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Rosetta protein

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https://www.readbyqxmd.com/read/29336241/generation-of-the-fluorescent-hpv16-e7-protein-for-detection-of-delivery-in-vitro
#1
Sepideh Shahbazi, Azam Bolhassani, Arash Arashkia, Esmaeil Sadroddiny
Immunotherapies targeting the human papillomavirus (HPV) oncogenic proteins, E6 and E7, are effective to treat HPV-associated cervical malignancies. In this study, two types of the fusion E7-GFP proteins (i.e., with or without linker) were expressed in different E. coli strains. Then, the efficiency of GFP and E7-GFP transfection was compared with FITC-antibody protein control using TurboFect reagent in the HEK-293T cell line. Our data indicated that both E7-GFP fusion proteins were efficiently produced in M15 E...
January 15, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/29295930/identification-of-a-ubiquitin-binding-interface-using-rosetta-and-deer
#2
Maxx H Tessmer, David M Anderson, Adam M Pickrum, Molly O Riegert, Rocco Moretti, Jens Meiler, Jimmy B Feix, Dara W Frank
ExoU is a type III-secreted cytotoxin expressing A2 phospholipase activity when injected into eukaryotic target cells by the bacterium Pseudomonas aeruginosa The enzymatic activity of ExoU is undetectable in vitro unless ubiquitin, a required cofactor, is added to the reaction. The role of ubiquitin in facilitating ExoU enzymatic activity is poorly understood but of significance for designing inhibitors to prevent tissue injury during infections with strains of P. aeruginosa producing this toxin. Most ubiquitin-binding proteins, including ExoU, demonstrate a low (micromolar) affinity for monoubiquitin (monoUb)...
January 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29281622/high-resolution-global-peptide-protein-docking-using-fragments-based-piper-flexpepdock
#3
Nawsad Alam, Oriel Goldstein, Bing Xia, Kathryn A Porter, Dima Kozakov, Ora Schueler-Furman
Peptide-protein interactions contribute a significant fraction of the protein-protein interactome. Accurate modeling of these interactions is challenging due to the vast conformational space associated with interactions of highly flexible peptides with large receptor surfaces. To address this challenge we developed a fragment based high-resolution peptide-protein docking protocol. By streamlining the Rosetta fragment picker for accurate peptide fragment ensemble generation, the PIPER docking algorithm for exhaustive fragment-receptor rigid-body docking and Rosetta FlexPepDock for flexible full-atom refinement of PIPER docked models, we successfully addressed the challenge of accurate and efficient global peptide-protein docking at high-resolution with remarkable accuracy, as validated on a small but representative set of peptide-protein complex structures well resolved by X-ray crystallography...
December 27, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29250820/a-computational-method-for-the-design-of-nested-proteins-by-loop-directed-domain-insertion
#4
Kristin Blacklock, Lu Yang, Vikram K Mulligan, Sagar D Khare
The computational design of novel nested proteins - in which the primary structure of one protein domain (insert) is flanked by the primary structure segments of another (parent) - would enable the generation of multifunctional proteins. Here we present a new algorithm, called Loop-Directed Domain Insertion (LooDo), implemented within the Rosetta software suite, for the purpose of designing nested protein domain combinations connected by flexible linker regions. Conformational space for the insert domain is sampled using large libraries of linker fragments for linker-to-parent domain superimposition followed by insert-to-linker superimposition...
December 18, 2017: Proteins
https://www.readbyqxmd.com/read/29216185/a-cyber-linked-undergraduate-research-experience-in-computational-biomolecular-structure-prediction-and-design
#5
Rebecca F Alford, Andrew Leaver-Fay, Lynda Gonzales, Erin L Dolan, Jeffrey J Gray
Computational biology is an interdisciplinary field, and many computational biology research projects involve distributed teams of scientists. To accomplish their work, these teams must overcome both disciplinary and geographic barriers. Introducing new training paradigms is one way to facilitate research progress in computational biology. Here, we describe a new undergraduate program in biomolecular structure prediction and design in which students conduct research at labs located at geographically-distributed institutions while remaining connected through an online community...
December 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29160840/cloning-and-molecular-characterization-of-an-alpha-glucosidase-malh-from-the-halophilic-archaeon-haloquadratum-walsbyi
#6
Mara F Cuebas-Irizarry, Ricardo A Irizarry-Caro, Carol López-Morales, Keyla M Badillo-Rivera, Carlos M Rodríguez-Minguela, Rafael Montalvo-Rodríguez
We report the heterologous expression and molecular characterization of the first extremely halophilic alpha-glucosidase (EC 3.2.1.20) from the archaeon Haloquadratum walsbyi. A 2349 bp region (Hqrw_2071) from the Hqr. walsbyi C23 annotated genome was PCR-amplified and the resulting amplicon ligated into plasmid pET28b(+), expressed in E. coli Rosetta cells, and the resulting protein purified by Ni-NTA affinity chromatography. The recombinant protein showed an estimated molecular mass of 87 kDa, consistent with the expected value of the annotated protein, and an optimal activity for the hydrolysis of α-PNPG was detected at 40 °C, and at pH 6...
November 21, 2017: Life
https://www.readbyqxmd.com/read/29155876/docking-analysis-and-the-possibility-of-prediction-efficacy-for-an-anti-il-13-biopharmaceutical-treatment-with-tralokinumab-and-lebrikizumab-for-bronchial-asthma
#7
Yutaka Nakamura, Aki Sugano, Mika Ohta, Yutaka Takaoka
Interleukin-13 (IL-13) is associated with allergic airway inflammation and airway remodeling. Our group found a variant with a single nucleotide polymorphism in the IL13 gene at position +2044G>A (rs20541) that was expected to result in the non-conservative replacement of a positively charged arginine (R) with a neutral glutamine (Q) at position 144. IL-13Q144 was associated with augmented allergic airway inflammation and bronchial asthma remodeling. There is some indication that anti-IL-13 monoclonal antibodies can demonstrate a positive effect on the clinical course of refractory asthmatic patients...
2017: PloS One
https://www.readbyqxmd.com/read/29151205/filamentous-bacteriophage-viruses-preparation-magic-angle-spinning-solid-state-nmr-experiments-and-structure-determination
#8
Omry Morag, Nikolaos G Sgourakis, Gili Abramov, Amir Goldbourt
Filamentous bacteriophages are elongated semi-flexible viruses that infect bacteria. They consist of a circular single-stranded DNA (ssDNA) wrapped by a capsid consisting of thousands of copies of a major coat protein subunit. Given the increasing number of discovered phages and the existence of only a handful of structures, the development of methods for phage structure determination is valuable for biophysics and structural virology. In recent years, we developed and applied techniques to elucidate the 3D atomic-resolution structures of intact bacteriophages using experimental magic-angle spinning (MAS) solid-state NMR data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29148426/stabilization-and-structural-analysis-of-a-membrane-associated-hiapp-aggregation-intermediate
#9
Diana C Rodriguez Camargo, Kyle J Korshavn, Alexander Jussupow, Kolio Raltchev, David Goricanec, Markus Fleisch, Riddhiman Sarkar, Kai Xue, Michaela Aichler, Gabriele Mettenleiter, Axel Karl Walch, Carlo Camilloni, Franz Hagn, Bernd Reif, Ayyalusamy Ramamoorthy
Membrane-assisted amyloid formation is implicated in human diseases, and many of the aggregating species accelerate amyloid formation and induce cell death. While structures of membrane-associated intermediates would provide tremendous insights into the pathology and aid in the design of compounds to potentially treat the diseases, it has not been feasible to overcome the challenges posed by the cell membrane. Here we use NMR experimental constraints to solve the structure of a type-2 diabetes related human islet amyloid polypeptide intermediate stabilized in nanodiscs...
November 17, 2017: ELife
https://www.readbyqxmd.com/read/29146152/improved-antifungal-activity-of-barley-derived-chitinase-i-gene-that-overexpress-a-32kda-recombinant-chitinase-in-escherichia-coli-host
#10
Nida Toufiq, Bushra Tabassum, Muhammad Umar Bhatti, Anwar Khan, Muhammad Tariq, Naila Shahid, Idrees Ahmad Nasir, Tayyab Husnain
Agricultural crops suffer many diseases, including fungal and bacterial infections, causing significant yield losses. The identification and characterisation of pathogenesis-related protein genes, such as chitinases, can lead to reduction in pathogen growth, thereby increasing tolerance against fungal pathogens. In the present study, the chitinase I gene was isolated from the genomic DNA of Barley (Hordeum vulgare L.) cultivar, Haider-93. The isolated DNA was used as template for the amplification of the ∼935bp full-length chitinase I gene...
October 31, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29090504/computational-design-of-membrane-proteins-using-rosettamembrane
#11
Amanda M Duran, Jens Meiler
Computational membrane protein design is challenging due to the small number of high-resolution structures available to elucidate the physical basis of membrane protein structure, multiple functionally important conformational states, and a limited number of high-throughput biophysical assays to monitor function. However, structural determination of membrane proteins has made tremendous progress in the past years. Concurrently the field of soluble computational design has made impressive inroads. These developments allow us to tackle the formidable challenge of designing functional membrane proteins...
November 1, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28976747/purification-and-characterization-of-rhopde-a-retinylidene-phosphodiesterase-fusion-protein-and-potential-optogenetic-tool-from-the-choanoflagellate-salpingoeca-rosetta
#12
Lindsey B Lamarche, Ramasamy P Kumar, Melissa M Trieu, Erin L Devine, Luke E Cohen-Abeles, Douglas L Theobald, Daniel D Oprian
RhoPDE is a type I rhodopsin/phosphodiesterase gene fusion product from the choanoflagellate Salpingoeca rosetta. The gene was discovered around the time that a similar type I rhodopsin/guanylyl cyclase fusion protein, RhoGC, was shown to control phototaxis of an aquatic fungus through a cGMP signaling pathway. RhoPDE has potential as an optogenetic tool catalyzing the hydrolysis of cyclic nucleotides. Here we provide an expression and purification system for RhoPDE, as well as a crystal structure of the C-terminal phosphodiesterase catalytic domain...
October 31, 2017: Biochemistry
https://www.readbyqxmd.com/read/28973862/de-novo-design-of-covalently-constrained-mesosize-protein-scaffolds-with-unique-tertiary-structures
#13
Bobo Dang, Haifan Wu, Vikram Khipple Mulligan, Marco Mravic, Yibing Wu, Thomas Lemmin, Alexander Ford, Daniel-Adriano Silva, David Baker, William F DeGrado
The folding of natural proteins typically relies on hydrophobic packing, metal binding, or disulfide bond formation in the protein core. Alternatively, a 3D structure can be defined by incorporating a multivalent cross-linking agent, and this approach has been successfully developed for the selection of bicyclic peptides from large random-sequence libraries. By contrast, there is no general method for the de novo computational design of multicross-linked proteins with predictable and well-defined folds, including ones not found in nature...
October 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28968726/graddock-rapid-simulation-and-tailored-ranking-functions-for-peptide-mhc-class-i-docking
#14
Hyun-Ho Kyeong, Yoonjoo Choi, Hak-Sung Kim
Motivation: The identification of T-cell epitopes has many profound translational applications in the areas of transplantation, disease diagnosis, vaccine/therapeutic protein development and personalized immunotherapy. While data-driven methods have been widely used for the prediction of peptide binders with notable successes, the structural modeling of peptide binding to MHC molecules is crucial for understanding the underlying molecular mechanism of the immunological processes. Results: We developed GradDock, a structure-based method for the rapid and accurate modeling of peptide binding to MHC class I (pMHC-I)...
September 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28968723/ccfold-rapid-and-accurate-prediction-of-coiled-coil-structures-and-application-to-modeling-intermediate-filaments
#15
Dmytro Guzenko, Sergei V Strelkov
Motivation: Accurate molecular structure of the protein dimer representing the elementary building block of intermediate filaments (IFs) is essential towards the understanding of the filament assembly, rationalizing their mechanical properties and explaining the effect of disease-related IF mutations. The dimer contains a ~300-residue long α-helical coiled coil which cannot be assessed by either direct experimental structure determination or modelling using standard approaches. At the same time, coiled coils are well-represented in structural databases...
September 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28960691/web-accessible-molecular-modeling-with-rosetta-the-rosetta-online-server-that-includes-everyone-rosie
#16
Rocco Moretti, Sergey Lyskov, Rhiju Das, Jens Meiler, Jeffrey J Gray
The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called Rosetta Online Server that Includes Everyone (ROSIE), which provides a common environment for hosting web-accessible Rosetta protocols...
September 28, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28959351/cloning-overexpression-and-in-vitro-antifungal-activity-of-zea-mays-pr10-protein
#17
Niloofar Zandvakili, Mohammadreza Zamani, Mostafa Motallebi, Zahra Moghaddassi Jahromi
BACKGROUND: Plants have various defense mechanisms such as production of antimicrobial peptides, particularly pathogenesis related proteins (PR proteins). PR10 family is an essential member of this group, with antifungal, antibacterial and antiviral activities. OBJECTIVE: The goal of this study is to assess the antifungal activity of maize PR10 against some of fungal phytopathogens. MATERIALS AND METHODS: Zea mays PR10 gene (TN-05-147) was cloned from genomic DNA and cDNA and overexpressed in Escherichia coli...
March 2017: Iranian Journal of Biotechnology
https://www.readbyqxmd.com/read/28949136/iterative-molecular-dynamics-rosetta-membrane-protein-structure-refinement-guided-by-cryo-em-densities
#18
Sumudu P Leelananda, Steffen Lindert
Knowing atomistic details of proteins is essential not only for the understanding of protein function but also for the development of drugs. Experimental methods such as X-ray crystallography, NMR, and cryo-electron microscopy (cryo-EM) are the preferred forms of protein structure determination and have achieved great success over the most recent decades. Computational methods may be an alternative when experimental techniques fail. However, computational methods are severely limited when it comes to predicting larger macromolecule structures with little sequence similarity to known structures...
October 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28940798/protein-structure-prediction-using-rosetta-in-casp12
#19
Sergey Ovchinnikov, Hahnbeom Park, David E 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
#20
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
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