keyword
MENU ▼
Read by QxMD icon Read
search

Structural bioinformatics

keyword
https://www.readbyqxmd.com/read/28748912/a-novel-allosteric-site-in-casein-kinase-2%C3%AE-discovered-using-combining-bioinformatics-and-biochemistry-methods
#1
Hai-Ming Jiang, Jiang-Kai Dong, Kun Song, Tong-Dan Wang, Wen-Kang Huang, Jing-Miao Zhang, Xiu-Yan Yang, Ying Shen, Jian Zhang
Casein kinase 2 (CK2) is a highly pleiotropic serine-threonine kinase, which catalyzed phosphorylation of more than 300 proteins that are implicated in regulation of many cellular functions, such as signal transduction, transcriptional control, apoptosis and the cell cycle. On the other hand, CK2 is abnormally elevated in a variety of tumors, and is considered as a promising therapeutic target. The currently available ATP-competitive CK2 inhibitors, however, lack selectivity, which has impeded their development in cancer therapy...
July 27, 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/28748551/identification-of-a-dimeric-kdg-aldolase-from-agrobacterium-tumefaciens
#2
Tatiana P Soares da Costa, Madhvi Patel, Sebastien Desbois, Ruchi Gupta, Pierre Faou, Matthew A Perugini
Agrobacterium tumefaciens is a Gram-negative bacterium and causative agent of Crown Gall disease that infects a variety of economically-important plants. The annotated A. tumefaciens genome contains 10 putative dapA genes, which code for dihydrodipicolinate synthase (DHDPS). However, we have recently demonstrated that only one of these genes (dapA7) encodes a functional DHDPS. The function of the other nine putative dapA genes is yet to be determined. Here, we demonstrate using bioinformatics that the product of the dapA5 gene (DapA5) possesses all the catalytic residues canonical to 2-keto-3-deoxygluconate (KDG) aldolase, which is a class I aldolase involved in glucose metabolism...
July 27, 2017: Proteins
https://www.readbyqxmd.com/read/28748209/metagenomic-data-of-free-cyanide-and-thiocyanate-degrading-bacterial-communities
#3
Lukhanyo Mekuto, Seteno K O Ntwampe, John B N Mudumbi, Enoch A Akinpelu, Maxwell Mewa-Ngongang
The data presented in this article contains the bacterial community structure of the free cyanide (CN(-)) and thiocyanate (SCN(-)) degrading organisms that were isolated from electroplating wastewater and synthetic SCN(-) containing wastewater. PCR amplification of the 16S rRNA V1-V3 regions was undertaken using the 27F and 518R oligonucleotide primers following the metacommunity DNA extraction procedure. The PCR amplicons were processed using the illumina® reaction kits as per manufacturer׳s instruction and sequenced using the illumina® MiSeq-2000, using the MiSeq V3 kit...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28744787/on-the-possibility-of-an-early-evolutionary-origin-for-the-spliced-leader-trans-splicing
#4
Zuzana Krchňáková, Juraj Krajčovič, Matej Vesteg
Trans-splicing is a process by which 5'- and 3'-ends of two pre-RNA molecules transcribed from different sites of the genome can be joined together to form a single RNA molecule. The spliced leader (SL) trans-splicing is mediated by the spliceosome and it allows the replacement of 5'-end of pre-mRNA by 5'(SL)-end of SL-RNA. This form of splicing has been observed in many phylogenetically unrelated eukaryotes. Either the SL trans-splicing (SLTS) originated in the last eukaryotic common ancestor (LECA) (or even earlier) and it was lost in most eukaryotic lineages, or this mechanism of RNA processing evolved several times independently in various unrelated eukaryotic taxa...
July 25, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28743673/genomic-landscape-of-copy-number-variation-and-copy-neutral-loss-of-heterozygosity-events-in-equine-sarcoids-reveals-increased-instability-of-the-sarcoid-genome
#5
Klaudia Pawlina, Artur Gurgul, Tomasz Szmatoła, Katarzyna Ropka-Molik, Ewelina Semik, Jolanta Klukowska-Rötzler, Christoph Koch, Kathrin Mählmann, Monika Bugno-Poniewierska
Although they are the most common neoplasms in equids, sarcoids are not fully characterized at the molecular level. Therefore, the objective of this study was to characterize the landscape of structural rearrangements, such as copy number variation (CNV) and copy neutral loss of heterozygosity (cnLOH), in the genomes of sarcoid tumor cells. This information will not only broaden our understanding of the characteristics of this genome but will also improve the general knowledge of this tumor and the mechanisms involved in its generation...
July 22, 2017: Biochimie
https://www.readbyqxmd.com/read/28743644/species-trees-from-consensus-single-nucleotide-polymorphism-snp-data-testing-phylogenetic-approaches-with-simulated-and-empirical-data
#6
Alexander N Schmidt-Lebuhn, Nicola C Aitken, Aaron Chuah
Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species...
July 22, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28736756/advancing-the-science-of-myocardial-recovery-with-mechanical-circulatory-support-a-working-group-of-the-national-heart-lung-and-blood-institute
#7
Stavros G Drakos, Francis D Pagani, Martha S Lundberg, J Timothy Baldwin
The medical burden of heart failure (HF) has spurred interest in clinicians and scientists to develop therapies to restore the function of a failing heart. To advance this agenda, the National Heart Lung Blood Institute (NHLBI) convened a Working Group of experts on June 2-3, 2016 in Bethesda Maryland to develop recommendations for the NHLBI aimed at advancing the science of cardiac recovery in the setting of mechanical circulatory support (MCS). MSC devices effectively reduce volume and pressure overload that drives the cycle of progressive myocardial dysfunction, thereby triggering structural and functional reverse remodeling...
June 2017: JACC. Basic to Translational Science
https://www.readbyqxmd.com/read/28736529/detection-of-ros-induced-proteomic-signatures-by-mass-spectrometry
#8
REVIEW
Brian McDonagh
Reversible and irreversible post-translational modifications (PTMs) induced by endogenously generated reactive oxygen species (ROS) in regulatory enzymes and proteins plays an essential role in cellular signaling. Almost all cellular processes including metabolism, transcription, translation and degradation have been identified as containing redox regulated proteins. Specific redox modifications of key amino acids generated by ROS offers a dynamic and versatile means to rapidly alter the activity or functional structure of proteins in response to biochemical, environmental, genetic and pathological perturbations...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28735622/modeling-rna-secondary-structure-with-sequence-comparison-and-experimental-mapping-data
#9
Zhen Tan, Gaurav Sharma, David H Mathews
Secondary structure prediction is an important problem in RNA bioinformatics because knowledge of structure is critical to understanding the functions of RNA sequences. Significant improvements in prediction accuracy have recently been demonstrated though the incorporation of experimentally obtained structural information, for instance using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) mapping. However, such mapping data is currently available only for a limited number of RNA sequences...
July 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28735540/the-n%C3%A2-%C3%AF-interaction
#10
Robert W Newberry, Ronald T Raines
The carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group...
July 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28733845/genome-wide-identification-in-silico-characterization-and-expression-analysis-of-zip-like-genes-from-trichomonas-vaginalis-in-response-to-zinc-and-iron
#11
K G Fernández-Martín, M E Alvarez-Sánchez, V E Arana-Argáez, L C Alvarez-Sánchez, J C Lara-Riegos, J C Torres-Romero
Trace elements such as Zinc and Iron are essential components of metalloproteins and serve as cofactors or structural elements for enzymes involved in several important biological processes in almost all organisms. Because either excess or insufficient levels of Zn and Fe can be harmful for the cells, the homeostatic levels of these trace minerals must be tightly regulated. The Zinc regulated transporter, Iron regulated transporter-like Proteins (ZIP) comprise a diverse family, with several paralogues in diverse organisms and are considered essential for the Zn and Fe uptake and homeostasis...
July 21, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28732007/a-data-driven-modeling-approach-to-identify-disease-specific-multi-organ-networks-driving-physiological-dysregulation
#12
Warren D Anderson, Danielle DeCicco, James S Schwaber, Rajanikanth Vadigepalli
Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension). We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28730979/adsorption-of-staphylococcus-viruses-s13-and-s24-1-on-staphylococcus-aureus-strains-with-different-glycosidic-linkage-patterns-of-wall-teichoic-acids
#13
Jumpei Uchiyama, Maya Taniguchi, Kenji Kurokawa, Iyo Takemura-Uchiyama, Takako Ujihara, Hidekatsu Shimakura, Yoshihiko Sakaguchi, Hironobu Murakami, Masahiro Sakaguchi, Shigenobu Matsuzaki
The group of phages belonging to the family Podoviridae, genus P68virus, including Staphylococcus viruses S13' and S24-1, are important because of their benefits in phage therapy against Staphylococcus aureus infections. The O-glycosidic linkage patterns of wall teichoic acids (WTAs) in S. aureus cell walls seem to be important for adsorption of this phage group. In this study, the adsorption of Staphylococcus viruses S13' and S24-1 to S. aureus was examined using strains with modified WTA glycosidic linkage patterns...
July 21, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28728879/identification-of-universal-diagnostic-peptide-candidates-for-neglected-tropical-diseases-caused-by-cestodes-through-the-integration-of-multi-genome-wide-analyses-and-immunoinformatic-predictions
#14
Sebastián Miles, Marco Navatta, Sylvia Dematteis, Gustavo Mourglia-Ettlin
Neglected tropical diseases caused by helminth infections currently affect millions of people worldwide. Among them, there are three tapeworm species of outstanding importance: Echinococcus granulosus, E. multilocularis, and Taenia solium, which are responsible for cystic echinococcosis, alveolar echinococcosis, and cysticercosis, respectively. Despite several attempts, there is still a need for an effective and low-cost serological diagnostic test that can be used in endemic countries. In the present work, we described an innovative bioinformatic workflow for a rational prediction of putative peptide candidates for one-step serological diagnosis of any of these infections...
July 17, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28727099/identification-of-differentially-expressed-proteins-in-testicular-semen-of-sex-reversed-female-xx-and-normal-male-xy-rainbow-trout
#15
J Nynca, M Adamek, A Ciereszko
Masculinized females, named sex-reversed females (SRF), have a male phenotype but retain the female genotype (XX) and all spermatozoa produced in their testes carry the X chromosome. Masculinization of females leads to incomplete testicular development and the production of lower-quality semen. The mechanism of masculinization is unknown at present. Therefore, the aim of our study was to identify differentially abundant proteins in testicular semen of normal males and SRF using a difference in-gel electrophoresis approach...
July 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28724407/characterization-of-the-cytochrome-p450-monooxygenase-genes-p450ome-from-the-carotenogenic-yeast-xanthophyllomyces-dendrorhous
#16
Pamela Córdova, Ana-María Gonzalez, David R Nelson, María-Soledad Gutiérrez, Marcelo Baeza, Víctor Cifuentes, Jennifer Alcaíno
BACKGROUND: The cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases involved in the oxidative metabolism of an enormous diversity of substrates. These enzymes require electrons for their activity, and the electrons are supplied by NAD(P)H through a P450 electron donor system, which is generally a cytochrome P450 reductase (CPR). The yeast Xanthophyllomyces dendrorhous has evolved an exclusive P450-CPR system that specializes in the synthesis of astaxanthin, a carotenoid with commercial potential...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28720122/enhance-the-performance-of-current-scoring-functions-with-the-aid-of-3d-protein-ligand-interaction-fingerprints
#17
Jie Liu, Minyi Su, Zhihai Liu, Jie Li, Yan Li, Renxiao Wang
BACKGROUND: In structure-based drug design, binding affinity prediction remains as a challenging goal for current scoring functions. Development of target-biased scoring functions provides a new possibility for tackling this problem, but this approach is also associated with certain technical difficulties. We previously reported the Knowledge-Guided Scoring (KGS) method as an alternative approach (BMC Bioinformatics, 2010, 11, 193-208). The key idea is to compute the binding affinity of a given protein-ligand complex based on the known binding data of an appropriate reference complex, so the error in binding affinity prediction can be reduced effectively...
July 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28716709/isolation-and-characterization-of-the-5-flanking-region-of-the-human-pdxk-gene
#18
ShuoHao Huang, ZhengQing Liu, ZhenQiao Ma, JianYun Zhang, LongQuan Huang
Pyridoxal kinase is a key enzyme for the biosynthesis of pyridoxal 5'-phosphate. Pyridoxal 5'-phosphate is the catalytically active form of vitamin B6, and acts as a cofactor in >140 different enzyme reactions. It is still unknown how the kinase synthesis is regulated in the cells, and nothing has been reported about the gene promoter. In the present study, based on the bioinformatics analysis of the 5'-flanking region of the human PDXK gene, we cloned the promoter region by PCR. Through the construction of a series of luciferase expression vectors containing the human PDXK promoter region, we characterized the promoter in terms of its structure and function...
July 14, 2017: Gene
https://www.readbyqxmd.com/read/28715844/effects-of-pathogenic-variations-in-the-human-rhodopsin-gene-hrho-on-the-predicted-accessibility-for-a-lead-candidate-ribozyme
#19
Beau R Froebel, Alexandria J Trujillo, Jack M Sullivan
Purpose: The mutation-independent strategy for hammerhead ribozyme (hhRz) or RNA interference (RNAi)-based gene therapeutics to treat autosomal dominant diseases is predicated on the hypothesis that a single therapeutic would equivalently suppress all/most of the diverse mutant mRNAs in patients with the disease phenotype. However, the hypothesis has not been formally tested. We address this through a comprehensive bioinformatics study of how mutations affect target mRNA structure accessibility for a single lead hhRz therapeutic (725GUC↓), designed against human rod rhodopsin mRNA (hRHO), for patients with hRHO mutations that cause autosomal dominant retinitis pigmentosa...
July 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28715614/intraperitoneal-administration-of-adipose-tissue-derived-stem-cells-for-the-rescue-of-retinal-degeneration-in-a-mouse-model-via-indigenous-cntf-up-regulation-by-il-6
#20
Jeong Hoon Heo, Jung Ae Yoon, Eun Kyung Ahn, Hyun Kim, Sang Hwa Urm, Chul Oh Oak, Byeng Chul Yu, Sang Joon Lee
As the world's population begins to age, retinal degeneration is an increasing problem, and various treatment modalities are being developed. However, there have been no therapies for degenerative retinal conditions that are not characterized by neovascularization. We investigated whether transplantation of mouse adipose tissue-derived stem cells (mADSC) into the intraperitoneal space has a rescue effect on NaIO3 -induced retinal degeneration in mice. In this study, mADSC transplantation recovered visual function and preserved the retinal outer layer structure compared to the control group without any integration of mADSC into the retina...
July 17, 2017: Journal of Tissue Engineering and Regenerative Medicine
keyword
keyword
13141
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"