keyword
MENU ▼
Read by QxMD icon Read
search

folding

keyword
https://www.readbyqxmd.com/read/28335582/nonradiative-relaxation-mechanisms-of-uv-excited-phenylalanine-residues-a-comparative-computational-study
#1
Momir Mališ, Nađa Došlić
The present work is directed toward understanding the mechanisms of excited state deactivation in three neutral model peptides containing the phenylalanine residue. The excited state dynamics of theγL(g+)folded form of N-acetylphenylalaninylamide (NAPA B) and its amide-N-methylated derivative (NAPMA B) is reviewed and compared to the dynamics of the monohydrated structure of NAPA (NAPAH). The goal is to unravel how the environment, and in particular solvation, impacts the photodynamics of peptides. The systems are investigated using reaction path calculations and surface hopping nonadiabatic dynamics based on the coupled cluster doubles (CC2) method and time-dependent density functional theory...
March 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335556/trm5-and-trmd-two-enzymes-from-distinct-origins-catalyze-the-identical-trna-modification-m%C3%A2-g37
#2
REVIEW
Sakurako Goto-Ito, Takuhiro Ito, Shigeyuki Yokoyama
The N¹-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m¹G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs...
March 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28335520/endoplasmic-reticulum-stress-and-unfolded-protein-response-in-cartilage-pathophysiology-contributing-factors-to-apoptosis-and-osteoarthritis
#3
REVIEW
Alexandria Hughes, Alexandra E Oxford, Ken Tawara, Cheryl L Jorcyk, Julia Thom Oxford
Chondrocytes of the growth plate undergo apoptosis during the process of endochondral ossification, as well as during the progression of osteoarthritis. Although the regulation of this process is not completely understood, alterations in the precisely orchestrated programmed cell death during development can have catastrophic results, as exemplified by several chondrodystrophies which are frequently accompanied by early onset osteoarthritis. Understanding the mechanisms that underlie chondrocyte apoptosis during endochondral ossification in the growth plate has the potential to impact the development of therapeutic applications for chondrodystrophies and associated early onset osteoarthritis...
March 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335441/dietary-intake-of-individual-free-and-intrinsic-sugars-and-food-sources-in-the-spanish-population-findings-from-the-anibes-study
#4
Emma Ruiz, Paula Rodriguez, Teresa Valero, José M Ávila, Javier Aranceta-Bartrina, Ángel Gil, Marcela González-Gross, Rosa M Ortega, Lluis Serra-Majem, Gregorio Varela-Moreiras
The consumption of total and individual sugars is controversial and little is known about consumption and dietary sources in Spain. The purpose was to examine free and intrinsic sugar intake and food and beverage sources. The ANIBES Study (Anthropometry, Intake and Energy Balance in Spain), a cross-sectional study of a representative sample of the Spanish population (9-75 years old; n = 2009) carried out in 2013, was used. Food and beverage records were obtained by a three-day dietary record by using a tablet device...
March 14, 2017: Nutrients
https://www.readbyqxmd.com/read/28335390/a-simple-metallothionein-based-biosensor-for-enhanced-detection-of-arsenic-and-mercury
#5
Gordon W Irvine, Swee Ngin Tan, Martin J Stillman
Metallothioneins (MTs) are a family of cysteine-rich proteins whose biological roles include the regulation of essential metal ions and protection against the harmful effects of toxic metals. Due to its high affinity for many toxic, soft metals, recombinant human MT isoform 1a was incorporated into an electrochemical-based biosensor for the detection of As(3+) and Hg(2+). A simple design was chosen to maximize its potential in environmental monitoring and MT was physically adsorbed onto paper discs placed on screen-printed carbon electrodes (SPCEs)...
March 13, 2017: Biosensors
https://www.readbyqxmd.com/read/28335304/silver-nanoparticle-embedded-thin-silica-coated-graphene-oxide-as-an-sers-substrate
#6
Xuan-Hung Pham, Eunil Hahm, Hyung-Mo Kim, Seongbo Shim, Tae Han Kim, Dae Hong Jeong, Yoon-Sik Lee, Bong-Hyun Jun
A hybrid of Ag nanoparticle (NP)-embedded thin silica-coated graphene oxide (GO@SiO₂@Ag NPs) was prepared as a surface-enhanced Raman scattering (SERS) substrate. A 6 nm layer of silica was successfully coated on the surface of GO by the physical adsorption of sodium silicate, followed by the hydrolysis of 3-mercaptopropyl trimethoxysilane. Ag NPs were introduced onto the thin silica-coated graphene oxide by the reduction of Ag⁺ to prepare GO@SiO₂@Ag NPs. The GO@SiO₂@Ag NPs exhibited a 1.8-fold enhanced Raman signal compared to GO without a silica coating...
September 22, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335195/pmn-pt-pvdf-nanocomposite-for-high-output-nanogenerator-applications
#7
Chuan Li, Wenbo Luo, Xingzhao Liu, Dong Xu, Kai He
The 0.7Pb(Mg1/3Nb2/3)O₃-0.3PbTiO₃(0.7PMN-0.3PT) nanorods were obtained via hydrothermal method with high yield (over 78%). Then, new piezoelectric nanocomposites based on (1-x)Pb(Mg1/3Nb2/3)O₃-xPbTiO₃ (PMN-PT) nanorods were fabricated by dispersing the 0.7PMN-0.3PT nanorods into piezoelectric poly(vinylidene fluoride) (PVDF) polymer. The mechanical behaviors of the nanocomposites were investigated. The voltage and current generation of PMN-PT/PVDF nanocomposites were also measured. The results showed that the tensile strength, yield strength, and Young's modulus of nanocomposites were enhanced as compared to that of the pure PVDF...
April 11, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335003/identification-of-genetic-variants-affecting-vitamin-d-receptor-binding-and-associations-with-autoimmune-disease
#8
Giuseppe Gallone, Wilfried Haerty, Giulio Disanto, Sreeram V Ramagopalan, Chris P Ponting, Antonio J Berlanga-Taylor
Large numbers of statistically significant associations between sentinel SNPs and case-control status have been replicated by genome-wide association studies. Nevertheless, few underlying molecular mechanisms of complex disease are currently known. We investigated whether variation in binding of a transcription factor, the vitamin D receptor (VDR) whose activating ligand vitamin D has been proposed as a modifiable factor in multiple disorders, could explain any of these associations. VDR modifies gene expression by binding DNA as a heterodimer with the Retinoid X receptor (RXR)...
March 9, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28335001/fastkd1-and-fastkd4-have-opposite-effects-on-expression-of-specific-mitochondrial-rnas-depending-upon-their-endonuclease-like-rap-domain
#9
Erik Boehm, Sofia Zaganelli, Kinsey Maundrell, Alexis A Jourdain, Stéphane Thore, Jean-Claude Martinou
FASTK family proteins have been identified as regulators of mitochondrial RNA homeostasis linked to mitochondrial diseases, but much remains unknown about these proteins. We show that CRISPR-mediated disruption of FASTKD1 increases ND3 mRNA level, while disruption of FASTKD4 reduces the level of ND3 and of other mature mRNAs including ND5 and CYB, and causes accumulation of ND5-CYB precursor RNA. Disrupting both FASTKD1 and FASTKD4 in the same cell results in decreased ND3 mRNA similar to the effect of depleting FASTKD4 alone, indicating that FASTKD4 loss is epistatic...
March 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334976/a-sensitivity-analysis-of-rna-folding-nearest-neighbor-parameters-identifies-a-subset-of-free-energy-parameters-with-the-greatest-impact-on-rna-secondary-structure-prediction
#10
Jeffrey Zuber, Hongying Sun, Xiaoju Zhang, Iain McFadyen, David H Mathews
Nearest neighbor parameters for estimating the folding energy changes of RNA secondary structures are used in structure prediction and analysis. Despite their widespread application, a comprehensive analysis of the impact of each parameter on the precision of calculations had not been conducted. To identify the parameters with greatest impact, a sensitivity analysis was performed on the 291 parameters that compose the 2004 version of the free energy nearest neighbor rules. Perturbed parameter sets were generated by perturbing each parameter independently...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334968/postoperative-stridor-following-repair-of-tracheoesophageal-fistula-a-case-report
#11
Showkat Hussain Tali, Nandkishore Shrikishanji Kabra, Javed Ahmed, Jui Mandke, Haribalakrishna Balasubramanian, Manohar Shaan, Swarup Kumar Dash, Shagufta Yousuf
We report a case of prolonged post-operative stridor in a full-term neonate who was operated for tracheoesophageal fistula. Initial evaluation including an endoscopy and contrast-enhanced computed tomography scan was normal. Repeat endoscopic evaluation under anesthesia revealed tight aryepiglottic folds. Aryepiglottic split was performed and stridor improved dramatically. Tight aryepiglottic folds should be kept in differential diagnosis in a case of postoperative stridor in an infant.
March 8, 2017: Journal of Tropical Pediatrics
https://www.readbyqxmd.com/read/28334932/ribosome-dependent-vibrio-cholerae-mrnase-higb2-is-regulated-by-a-%C3%AE-strand-sliding-mechanism
#12
San Hadži, Abel Garcia-Pino, Sarah Haesaerts, Dukas Jurenas, Kenn Gerdes, Jurij Lah, Remy Loris
Toxin-antitoxin (TA) modules are small operons involved in bacterial stress response and persistence. higBA operons form a family of TA modules with an inverted gene organization and a toxin belonging to the RelE/ParE superfamily. Here, we present the crystal structures of chromosomally encoded Vibrio cholerae antitoxin (VcHigA2), toxin (VcHigB2) and their complex, which show significant differences in structure and mechanisms of function compared to the higBA module from plasmid Rts1, the defining member of the family...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334926/can-memory-assessment-services-mas-in-england-be-categorized-a-national-survey
#13
T Chrysanthaki, B Fernandes, S Smith, N Black
Background: The effectiveness and efficiency of memory assessment services (MASs) is unknown. Our aim was to determine if a typology can be constructed, based on shared structural and process characteristics, as a basis for a non-randomized evaluation of their effectiveness and cost-effectiveness. Methods: Survey of random sample of 73 MASs in 2015; comparison of characteristics and investigation of inter-correlation. Results: It was not possible to group characteristics to form the basis of a typology of MASs...
March 2, 2017: Journal of Public Health
https://www.readbyqxmd.com/read/28334922/scn2a-deletion-improves-survival-and-brain-heart-dynamics-in-the-kcna1-null-mouse-model-of-sudden-unexpected-death-in-epilepsy-sudep
#14
Vikas Mishra, Bharat K Karumuri, Nicole M Gautier, Rui Liu, Timothy N Hutson, Stephanie L Vanhoof-Villalba, Ioannis Vlachos, Leonidas Iasemidis, Edward Glasscock
People with epilepsy have greatly increased probability of premature mortality due to sudden unexpected death in epilepsy (SUDEP). Identifying which patients are most at risk of SUDEP is hindered by a complex genetic etiology, incomplete understanding of the underlying pathophysiology, and lack of prognostic biomarkers. Here we evaluated heterozygous Scn2a gene deletion (Scn2a+/-) as a protective genetic modifier in the Kcna1 knockout mouse (Kcna1-/-) model of SUDEP, while searching for biomarkers of SUDEP risk embedded in electroencephalography (EEG) and electrocardiography (ECG) recordings...
March 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334887/avoidance-of-apobec3b-induced-mutation-by-error-free-lesion-bypass
#15
James I Hoopes, Amber L Hughes, Lauren A Hobson, Luis M Cortez, Alexander J Brown, Steven A Roberts
APOBEC cytidine deaminases mutate cancer genomes by converting cytidines into uridines within ssDNA during replication. Although uracil DNA glycosylases limit APOBEC-induced mutation, it is unknown if subsequent base excision repair (BER) steps function on replication-associated ssDNA. Hence, we measured APOBEC3B-induced CAN1 mutation frequencies in yeast deficient in BER endonucleases or DNA damage tolerance proteins. Strains lacking Apn1, Apn2, Ntg1, Ntg2 or Rev3 displayed wild-type frequencies of APOBEC3B-induced canavanine resistance (CanR)...
March 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334881/random-pseuoduridylation-in-vivo-reveals-critical-region-of-escherichia-coli-23s-rrna-for-ribosome-assembly
#16
Margus Leppik, Aivar Liiv, Jaanus Remme
Pseudouridine is the most common modified nucleoside in RNA, which is found in stable RNA species and in eukaryotic mRNAs. Functional analysis of pseudouridine is complicated by marginal effect of its absence. We demonstrate that excessive pseudouridines in rRNA inhibit ribosome assembly. Ten-fold increase of pseudouridines in the 16S and 23S rRNA made by a chimeric pseudouridine synthase leads to accumulation of the incompletely assembled large ribosome subunits. Hyper modified 23S rRNA is found in the r-protein assembly defective particles and are selected against in the 70S and polysome fractions showing modification interference...
March 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334877/iron-mediates-catalysis-of-nucleic-acid-processing-enzymes-support-for-fe-ii-as-a-cofactor-before-the-great-oxidation-event
#17
C Denise Okafor, Kathryn A Lanier, Anton S Petrov, Shreyas S Athavale, Jessica C Bowman, Nicholas V Hud, Loren Dean Williams
Life originated in an anoxic, Fe2+-rich environment. We hypothesize that on early Earth, Fe2+ was a ubiquitous cofactor for nucleic acids, with roles in RNA folding and catalysis as well as in processing of nucleic acids by protein enzymes. In this model, Mg2+ replaced Fe2+ as the primary cofactor for nucleic acids in parallel with known metal substitutions of metalloproteins, driven by the Great Oxidation Event. To test predictions of this model, we assay the ability of nucleic acid processing enzymes, including a DNA polymerase, an RNA polymerase and a DNA ligase, to use Fe2+ in place of Mg2+ as a cofactor during catalysis...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334873/alternative-dna-structure-formation-in-the-mutagenic-human-c-myc-promoter
#18
Imee Marie A Del Mundo, Maha Zewail-Foote, Sean M Kerwin, Karen M Vasquez
Mutation 'hotspot' regions in the genome are susceptible to genetic instability, implicating them in diseases. These hotspots are not random and often co-localize with DNA sequences potentially capable of adopting alternative DNA structures (non-B DNA, e.g. H-DNA and G4-DNA), which have been identified as endogenous sources of genomic instability. There are regions that contain overlapping sequences that may form more than one non-B DNA structure. The extent to which one structure impacts the formation/stability of another, within the sequence, is not fully understood...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334779/targeted-gene-knock-in-by-homology-directed-genome-editing-using-cas9-ribonucleoprotein-and-aav-donor-delivery
#19
Thomas Gaj, Brett T Staahl, Gonçalo M C Rodrigues, Prajit Limsirichai, Freja K Ekman, Jennifer A Doudna, David V Schaffer
Realizing the full potential of genome editing requires the development of efficient and broadly applicable methods for delivering programmable nucleases and donor templates for homology-directed repair (HDR). The RNA-guided Cas9 endonuclease can be introduced into cells as a purified protein in complex with a single guide RNA (sgRNA). Such ribonucleoproteins (RNPs) can facilitate the high-fidelity introduction of single-base substitutions via HDR following co-delivery with a single-stranded DNA oligonucleotide...
March 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334773/a-critical-assessment-of-topologically-associating-domain-prediction-tools
#20
Rola Dali, Mathieu Blanchette
Topologically associating domains (TADs) have been proposed to be the basic unit of chromosome folding and have been shown to play key roles in genome organization and gene regulation. Several different tools are available for TAD prediction, but their properties have never been thoroughly assessed. In this manuscript, we compare the output of seven different TAD prediction tools on two published Hi-C data sets. TAD predictions varied greatly between tools in number, size distribution and other biological properties...
March 2, 2017: Nucleic Acids Research
keyword
keyword
38814
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"