keyword
MENU ▼
Read by QxMD icon Read
search

Rosetta

keyword
https://www.readbyqxmd.com/read/29151205/filamentous-bacteriophage-viruses-preparation-magic-angle-spinning-solid-state-nmr-experiments-and-structure-determination
#1
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/29149090/computational-methods-for-modeling-aptamers-and-designing-riboswitches
#2
REVIEW
Sha Gong, Yanli Wang, Zhen Wang, Wenbing Zhang
Riboswitches, which are located within certain noncoding RNA region perform functions as genetic "switches", regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the aptamer domains. Although aptamers often form a complex structure, computational approaches, such as RNAComposer and Rosetta, have already been applied to model the tertiary (three-dimensional (3D)) structure for several aptamers...
November 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29148426/stabilization-and-structural-analysis-of-a-membrane-associated-hiapp-aggregation-intermediate
#3
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
#4
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/29123148/radiological-investigation-of-high-background-radiation-areas
#5
Fawzia Mubarak, M Fayez-Hassan, N A Mansour, Talaat Salah Ahmed, Abdallah Ali
In this paper, we used the Hyper-Pure Germanium (HPGe) detector to measure 30 samples which are collected from north of Nile Delta near Rosetta beach in Egypt. The activity of primordial radionuclides, such as (238)U, (235)U, (232)Th, and (40)K was estimated. Concentrations ranged between 36.5-177.4, 50-397.5 and 56.1-168.9 Bq.kg(-1) for (238)U, (232)Th and (40)K respectively. Activity concentration of (235)U and the variation in uranium isotopic ratio (235)U/(238)U was calculated. External hazard indices (Hex) (or radium equivalent activity Raeq), activity concentration indices (I), alpha index (Iα), absorbed outdoor gamma dose rate (Dout), effective outdoor gamma dose rate (Eout) and Excess Lifetime Cancer Risk (ELCR) due to different samples are estimated...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29122431/nonsurgical-strategies-to-reduce-mortality-in-patients-undergoing-cardiac-surgery-an-updated-consensus-process
#6
Giovanni Landoni, Vladimir Lomivorotov, Simona Silvietti, Caetano Nigro Neto, Antonio Pisano, Gabriele Alvaro, Ludmilla Abrahao Hajjar, Gianluca Paternoster, Hynek Riha, Fabrizio Monaco, Andrea Szekely, Rosalba Lembo, Nesrin A Aslan, Giovanni Affronti, Valery Likhvantsev, Cristiano Amarelli, Evgeny Fominskiy, Martina Baiardo Redaelli, Alessandro Putzu, Massimo Baiocchi, Jun Ma, Giuseppe Bono, Valentina Camarda, Remo Daniel Covello, Nora Di Tomasso, Miriam Labonia, Carlo Leggieri, Rosetta Lobreglio, Giacomo Monti, Paolo Mura, Anna Mara Scandroglio, Daniela Pasero, Stefano Turi, Agostino Roasio, Carmine D Votta, Emanuela Saporito, Claudio Riefolo, Chiara Sartini, Luca Brazzi, Rinaldo Bellomo, Alberto Zangrillo
OBJECTIVE: A careful choice of perioperative care strategies is pivotal to improve survival in cardiac surgery. However, there is no general agreement or particular attention to which nonsurgical interventions can reduce mortality in this setting. The authors sought to address this issue with a consensus-based approach. DESIGN: A systematic review of the literature followed by a consensus-based voting process. SETTING: A web-based international consensus conference...
June 7, 2017: Journal of Cardiothoracic and Vascular Anesthesia
https://www.readbyqxmd.com/read/29090504/computational-design-of-membrane-proteins-using-rosettamembrane
#7
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/29080703/hormesis-as-a-mechanistic-approach-to-understanding-herbal-treatments-in-traditional-chinese-medicine
#8
REVIEW
Dali Wang, Edward J Calabrese, Baoling Lian, Zhifen Lin, Vittorio Calabrese
Traditional Chinese medicine (TCM) has been long practiced and is becoming ever more widely recognized as providing curative and/or healing treatments for a number of diseases and physiological conditions. This paper posits that herbal medicines used in TCM treatments may act through hormetic dose-response mechanisms. It is proposed that the stimulatory (i.e., low dose) and inhibitory (i.e., high dose) components of the hormetic dose response correspond to respective "regulating" and "curing" aspects of TCM herbal treatments...
October 25, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/29073038/actin-retrograde-flow-actively-aligns-and-orients-ligand-engaged-integrins-in-focal-adhesions
#9
Vinay Swaminathan, Joseph Mathew Kalappurakkal, Shalin B Mehta, Pontus Nordenfelt, Travis I Moore, Nobuyasu Koga, David A Baker, Rudolf Oldenbourg, Tomomi Tani, Satyajit Mayor, Timothy A Springer, Clare M Waterman
Integrins are transmembrane receptors that, upon activation, bind extracellular ligands and link them to the actin filament (F-actin) cytoskeleton to mediate cell adhesion and migration. Cytoskeletal forces in migrating cells generated by polymerization- or contractility-driven "retrograde flow" of F-actin from the cell leading edge have been hypothesized to mediate integrin activation for ligand binding. This predicts that these forces should align and orient activated, ligand-bound integrins at the leading edge...
October 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29071738/assessment-of-contact-predictions-in-casp12-co-evolution-and-deep-learning-coming-of-age
#10
Joerg Schaarschmidt, Bohdan Monastyrskyy, Andriy Kryshtafovych, Alexandre M J J Bonvin
Following up on the encouraging results of residue-residue contact prediction in the CASP11 experiment, we present the analysis of predictions submitted for CASP12. The submissions include predictions of thirty-four groups for thirty-eight domains classified as free modelling targets which are not accessible to homology-based modelling due to a lack of structural templates. CASP11 saw a rise of coevolution-based methods outperforming other approaches. The improvement of these methods coupled to machine learning and sequence database growth are most likely the main driver for a significant improvement in average precision from 27% in CASP11 to 47% in CASP12...
October 26, 2017: Proteins
https://www.readbyqxmd.com/read/29052843/animal-models-in-translational-research-rosetta-stone-or-stumbling-block
#11
REVIEW
Jessica A Bolker
Leading animal models are powerful tools for translational research, but they also present obstacles. Poorly conducted preclinical research in animals is a common cause of translational failure, but even when such research is well-designed and carefully executed, challenges remain. In particular, dominant models may bias research directions, elide essential aspects of human disease, omit important context, or subtly shift research targets. Recognizing these stumbling blocks can help us find ways to avoid them: employing a wider range of models, incorporating more realistic environmental conditions, better aligning studies between animals and patients, and focusing on human biology and therapeutic goals...
October 20, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29033287/rotamer-libraries-for-the-high-resolution-design-of-%C3%AE-amino-acid-foldamers
#12
Andrew M Watkins, Timothy W Craven, P Douglas Renfrew, Paramjit S Arora, Richard Bonneau
β-Amino acids offer attractive opportunities to develop biologically active peptidomimetics, either employed alone or in conjunction with natural α-amino acids. Owing to their potential for unique conformational preferences that deviate considerably from α-peptide geometries, β-amino acids greatly expand the possible chemistries and physical properties available to polyamide foldamers. Complete in silico support for designing new molecules incorporating non-natural amino acids typically requires representing their side-chain conformations as sets of discrete rotamers for model refinement and sequence optimization...
November 7, 2017: Structure
https://www.readbyqxmd.com/read/29028645/an-update-on-the-status-of-molecular-testing-for-the-indeterminate-thyroid-nodule-and-risk-stratification-of-differentiated-thyroid-cancer
#13
Kristina J Nicholson, Linwah Yip
PURPOSE OF REVIEW: Correct identification of malignancy in cytologically indeterminate thyroid nodules is a diagnostic challenge, leading to potentially unnecessary surgery in patients for whom final histology is benign. Similarly, many patients with differentiated thyroid cancer (DTC) undergo aggressive surgical management of tumors, which may ultimately have low-risk histologic features. Use of molecular testing strategies can aid in both the diagnosis of indeterminate thyroid nodules and preoperative risk stratification of DTC...
October 11, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/29024415/eros-enzyme-from-aliivibrio-fischeri-plays-cupid-to-choanoflagellates
#14
Sean E Rossiter, William M Wuest
Cupid's bow: A collaborative effort by the King and Clardy laboratories has serendipitously identified a bacterial chondroitinase that triggers the choanoflagellate S. rosetta to swarm and sexually reproduce. This unprecedented interaction between a bacterium and a choanoflagellate could give insights into a key evolutionary leap-sexual reproduction.
October 11, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28990197/pollen-tube-growth-and-guidance-occam-s-razor-sharpened-on-a-molecular-arabinogalactan-glycoprotein-rosetta-stone
#15
Derek T A Lamport, Li Tan, Michael Held, Marcia J Kieliszewski
Occam's Razor suggests a new model of pollen tube tip growth based on a novel Hechtian oscillator that integrates a periplasmic arabinogalactan glycoprotein-calcium (AGP-Ca(2+) ) capacitor with tip-localized AGPs as the source of tip-focussed cytosolic Ca(2+) oscillations: Hechtian adhesion between the plasma membrane and the cell wall of the growing tip acts as a piconewton force transducer that couples the internal stress of a rapidly growing wall to the plasma membrane. Such Hechtian transduction opens stretch-activated Ca(2+) channels and activates H(+) -ATPase proton pump efflux that dissociates periplasmic AGP-Ca(2+) resulting in a Ca(2+) influx that activates exocytosis of wall precursors...
October 9, 2017: New Phytologist
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
#16
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
#17
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
#18
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
#19
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/28964997/screening-for-attention-deficit-hyperactivity-disorder-in-borderline-personality-disorder
#20
Sébastien Weibel, Rosetta Nicastro, Paco Prada, Pierre Cole, Eva Rüfenacht, Eléonore Pham, Alexandre Dayer, Nader Perroud
BACKGROUND: A valid screening instrument is needed to detect attention-deficit/hyperactivity disorder (ADHD) in treatment-seeking borderline personality disorder (BPD) patients. We aimed to test the performance of the widely-used Adult ADHD Self-Report Scale v1.1 screener (ASRS-v1.1). METHODS: 317 BPD subjects were systematically assessed for comorbid ADHD and completed the ASRS-v1.1. 79 BPD patients also completed the Wender Utah Rating Scale (WURS-25). RESULTS: The prevalence of adult ADHD was of 32...
September 23, 2017: Journal of Affective Disorders
keyword
keyword
73295
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"