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https://www.readbyqxmd.com/read/27926874/multivalent-histone-and-dna-engagement-by-a-phd-brd-pwwp-triple-reader-cassette-recruits-zmynd8-to-k14ac-rich-chromatin
#1
Pavel Savitsky, Tobias Krojer, Takao Fujisawa, Jean-Philippe Lambert, Sarah Picaud, Chen-Yi Wang, Erin K Shanle, Krzysztof Krajewski, Hans Friedrichsen, Alexander Kanapin, Colin Goding, Matthieu Schapira, Anastasia Samsonova, Brian D Strahl, Anne-Claude Gingras, Panagis Filippakopoulos
Elucidation of interactions involving DNA and histone post-translational-modifications (PTMs) is essential for providing insights into complex biological functions. Reader assemblies connected by flexible linkages facilitate avidity and increase affinity; however, little is known about the contribution to the recognition process of multiple PTMs because of rigidity in the absence of conformational flexibility. Here, we resolve the crystal structure of the triple reader module (PHD-BRD-PWWP) of ZMYND8, which forms a stable unit capable of simultaneously recognizing multiple histone PTMs while presenting a charged platform for association with DNA...
December 6, 2016: Cell Reports
https://www.readbyqxmd.com/read/27926840/calcium-dependent-structural-dynamics-of-a-spin-labeled-ryr-peptide-bound-to-calmodulin
#2
Cheng Her, Jesse E McCaffrey, David D Thomas, Christine B Karim
We have used chemical synthesis, electron paramagnetic resonance (EPR), and circular dichroism to detect and analyze the structural dynamics of a ryanodine receptor (RyR) peptide bound to calmodulin (CaM). The skeletal muscle calcium release channel RyR1 is activated by Ca(2+)-free CaM and inhibited by Ca(2+)-bound CaM. To probe the structural mechanism for this regulation, wild-type RyRp and four spin-labeled derivatives were synthesized, each containing the nitroxide probe 2,2,6,6-tetramethyl-piperidine-1-oxyl-4-amino-4-carboxylic acid substituted for a single amino acid...
December 6, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27926838/high-resolution-mapping-of-a-repeat-protein-folding-free-energy-landscape
#3
Martin J Fossat, Thuy P Dao, Kelly Jenkins, Mariano Dellarole, Yinshan Yang, Scott A McCallum, Angel E Garcia, Doug Barrick, Christian Roumestand, Catherine A Royer
A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the conformational ensemble along the entire folding reaction coordinate. Simulations can provide this level of insight for small proteins. In contrast, with the exception of hydrogen exchange, which does not monitor folding directly, experimental studies of protein folding have not yielded such structural and energetic detail. NMR can provide residue specific atomic level structural information, but its implementation in protein folding studies using chemical or temperature perturbation is problematic...
December 6, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27926430/insights-in-waste-management-bioprocesses-using-genomic-tools
#4
H J Purohit, A Kapley, A Khardenavis, A Qureshi, N A Dafale
Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities...
2016: Advances in Applied Microbiology
https://www.readbyqxmd.com/read/27925795/oxidants-at-the-surface-of-mars-a-review-in-light-of-recent-exploration-results
#5
J Lasne, A Noblet, C Szopa, R Navarro-González, M Cabane, O Poch, F Stalport, P François, S K Atreya, P Coll
In 1976, the Viking landers carried out the most comprehensive search for organics and microbial life in the martian regolith. Their results indicate that Mars' surface is lifeless and, surprisingly, depleted in organics at part-per-billion levels. Several biology experiments on the Viking landers gave controversial results that have since been explained by the presence of oxidizing agents on the surface of Mars. These oxidants may degrade abiotic or biological organics, resulting in their nondetection in the regolith...
December 7, 2016: Astrobiology
https://www.readbyqxmd.com/read/27925472/image-guided-radiotherapy-for-prostate-cancer-in-the-united-kingdom-a-national-survey
#6
Hemal Ariyaratne, Hayley Chesham, Roberto Alonzi
OBJECTIVES: To survey the technology and practice of image-guided radiotherapy for prostate cancer in the United Kingdom Methods: A pre-tested semi-structured online questionnaire was sent to NHS and private radiotherapy providers in the United Kingdom between March and April 2014. The survey was carried out on the Opinio© online platform. RESULTS: There was a high survey response rate of 83%. There is widespread use of intensity-modulated radiotherapy and advanced verification imaging modalities...
December 7, 2016: British Journal of Radiology
https://www.readbyqxmd.com/read/27925218/insights-into-light-driven-dna-repair-by-photolyases-challenges-and-opportunities-for-electronic-structure-theory
#7
Shirin Faraji, Andreas Dreuw
UV radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photoproducts. (6-4) photolyases are light-activated enzymes that selectively bind to DNA and trigger repair of mutagenic 6-4 photoproducts via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH(-) ) to the lesion triggering repair. This review provides an overview of the sequential steps of the repair process, i.e. light absorption and resonance energy transfer, photo-induced electron transfer, and electron-induced splitting mechanisms, with an emphasis on the role of theory and computation...
December 7, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27924981/hts-ftir-spectroscopy-allows-the-classification-of-polyphenols-according-to-their-differential-effects-on-the-mda-mb-231-breast-cancer-cell-line
#8
A Mignolet, V Mathieu, E Goormaghtigh
Breast cancer is a major public health issue among women in the world. Meanwhile new anticancer treatments struggle more and more to be accepted in the pharmaceutical market and research costs still increase. There is therefore a need to find new treatments and new screening methods to test them more quickly and efficiently. Among natural compounds, an increasing interest has been given to polyphenols as they can take action at the different stages of carcinogenesis, from tumour initiation to metastasis formation, by disturbing multiple cellular signalling pathways...
December 7, 2016: Analyst
https://www.readbyqxmd.com/read/27924857/electrohydrodynamic-assisted-assembly-of-hierarchically-structured-3d-crumpled-nanostructures-for-efficient-solar-conversions
#9
Hidetaka Ishihara, Yen-Chang Chen, Nicholas De Marco, Oliver Lin, Chih-Meng Huang, Vipawee Limsakoune, Yi-Chia Chou, Yang Yang, Vincent Tung
The tantalizing prospect of harnessing the unique properties of graphene crumpled nanostructures continues to fuel tremendous interest in energy storage and harvesting applications. However, the paper ball-like, hard texture, and closed-sphere morphology of current 3D graphitic nanostructure production not only constricts the conductive pathways but also limits the accessible surface area. Here, we report new insights into electrohydrodynamically-generated droplets as colloidal nanoreactors in that the stimuli-responsive nature of reduced graphene oxide can lead to the formation of crumpled nanostructures with a combination of open structures and doubly curved, saddle-shaped edges...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924846/structure-and-dynamics-of-a-constitutively-active-neurotensin-receptor
#10
Brian E Krumm, Sangbae Lee, Supriyo Bhattacharya, Istvan Botos, Courtney F White, Haijuan Du, Nagarajan Vaidehi, Reinhard Grisshammer
Many G protein-coupled receptors show constitutive activity, resulting in the production of a second messenger in the absence of an agonist; and naturally occurring constitutively active mutations in receptors have been implicated in diseases. To gain insight into mechanistic aspects of constitutive activity, we report here the 3.3 Å crystal structure of a constitutively active, agonist-bound neurotensin receptor (NTSR1) and molecular dynamics simulations of agonist-occupied and ligand-free receptor. Comparison with the structure of a NTSR1 variant that has little constitutive activity reveals uncoupling of the ligand-binding domain from conserved connector residues, that effect conformational changes during GPCR activation...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924840/atmospheric-pressure-non-equilibrium-plasma-as-a-green-tool-to-crosslink-gelatin-nanofibers
#11
Anna Liguori, Adriana Bigi, Vittorio Colombo, Maria Letizia Focarete, Matteo Gherardi, Chiara Gualandi, Maria Chiara Oleari, Silvia Panzavolta
Electrospun gelatin nanofibers attract great interest as a natural biomaterial for cartilage and tendon repair despite their high solubility in aqueous solution, which makes them also difficult to crosslink by means of chemical agents. In this work, we explore the efficiency of non-equilibrium atmospheric pressure plasma in stabilizing gelatin nanofibers. We demonstrate that plasma represents an innovative, easy and environmentally friendly approach to successfully crosslink gelatin electrospun mats directly in the solid state...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924680/atomic-insight-into-designed-carbamate-based-derivatives-as-acetylcholine-esterase-ache-inhibitors-a-computational-study-by-multiple-molecular-docking-and-molecular-dynamics-simulation
#12
Tecush Mohammadi, Yousef Ghayeb
Over 100 variants have been designed and studied, using multiple docking methods such as Autodock Vina, ArgusLab, Molegro Virtual Docker (MVD), and Hex-Cuda, to study the effect of alteration in the structure of carbamate based acetylcholyne esterase (AChE) inhibitors. 16 selected systems were then subjected to 14 ns molecular dynamics (MD) simulations. Results from all the docking methods are in agreement. Variants that involved biphenyl substituents possess the most negative binding energies in the -37.64 to -39...
December 7, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27924412/atomistic-study-of-mono-multi-atomic-vacancy-defects-on-the-mechanical-characterization-of-boron-doped-graphene-sheets
#13
A R Setoodeh, H Badjian, H Shirzadi Jahromi
Graphene is known for its exceptional mechanical and electrical properties when in the form of a hexagonal monolayer of carbon atoms. In this study, the mechanical properties of hexagonal boron-doped graphene (h-BdGr) sheets with a 2% concentration of boron atoms distributed randomly throughout the layer were investigated. The effects of mono/multi-atomic vacancy defects, with different concentrations and various orientations, as well as temperature, on the tensile behavior of the sheets were examined utilizing molecular dynamic simulations...
January 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/27924325/lirb2lab2o6-a-new-rare-earth-borate-with-a-mof-5-like-topological-structure-and-a-short-uv-cut-off-edge
#14
Dongdong Xu, Fangfang Zhang, Yanzhou Sun, Zhihua Yang, Binghua Lei, Lili Liu, Shilie Pan
A new rare-earth borate LiRb2LaB2O6 (LB-1) has been synthesized using a high-temperature solution method. Interestingly, it shares its topological structure with the famous porous material MOF-5, which is formed from Zn4O(BDC)3 (BDC = 1,4-benzenedicarboxylate). The nodes [OZn4] and organic linkers [BDC] of MOF-5 are carefully substituted with La(3+) rare-earth cations and the inorganic linkers [BO3] and [LiO4], respectively, in order to construct a pure inorganic open framework. LB-1 exhibits good thermal and water stability...
December 7, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27924191/a-decade-of-biochemical-and-structural-studies-of-the-dna-repair-machinery-of-deinococcus-radiodurans-major-findings-functional-and-mechanistic-insight-and-challenges
#15
REVIEW
Joanna Timmins, Elin Moe
No abstract text is available yet for this article.
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27924027/crystal-structure-of-pseudomonas-aeruginosa-rsal-bound-to-promoter-dna-reaffirms-its-role-as-a-global-regulator-involved-in-quorum-sensing
#16
Huaping Kang, Jianhua Gan, Jingru Zhao, Weina Kong, Jing Zhang, Miao Zhu, Fan Li, Yaqin Song, Jin Qin, Haihua Liang
Pseudomonas aeruginosa possesses at least three well-defined quorum-sensing (QS) (las, rhl and pqs) systems that control a variety of important functions including virulence. RsaL is a QS repressor that reduces QS signal production and ensures homeostasis by functioning in opposition to LasR. However, its regulatory role in signal homeostasis remains elusive. Here, we conducted a ChIP-seq assay and revealed that RsaL bound to two new targets, the intergenic regions of PA2228/PA2229 and pqsH/cdpR, which are required for PQS synthesis...
October 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923993/specific-targeting-of-telomeric-multimeric-g-quadruplexes-by-a-new-triaryl-substituted-imidazole
#17
Ming-Hao Hu, Shuo-Bin Chen, Bo Wang, Tian-Miao Ou, Lian-Quan Gu, Jia-Heng Tan, Zhi-Shu Huang
Multiple G-quadruplex units in the 3'-terminal overhang of human telomeric DNA can associate and form multimeric structures. The specific targeting of such distinctive higher-order G-quadruplexes might be a promising strategy for developing selective anticancer agents with fewer side effects. However, thus far, only a few molecules were found to selectively bind to telomeric multimeric G-quadruplexes, and their effects on cancer cells were unknown. In this study, a new triaryl-substituted imidazole derivative called IZNP-1: was synthesized and found to specifically bind to and strongly stabilize telomeric multimeric G-quadruplexes through intercalating into the pocket between the two quadruplex units...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923813/the-chemical-basis-of-thiol-addition-to-nitro-conjugated-linoleic-acid-a-protective-cell-signaling-lipid
#18
Lucia Turell, Dario A Vitturi, E Laura Coitiño, Lourdes Lebrato, Matias N Moller, Camila Sagasti, Sonia R Salvatore, Steven R Woodcock, Beatriz Alvarez, Francisco J Schopfer
Nitroalkene fatty acids are formed in vivo and exert protective and anti-inflammatory effects via reversible Michael addition to thiol-containing proteins in key signaling pathways. Nitro-conjugated linoleic acid (NO2-CLA) is preferentially formed, constitutes the most abundant nitrated fatty acid in humans and contains two carbons that could potentially react with thiols, modulating signaling actions and levels. In this work, we examined the reactions of NO2-CLA with low molecular weight thiols (glutathione, cysteine, homocysteine, cysteinylglycine and β mercaptoethanol) and human serum albumin (HSA)...
December 6, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27923619/synthesis-and-application-of-%C3%AE-carbolines-as-novel-multi-functional-anti-alzheimer-s-disease-agents
#19
William Horton, Abha Sood, Swarada Peerannawar, Nandor Kugyela, Aditya Kulkarni, Rekha Tulsan, Chris D Tran, Jessica Soule, Harry LeVine, Béla Török, Marianna Török
The design, synthesis and assessment of β-carboline core-based compounds as potential multifunctional agents against several processes that are believed to play a significant role in Alzheimer's disease (AD) pathology, are described. The activity of the compounds was determined in Aβ self-assembly (fibril and oligomer formation) and cholinesterase (AChE, BuChE) activity inhibition, and their antioxidant properties were also assessed. To obtain insight into the mode of action of the compounds, HR-MS studies were carried out on the inhibitor-Aβ complex formation and molecular docking was performed on inhibitor-BuChE interactions...
November 24, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27923350/coneva-a-toolbox-for-comprehensive-assessment-of-protein-contacts
#20
Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
BACKGROUND: In recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein structure prediction methods. It is also observed that for almost all globular proteins, the quality of contact prediction dictates the accuracy of structure prediction. Hence, like many existing evaluation measures for evaluating 3D protein models, various measures are currently used to evaluate predicted contacts, with the most popular ones being precision, coverage and distance distribution score (Xd)...
December 7, 2016: BMC Bioinformatics
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