray, Sarah A Woodson
The RNA chaperone Hfq is an Sm protein that facilitates base pairing between bacterial small RNAs (sRNAs) and mRNAs involved in stress response and pathogenesis. Hfq possesses an intrinsically disordered C-terminal domain (CTD) that may tune the function of the Sm domain in different organisms. In Escherichia coli, the Hfq CTD increases kinetic competition between sRNAs and recycles Hfq from the sRNA-mRNA duplex. Here, de novo Rosetta modeling and competitive binding experiments show that the acidic tip of the E...
August 9, 2017: ELife
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
#12
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 29, 2017: Proceedings of the National Academy of Sciences of the United States of America
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
#13
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/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
#14
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
#15
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/28671122/rosetta-stone-for-amyloid-fibrils-the-key-role-of-ring-like-oligomers-in-amyloidogenesis
#16
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
#17
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/28628127/rosettaes-a-sampling-strategy-enabling-automated-interpretation-of-difficult-cryo-em-maps
#18
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
#19
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
#20
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
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