keyword
MENU ▼
Read by QxMD icon Read
search

Rosetta

keyword
https://www.readbyqxmd.com/read/28318014/-solvent-hydrogen-bond-occlusion-a-new-model-of-polar-desolvation-for-biomolecular-energetics
#1
Andrea Bazzoli, John Karanicolas
Water engages in two important types of interactions near biomolecules: it forms ordered "cages" around exposed hydrophobic regions, and it participates in hydrogen bonds with surface polar groups. Both types of interaction are critical to biomolecular structure and function, but explicitly including an appropriate number of solvent molecules makes many applications computationally intractable. A number of implicit solvent models have been developed to address this problem, many of which treat these two solvation effects separately...
March 20, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28302718/a-unique-choanoflagellate-enzyme-rhodopsin-with-cyclic-nucleotide-phosphodiesterase-activity
#2
Kazuho Yoshida, Satoshi P Tsunoda, Leonid S Brown, Hideki Kandori
Photoactivated adenylyl cyclase (PAC) and guanylyl cyclase rhodopsin (Rh-GC) increase the concentrations of intracellular cyclic nucleotides upon illumination, serving as promising second-generation tools in optogenetics. To broaden arsenal of such tools, it is desirable to have light-activatable enzymes which can decrease cyclic nucleotide concentrations in cells. Here, we report on an unusual microbial rhodopsin which may be able to meet the demand. It is found in the choanoflagellate Salpingoeca rosetta and contains a C-terminal cyclic nucleotide phosphodiesterase (PDE) domain...
March 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28300559/expression-purification-and-in-vitro-refolding-of-the-recombinant-truncated-saposin-like-protein-2-antigen-for-development-of-diagnosis-of-human-fascioliasis
#3
Abolfazl Mirzadeh, Zarrintaj Valadkhani, Asiyeh Yoosefy, Jalal Babaie, Majid Golkar, Ahmad Reza Esmaeili Rastaghi, Elham Kazemi-Rad, Keyhan Ashrafi
Early diagnosis of fascioliasis is critical in prevention of injury to the liver and bile ducts. Saposin-like protein (FhSAP-2) is probably the most ideal antigen of Fasciola hepatica for development of ELISA kits. SAP-2 has a conserved tertiary structure containing three disulfide bonds and conformational epitopes. Therefore, antigenicity of SAP-2 is greatly depends on disulfide bond formation and proper folding. We produced the recombinant truncated SAP-2 (rtSAP-2) in the SHuffle® T7 and Rosetta strain of E...
March 11, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28286974/natural-radioactivity-levels-and-associated-health-hazards-from-the-terrestrial-ecosystem-in-rosetta-branch-of-the-river-nile-egypt
#4
W M Abdellah, H M Diab, S U El-Kameesy, E Salama, S El-Framawy
Twenty soil and 25 sediment samples were collected from the banks and bottom of the River Nile in the surroundings of biggest cities located close to it. Natural radioactivity concentrations of (226)Ra, (232)Th and (40)K have been evaluated for all samples by means of γ spectrometric analysis. The radioactivity levels of soil and sediment samples fall within the internationally recommended values. Nevertheless, high natural background radiation zones are detected in the Kafr El-Zayat region due to the presence of a fertilizer factory, and in the Rosetta region due to the presence of black sand deposits...
March 13, 2017: Isotopes in Environmental and Health Studies
https://www.readbyqxmd.com/read/28282854/systematic-design-of-trypsin-cleavage-site-mutated-exendin4-cysteine-1-an-orally-bioavailable-glucagon-like-peptide-1-receptor-agonist
#5
Wenbo Sai, Hong Tian, Kangmin Yang, Daoqi Tang, Jinxiao Bao, Yang Ge, Xiaoda Song, Yu Zhang, Cheng Luo, Xiangdong Gao, Wenbing Yao
Exendin-4 is a strong therapeutic candidate for the treatment of metabolic syndrome. Related receptor agonist drugs have been on the market since 2005. However, technical limitations and the pain caused by subcutaneous injection have severely limited patient compliance. The goal of the study is to investigate a biologically active exendin-4 analog could be administered orally. Using intraperitoneal glucose tolerance tests, we discovered that exendin4-cysteine administered by oral gavage had a distinct hypoglycemic effect in C57BL/6J mice...
March 8, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28279194/crispr-targeted-genome-editing-of-mesenchymal-stem-cell-derived-therapies-for-type-1-diabetes-a-path-to-clinical-success
#6
REVIEW
Dario Gerace, Rosetta Martiniello-Wilks, Najah Therese Nassif, Sara Lal, Raymond Steptoe, Ann Margaret Simpson
Due to their ease of isolation, differentiation capabilities, and immunomodulatory properties, the therapeutic potential of mesenchymal stem cells (MSCs) has been assessed in numerous pre-clinical and clinical settings. Currently, whole pancreas or islet transplantation is the only cure for people with type 1 diabetes (T1D) and, due to the autoimmune nature of the disease, MSCs have been utilised either natively or transdifferentiated into insulin-producing cells (IPCs) as an alternative treatment. However, the initial success in pre-clinical animal models has not translated into successful clinical outcomes...
March 9, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/28274612/effects-of-obesity-on-il-33-st2-system-in-heart-adipose-tissue-and-liver-study-in-the-experimental-model-of-zucker-rats
#7
Rosetta Ragusa, Manuela Cabiati, Maria Angela Guzzardi, Andrea D'Amico, Daniela Giannessi, Silvia Del Ry, Chiara Caselli
Suppression of tumorigenicity 2 (ST2) mediates the effect of Interleukin-33 (IL-33). Few data are reported on the relationship between IL-33/ST2 and obesity. We aimed to investigate effects of obesity on IL-33/ST2 system in heart, adipose tissue and liver in a rodent model of obesity. The relationship of cardiac expression of IL-33/ST2 system with natriuretic peptides (NPs) system and inflammatory mediators was also studied. mRNA expression of IL-33/ST2 system was evaluated in cardiac, adipose and hepatic biopsies from obese Zucker rats (O) and controls (CO)...
March 6, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28263091/attachment-and-reflective-functioning-in-women-with-borderline-personality-disorder
#8
Deborah Badoud, Paco Prada, Rosetta Nicastro, Charlotte Germond, Patrick Luyten, Nader Perroud, Martin Debbané
Insecure attachment and impairments in reflective functioning (RF) are thought to play a critical role in borderline personality disorder (BPD). In particular, the mentalization-based model argues that insecure attachment indirectly accounts for increased BPD features, notably via disruption of RF capacities. Although the mediation relationship between attachment, RF, and BPD is supported by previous evidence, it remains to be directly tested in adults with BPD. In the current study, a sample of 55 female adult BPD patients and 105 female healthy controls completed a battery of self-report measures to investigate the interplay between attachment, RF capacities, and BPD clinical status...
March 6, 2017: Journal of Personality Disorders
https://www.readbyqxmd.com/read/28243985/efficient-synthesis-of-s-n-boc-3-hydroxypiperidine-using-an-r-specific-carbonyl-reductase-from-candida-parapsilosis
#9
Jingjing Chen, Ming Yan, Lin Xu
(S)-N-Boc-3-hydroxypiperidine (S-NBHP) is a critical chiral intermediate in the synthesis of pharmaceuticals, including ibrutinib, the active pharmaceutical ingredient of the new drug Imbruvica approved for the treatment of lymphoma. An (R)-specific carbonyl reductase from Candida parapsilosis (CprCR, also known as R-specific alcohol dehydrogenase) that catalyzes asymmetric reduction to produce (S)-N-Boc-3-hydroxypiperidine (S-NBHP) was identified for the first time. When co-expressed with a glucose dehydrogenase from Bacillus megaterium in Escherichia coli Rosetta (DE3), recombinant crude enzyme exhibited an activity of 9 U/mg with N-Boc-3-piperidone as the substrate and 12 U/mg with glucose as the substrate...
March 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28238619/application-of-the-rosetta-stone-to-understand-how-much-mvpa-preschoolers-accumulate-a-systematic-review
#10
REVIEW
Fabricio C P Ravagnani, Christianne F Coelho-Ravagnani, Keith Brazendale, Robert G Weaver, Daniel B Bornstein, Michael W Beets
OBJECTIVES: This study illustrates the utility of the Rosetta Stone equations for comparing estimates of preschool-age children's moderate-to-vigorous physical activity (MVPA) across studies utilizing different cutpoints. DESIGN: Systematic review. METHODS: A search of online databases was conducted to identify studies that reported daily minutes of MVPA in preschoolers using the cutpoints from which Rosetta Stone equations have been developed...
February 23, 2017: Journal of Science and Medicine in Sport
https://www.readbyqxmd.com/read/28236237/modeling-peptide-protein-structure-and-binding-using-monte-carlo-sampling-approaches-rosetta-flexpepdock-and-flexpepbind
#11
Nawsad Alam, Ora Schueler-Furman
Many signaling and regulatory processes involve peptide-mediated protein interactions, i.e., the binding of a short stretch in one protein to a domain in its partner. Computational tools that generate accurate models of peptide-receptor structures and binding improve characterization and manipulation of known interactions, help to discover yet unknown peptide-protein interactions and networks, and bring into reach the design of peptide-based drugs for targeting specific systems of medical interest.Here, we present a concise overview of the Rosetta FlexPepDock protocol and its derivatives that we have developed for the structure-based characterization of peptide-protein binding...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28223214/expression-studies-of-bacillus-licheniformis-chitin-deacetylase-in-e-coli-rosetta-cells
#12
Ritu Raval, Robin Simsa, Keyur Raval
Chitin, the biopolymer of the N-acetylglucosamine, is the most abundant biopolymer on the planet after cellulose. However owing to its crystalline nature, its deacetylated derivative; chitosan is industrially more potent. This conversion on an enzymatic scale can be made using chitin deacetylase. The metagenomics library constructed from the soil exposed to chitin and chitosan yielded chitin modifying enzymes, one of them being chitin deacetylase (CDA) utilized for the present study. The gene was amplified and expressed using the pET 22b vector in E...
February 20, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28219343/computing-structure-based-lipid-accessibility-of-membrane-proteins-with-mp_lipid_acc-in-rosettamp
#13
Julia Koehler Leman, Sergey Lyskov, Richard Bonneau
BACKGROUND: Membrane proteins are underrepresented in structural databases, which has led to a lack of computational tools and the corresponding inappropriate use of tools designed for soluble proteins. For membrane proteins, lipid accessibility is an essential property. Although programs are available for sequence-based prediction of lipid accessibility and structure-based identification of solvent-accessible surface area, the latter does not distinguish between water accessible and lipid accessible residues in membrane proteins...
February 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28216966/suppression-of-colorectal-tumorigenesis-by-recombinant-bacteroides-fragilis-enterotoxin-2-in-vivo
#14
You Lv, Tao Ye, Hui-Peng Wang, Jia-Ying Zhao, Wen-Jie Chen, Xin Wang, Chen-Xia Shen, Yi-Bin Wu, Yuan-Kun Cai
AIM: To evaluate the impact of recombinant Bacteroides fragilis enterotoxin-2 (BFT-2, or Fragilysin) on colorectal tumorigenesis in mice induced by azoxymethane/dextran sulfate sodium (AOM/DSS). METHODS: Recombinant proBFT-2 was expressed in Escherichia coli strain Rosetta (DE3) and BFT-2 was obtained and tested for its biological activity via colorectal adenocarcinoma cell strains SW-480. Seventy C57BL/6J mice were randomly divided into a blank (BC; n = 10), model (AD; n = 20), model + low-dose toxin (ADLT; n = 20, 10 μg), and a model + high-dose toxin (ADHT; n = 20, 20 μg) group...
January 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28210460/cloning-and-expression-of-clostridium-perfringens-type-d-vaccine-strain-epsilon-toxin-gene-in-e-coli-as-a-recombinant-vaccine-candidate
#15
Parastoo Aziminia, Reza Pilehchian-Langroudi, Kasra Esmaeilnia
BACKGROUND AND OBJECTIVES: Clostridium perfringens, a Gram-positive obligate anaerobic bacterium, is able to form resistant spores which are widely distributed in the environment. C. perfringens is subdivided into five types A to E based on its four major alpha, beta, epsilon and iota toxins. The aim of the present study was cloning and expression of C. perfringens type D vaccine strain epsilon toxin gene. MATERIALS AND METHODS: Genomic DNA was extracted and the epsilon toxin gene was amplified using Pfu DNA polymerase...
August 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/28202377/characterization-of-a-new-fungal-immunomodulatory-protein-fip-dsq2-from-dichomitus-squalens
#16
Shuying Li, Zhonghao Jiang, Lichao Sun, Xin Liu, Ying Huang, Fengzhong Wang, Fengjiao Xin
FIP-dsq2, a new immunomodulatory protein, was identified in Basidiomycota Dichomitus squalens by gene mining. FIP-dsq2 contained 111 amino acids with a molecular weight of 12.51kDa. FIP-dsq2 had a homology range of 51-65% to the reported FIPs. The predicted 3-dimensional model had more similar identical folding patterns in LZ-8 than for FIP-fve. Evolutionary analysis indicated substantial phylogenetic differences were existed with the other FIPs. Overexpression of a 14.07kDa soluble recombinant FIP-dsq2 (rFIP-dsq2) was achieved in Rosetta (pGEX-6P-1) and the purified recombinant protein was homodimer verified by gel filtration chromatography analysis...
March 20, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28160322/atlas-a-database-linking-binding-affinities-with-structures-for-wild-type-and-mutant-tcr-pmhc-complexes
#17
Tyler Borrman, Jennifer Cimons, Michael Cosiano, Michael Purcaro, Brian G Pierce, Brian M Baker, Zhiping Weng
The ATLAS (Altered TCR Ligand Affinities and Structures) database (https://zlab.umassmed.edu/atlas/web/) is a manually curated repository containing the binding affinities for wild-type and mutant T cell receptors (TCRs) and their antigens, peptides presented by the major histocompatibility complex (pMHC). The database links experimentally measured binding affinities with the corresponding three dimensional (3D) structures for TCR-pMHC complexes. The user can browse and search affinities, structures, and experimental details for TCRs, peptides, and MHCs of interest...
February 3, 2017: Proteins
https://www.readbyqxmd.com/read/28152669/psychometric-properties-and-factor-structure-of-the-short-form-of-the-affective-lability-scale-in-adult-patients-with-adhd
#18
Sébastien Weibel, Jean-Arthur Micoulaud-Franchi, Laura Brandejsky, Régis Lopez, Paco Prada, Rosetta Nicastro, Stefano Ardu, Alexandre Dayer, Christophe Lançon, Nader Perroud
OBJECTIVE: Affective lability is an important dimension of adult ADHD, associated with marked impairments and worse outcomes. A valid and quick tool to measure affective lability may therefore be of interest. METHOD: In 187 adult ADHD patients, we explored psychometric properties of the Affective Lability Scale-Short Form (ALS-18 items). We analyzed the construct validity and the external validity of the scale. Patients were compared with 48 healthy adult controls...
February 1, 2017: Journal of Attention Disorders
https://www.readbyqxmd.com/read/28145457/two-strategies-to-engineer-flexible-loops-for-improved-enzyme-thermostability
#19
Haoran Yu, Yihan Yan, Cheng Zhang, Paul A Dalby
Flexible sites are potential targets for engineering the stability of enzymes. Nevertheless, the success rate of the rigidifying flexible sites (RFS) strategy is still low due to a limited understanding of how to determine the best mutation candidates. In this study, two parallel strategies were applied to identify mutation candidates within the flexible loops of Escherichia coli transketolase (TK). The first was a "back to consensus mutations" approach, and the second was computational design based on ΔΔG calculations in Rosetta...
February 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28142198/incorporating-an-allosteric-regulatory-site-in-an-antibody-through-backbone-design
#20
Olga Khersonsky, Sarel J Fleishman
Allosteric regulation underlies living cells' ability to sense changes in nutrient and signaling-molecule concentrations, but the ability to computationally design allosteric regulation into non-allosteric proteins has been elusive. Allosteric-site design is complicated by the requirement to encode the relative stabilities of active and inactive conformations of the same protein in the presence and absence of both ligand and effector. To address this challenge, we used Rosetta to design the backbone of the flexible heavy-chain complementarity-determining region 3 (HCDR3), and used geometric matching and sequence optimization to place a Zn(2+) -coordination site in a fluorescein-binding antibody...
January 31, 2017: Protein Science: a Publication of the Protein Society
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"