keyword
MENU ▼
Read by QxMD icon Read
search

Rosetta

keyword
https://www.readbyqxmd.com/read/27918427/prolactin-friend-or-foe-in-central-nervous-system-autoimmune-inflammation
#1
REVIEW
Massimo Costanza, Rosetta Pedotti
The higher prevalence of multiple sclerosis (MS) in females, along with the modulation of disease activity observed during pregnancy and the post-partum period, has suggested a hormonal influence in MS. Even if prolactin (PRL) does not belong to the sex hormones family, its crucial role in female reproduction and lactation has prompted great efforts to understand if PRL could represent a gender factor in the pathogenesis of MS and experimental autoimmune encephalomyelitis (EAE), the animal model for this disease...
December 2, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27916743/clipping-of-the-tricuspid-valve-proposal-of-a-rosetta-stone-nomenclature-for-procedural-3d-transesophageal-guidance
#2
Maurizio Taramasso, Michel Zuber, Fabian Nietlispach, Francesco Maisano
No abstract text is available yet for this article.
December 6, 2016: EuroIntervention
https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#3
Christine E Tinberg, Sagar D Khare
The ability to design novel small-molecule binding sites in proteins is a stringent test of our understanding of the principles of molecular recognition, and would have many practical applications, in synthetic biology and medicine. Here, we describe a computational method in the context of the macromolecular modeling suite Rosetta to designing proteins with sites featuring predetermined interactions to ligands of choice. The required inputs for the method are a model of the small molecule and the desired interactions (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27908283/expression-of-a-fungal-manganese-peroxidase-in-escherichia-coli-a-comparison-between-the-soluble-and-refolded-enzymes
#4
Nan Wang, Kai Ren, Rong Jia, Wenting Chen, Ruirui Sun
BACKGROUND: Manganese peroxidase (MnP) from Irpex lacteus F17 has been shown to have a strong ability to degrade recalcitrant aromatic pollutants. In this study, a recombinant MnP from I. lacteus F17 was expressed in Escherichia coli Rosetta (DE3) in the form of inclusion bodies, which were refolded to achieve an active enzyme. Further, we optimized the in vitro refolding conditions to increase the recovery yield of the recombinant protein production. Additionally, we attempted to express recombinant MnP in soluble form in E...
December 1, 2016: BMC Biotechnology
https://www.readbyqxmd.com/read/27900782/residue-centric-modeling-and-design-of-saccharide-and-glycoconjugate-structures
#5
Jason W Labonte, Jared Adolf-Bryfogle, William R Schief, Jeffrey J Gray
The RosettaCarbohydrate framework is a new tool for modeling a wide variety of saccharide and glycoconjugate structures. This report describes the development of the framework and highlights its applications. The framework integrates with established protocols within the Rosetta modeling and design suite, and it handles the vast complexity and variety of carbohydrate molecules, including branching and sugar modifications. To address challenges of sampling and scoring, RosettaCarbohydrate can sample glycosidic bonds, side-chain conformations, and ring forms, and it utilizes a glycan-specific term within its scoring function...
November 30, 2016: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/27890597/identification-eukaryotic-expression-and-structure-function-characterizations-of-%C3%AE-defensin-like-homologues-from-pelodiscus-sinensis
#6
Haining Yu, Xuelian Liu, Hui Wang, Lan Feng, Xue Qiao, Shasha Cai, Nannan Shi, Yipeng Wang
Defensins are a group of host defense peptides that play a central role in host innate immune responses. Here, 26 genes encoding β-defensin-like peptides have been identified for the first time in Pelodiscus sinensis using database mining approach. Phylogenetic study confirmed that β-defensins are fast evolving genes with high rates of sequence substitutions. The expression level of several selected genes in different tissues was examined by RT-PCR. Ps-BDs mainly adopt β-strands and/or α-helix conformations homology modeled by Rosetta program...
November 24, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27882869/aerotaxis-in-the-closest-relatives-of-animals
#7
Julius B Kirkegaard, Ambre Bouillant, Alan O Marron, Kyriacos C Leptos, Raymond E Goldstein
As the closest unicellular relatives of animals, choanoflagellates serve as useful model organisms for understanding the evolution of animal multicellularity. An important factor in animal evolution was the increasing ocean oxygen levels in the Precambrian, which are thought to have influenced the emergence of complex multicellular life. As a first step in addressing these conditions, we study here the response of the colony-forming choanoflagellate Salpingoeca rosetta to oxygen gradients. Using a microfluidic device that allows spatio-temporal variations in oxygen concentrations, we report the discovery that S...
November 24, 2016: ELife
https://www.readbyqxmd.com/read/27856849/rosetta-s-comet-67p-churyumov-gerasimenko-sheds-its-dusty-mantle-to-reveal-its-icy-nature
#8
S Fornasier, S Mottola, H U Keller, M A Barucci, B Davidsson, C Feller, J D P Deshapriya, H Sierks, C Barbieri, P L Lamy, R Rodrigo, D Koschny, H Rickman, M A'Hearn, J Agarwal, J-L Bertaux, I Bertini, S Besse, G Cremonese, V Da Deppo, S Debei, M De Cecco, J Deller, M R El-Maarry, M Fulle, O Groussin, P J Gutierrez, C Güttler, M Hofmann, S F Hviid, W-H Ip, L Jorda, J Knollenberg, G Kovacs, R Kramm, E Kührt, M Küppers, M L Lara, M Lazzarin, J J Lopez Moreno, F Marzari, M Massironi, G Naletto, N Oklay, M Pajola, A Pommerol, F Preusker, F Scholten, X Shi, N Thomas, I Toth, C Tubiana, J-B Vincent
The Rosetta spacecraft has investigated comet 67P/Churyumov-Gerasimenko from large heliocentric distances to its perihelion passage and beyond. We trace the seasonal and diurnal evolution of the colors of the 67P nucleus, finding changes driven by sublimation and recondensation of water ice. The whole nucleus became relatively bluer near perihelion, as increasing activity removed the surface dust, implying that water ice is widespread underneath the surface. We identified large (1500 m(2)) ice-rich patches appearing and then vanishing in about 10 days, indicating small-scale heterogeneities on the nucleus...
November 17, 2016: Science
https://www.readbyqxmd.com/read/27829420/association-of-a-rare-notch4-coding-variant-with-systemic-sclerosis-a-family-based-whole-exome-sequencing-study
#9
Christopher J Cardinale, Dong Li, Lifeng Tian, John J Connolly, Michael E March, Cuiping Hou, Fengxiang Wang, James Snyder, Cecilia E Kim, Rosetta M Chiavacci, Patrick M Sleiman, Jon M Burnham, Hakon Hakonarson
BACKGROUND: Systemic sclerosis (SSc) is a rheumatologic disease with a multifactorial etiology. Genome-wide association studies imply a polygenic, complex mode of inheritance with contributions from variation at the human leukocyte antigen locus and non-coding variation at a locus on chromosome 6p21, among other modestly impactful loci. Here we describe an 8-year-old female proband presenting with diffuse cutaneous SSc/scleroderma and a family history of SSc in a grandfather and maternal aunt...
November 9, 2016: BMC Musculoskeletal Disorders
https://www.readbyqxmd.com/read/27805072/evaluation-of-an-albumin-binding-domain-protein-fused-to-recombinant-human-il-2-and-its-effects-on-the-bioactivity-and-serum-half-life-of-the-cytokine
#10
Elham Adabi, Fateme Saebi, Amin Moradi Hasan-Abad, Ladan Teimoori-Toolabi, Gholam Ali Kardar
BACKGROUND: Background: Cancer immunotherapy is a promising strategy for cancer treatment. In this strategy, the immune system is triggered to destroy cancer cells. IL-2 is an important factor in passive cancer immunotherapy that helps modulating some important immune functions. One of the IL-2 limitations is low serum half-life; therefore, repetitive high doses of the injections are required to maintain effective concentrations. High-dose IL-2 therapy results in severe side effects; thus, improvement of its serum half-life would provide therapeutic benefits...
November 2, 2016: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/27800552/lasso-peptide-biosynthetic-protein-larb1-binds-both-leader-and-core-peptide-regions-of-the-precursor-protein-lara
#11
Wai Ling Cheung, Maria Y Chen, Mikhail O Maksimov, A James Link
Lasso peptides are a member of the superclass of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Like all RiPPs, lasso peptides are derived from a gene-encoded precursor protein. The biosynthesis of lasso peptides requires two enzymatic activities: proteolytic cleavage between the leader peptide and the core peptide in the precursor protein, accomplished by the B enzymes, and ATP-dependent isopeptide bond formation, accomplished by the C enzymes. In a subset of lasso peptide biosynthetic gene clusters from Gram-positive organisms, the B enzyme is split between two proteins...
October 26, 2016: ACS Central Science
https://www.readbyqxmd.com/read/27769252/genomic-copy-number-variation-association-study-in-caucasian-patients-with-nonsyndromic-cryptorchidism
#12
Yanping Wang, Jin Li, Thomas F Kolon, Alicia Olivant Fisher, T Ernesto Figueroa, Ahmad H BaniHani, Jennifer A Hagerty, Ricardo Gonzalez, Paul H Noh, Rosetta M Chiavacci, Kisha R Harden, Debra J Abrams, Deborah Stabley, Cecilia E Kim, Katia Sol-Church, Hakon Hakonarson, Marcella Devoto, Julia Spencer Barthold
BACKGROUND: Copy number variation (CNV) is a potential contributing factor to many genetic diseases. Here we investigated the potential association of CNV with nonsyndromic cryptorchidism, the most common male congenital genitourinary defect, in a Caucasian population. METHODS: Genome wide genotyping were performed in 559 cases and 1772 controls (Group 1) using Illumina HumanHap550 v1, HumanHap550 v3 or Human610-Quad platforms and in 353 cases and 1149 controls (Group 2) using the Illumina Human OmniExpress 12v1 or Human OmniExpress 12v1-1...
October 21, 2016: BMC Urology
https://www.readbyqxmd.com/read/27768593/toward-the-development-of-a-novel-non-rgd-cyclic-peptide-drug-conjugate-for-treatment-of-human-metastatic-melanoma
#13
Boris Redko, Helena Tuchinsky, Tamar Segal, Dror Tobi, Galia Luboshits, Osnat Ashur-Fabian, Albert Pinhasov, Gabi Gerlitz, Gary Gellerman
The newly discovered short (9 amino acid) non-RGD S-S bridged cyclic peptide ALOS-4 (H-cycl(Cys-Ser-Ser-Ala-Gly-Ser-Leu-Phe-Cys)-OH), which binds to integrin αvβ3 is investigated as peptide carrier for targeted drug delivery against human metastatic melanoma. ALOS4 binds specifically the αvβ3 overexpressing human metastatic melanoma WM-266-4 cell line both in vitro and in ex vivo assays. Coupling ALOS4 to the topoisomerase I inhibitor Camptothecin (ALOS4-CPT) increases the cytotoxicity of CPT against human metastatic melanoma cells while reduces dramatically the cytotoxicity against non-cancerous cells as measured by the levels of γH2A...
October 19, 2016: Oncotarget
https://www.readbyqxmd.com/read/27766851/simultaneous-optimization-of-biomolecular-energy-function-on-features-from-small-molecules-and-macromolecules
#14
Hahnbeom Park, Philip Bradley, Per Greisen, Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, Frank DiMaio
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data...
October 21, 2016: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/27754489/in-silico-aptamer-docking-studies-from-a-retrospective-validation-to-a-prospective-case-study-tim3-aptamers-binding
#15
Obdulia Rabal, Fernando Pastor, Helena Villanueva, Mario M Soldevilla, Sandra Hervas-Stubbs, Julen Oyarzabal
Complementing Systematic Evolution of Ligands by EXponential Enrichment (SELEX) technologies with in silico prediction of aptamer binders has attracted a lot of interest in the recent years. We propose a workflow involving 2D structure prediction, 3D RNA modeling using Rosetta and docking to the target protein with 3dRPC for: (i) prediction of the binding mode of our two previously reported potent (Kd < 50 nmol/l) murine TIM3 aptamers, and (ii) the prioritization of TIM3 aptamers that were enriched in the SELEX workflow...
October 18, 2016: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/27752792/molecular-cloning-and-characterization-of-%C3%AE-amylase-subtilisin-inhibitor-from-rhizome-of-ligusticum-chuanxiong
#16
Ji-Hua Yu, Yang-Yang Li, Mian Xiang, Jian-Quan Zhu, Xin-He Huang, Wan-Jun Wang, Rui Tan, Jia-Yu Zhou, Hai Liao
OBJECTIVES: To clone and characterize a novel bi-functional α-amylase/subtilisin inhibitor (LASI) from the rhizome of Ligusticum chuanxiong, a traditional Chinese medicine. RESULTS: The LASI showed strong homology with members of the Kunitz trypsin inhibitor family. Its putative amino acid sequence has a 40 % identity with that of the α-amylase/subtilisin inhibitor from rice. LASI gene without signal peptide was expressed in E. coli Rosetta. After purification, the recombinant LASI protein was inhibitory against not only α-amylase from porcine pancreas, Helicoverpa armigera, Spodoptera litura and Plutella xylostella, but also subtilisin A, but not against trypsin or chymotrypsin...
October 17, 2016: Biotechnology Letters
https://www.readbyqxmd.com/read/27736019/computed-insight-into-a-peptide-inhibitor-preventing-the-induced-fit-mechanism-of-mura-enzyme-from-pseudomonas-aeruginosa
#17
Anderson H Lima, Alberto M Dos Santos, Cláudio Nahum Alves, Jerônimo Lameira
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is one of the key enzymes involved in peptidoglycan biosynthesis. The peptide HESFWYLPHQSY (called PEP 1354) is an inhibitor of MurA with an IC50 value of 200 μm. In this article, we have used the FlexPepDock ab-initio protocol from the Rosetta program homology modeling and molecular dynamics simulations to analyze, for the first time, the interaction of the PEP 1354 peptide with MurA enzyme from Pseudomonas aeruginosa (MurA-PA). Our modeling results suggest that the peptide binds to the same active site as the natural substrate UDP-N-acetylglucosamine (UNAG)...
October 13, 2016: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/27729545/the-structure-kinetics-and-interactions-of-the-%C3%AE-carboxysomal-%C3%AE-carbonic-anhydrase-ccaa
#18
Leah D McGurn, Maryam Moazami-Goudarzi, Sean A White, Tannu Suwal, Beant Brar, Jason Q Tang, George S Espie, Matthew S Kimber
CcaA is a b-carbonic anhydrase that is a component of the carboxysomes of a subset of b-cyanobacteria. This protein, which has a characteristic C-terminal extension of unknown function, is recruited to the carboxysome via interactions with CcmM, which is itself a γ-carbonic anhydrase homolog with enzymatic activity in many, but not all cyanobacteria. We have determined the structure of CcaA from Synechocystis sp. PCC 6803 at 1.45 Å. In contrast to the dimer of dimers organization of most bacterial β-carbonic anhydrases, or the loose dimer-of-dimers-of-dimers organization found in the plant enzymes, CcaA shows a well-packed trimer-of-dimers organization...
October 11, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27722754/transepithelial-iontophoresis-versus-standard-corneal-collagen-cross-linking-1-year-results-of-a-prospective-clinical-study
#19
Paolo Vinciguerra, Vito Romano, Pietro Rosetta, Emanuela F Legrottaglie, Raffaele Piscopo, Claudia Fabiani, Claudio Azzolini, Riccardo Vinciguerra
PURPOSE: To compare 1-year transepithelial corneal collagen cross-linking with iontophoresis (I-CXL) outcomes with standard CXL (S-CXL) epithelium-off for progressive keratoconus. METHODS: Forty eyes of 40 patients with progressive keratoconus were included in this comparative, prospective clinical study. Corrected distance visual acuity (CDVA), spherical equivalent, cylinder refraction, corneal topography, Scheimpflug tomography, aberrometry, and endothelial cell count were assessed at baseline and at 1, 3, 6, and 12 months of follow-up...
October 1, 2016: Journal of Refractive Surgery
https://www.readbyqxmd.com/read/27718569/production-and-directional-evolution-of-anti-sarafloxacin-scfv-antibody-for-immunoassay-of-fluoroquinolones-in-milk
#20
Jian Ping Wang, Jun Dong, Chang Fei Duan, Hui Cai Zhang, Xin He, Geng Nan Wang, Guo Xian Zhao, Jing Liu
A recombinant anti-sarafloxacin ScFv antibody was produced by direct transformation of its gene into Rosetta-gami(DE3) for expression, and then its recognition mechanisms for 12 fluoroquinolones were studied by using molecular docking method. Based on the results of virtual mutation, the ScFv antibody was evolved by directional mutagenesis of contact amino acid residue Tyr99 to His. The ScFv mutant showed highly increased affinity for the 12 drugs with up to 7-folds improved sensitivity. Finally, the mutant was used to develop an indirect competitive enzyme linked immunosorbent assay for determination of the 12 drugs in milk...
October 10, 2016: Journal of Agricultural and Food Chemistry
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"