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DNA molecular dynamics

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https://www.readbyqxmd.com/read/28231333/molecular-mechanisms-of-cooperative-binding-of-transcription-factors-runx1-cbf%C3%AE-ets1-on-the-tcr%C3%AE-gene-enhancer
#1
Kota Kasahara, Masaaki Shiina, Ikuo Fukuda, Kazuhiro Ogata, Haruki Nakamura
Ets1 is an essential transcription factor (TF) for several important physiological processes, including cell proliferation and differentiation. Its recognition of the enhancer region of the TCRα gene is enhanced by the cooperative binding of the Runx1-CBFβ heterodimer, with the cancelation of phosphorylation-dependent autoinhibition. The detailed mechanism of this interesting cooperativity between Ets1 and the Runx1-CBFβ heterodimer is still largely unclear. Here, we investigated the molecular mechanisms of this cooperativity, by using molecular dynamics simulations...
2017: PloS One
https://www.readbyqxmd.com/read/28231280/alkbh7-variant-related-to-prostate-cancer-exhibits-altered-substrate-binding
#2
Alice R Walker, Pavel Silvestrov, Tina A Müller, Robert H Podolsky, Gregory Dyson, Robert P Hausinger, Gerardo Andrés Cisneros
The search for prostate cancer biomarkers has received increased attention and several DNA repair related enzymes have been linked to this dysfunction. Here we report a targeted search for single nucleotide polymorphisms (SNPs) and functional impact characterization of human ALKBH family dioxygenases related to prostate cancer. Our results uncovered a SNP of ALKBH7, rs7540, which is associated with prostate cancer disease in a statistically significantly manner in two separate cohorts, and maintained in African American men...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28230082/tubz-filament-assembly-dynamics-requires-the-flexible-c-terminal-tail
#3
Maria E Fuentes-Pérez, Rafael Núñez-Ramírez, Alejandro Martín-González, David Juan-Rodríguez, Oscar Llorca, Fernando Moreno-Herrero, Maria A Oliva
Cytomotive filaments are essential for the spatial organization in cells, showing a dynamic behavior based on nucleotide hydrolysis. TubZ is a tubulin-like protein that functions in extrachromosomal DNA movement within bacteria. TubZ filaments grow in a helical fashion following treadmilling or dynamic instability, although the underlying mechanism is unclear. We have unraveled the molecular basis for filament assembly and dynamics combining electron and atomic force microscopy and biochemical analyses. Our findings suggest that GTP caps retain the filament helical structure and hydrolysis triggers filament stiffening upon disassembly...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223401/transcriptome-analyses-of-rhesus-monkey-pre-implantation-embryos-reveal-a-reduced-capacity-for-dna-double-strand-break-repair-in-primate-oocytes-and-early-embryos
#4
Xinyi Wang, Denghui Liu, Dajian He, Shengbo Suo, Xian Xia, Xiechao He, Jing-Dong Han, Ping Zheng
Pre-implantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA), and cell fate commitment, most of which remain mechanistically unclear in primates. In addition, primates display a high rate of embryo wastage without any clear molecular basis. Understanding the factors involved in genome reprogramming and ZGA will help the generation of induced pluripotent stem cells with high efficiency. Moreover, explaining the molecular basis responsible for embryo wastage in primates will greatly expand our knowledge of species evolution...
February 21, 2017: Genome Research
https://www.readbyqxmd.com/read/28222666/dynamic-tracing-for-epidermal-growth-factor-receptor-mutations-in-urinary-circulating-dna-in-gastric-cancer-patients
#5
Xiu-Qin Shi, Wen-Hua Xue, Song-Feng Zhao, Xiao-Jian Zhang, Wukong Sun
The mutations of epidermal growth factor receptor are detected in gastric cancer, indicating its suitability as a target for receptor tyrosine kinase inhibitors, as well as a marker for clinical outcome of chemotherapeutic treatments. However, extraction of quality tumor tissue for molecular processes remains challenging. Here, we aimed to examine the clinical relevance of urinary cell-free DNA as an alternative tumor material source used specifically for monitoring epidermal growth factor receptor mutations...
February 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28222192/blastocystis-subtyping-and-its-association-with-intestinal-parasites-in-children-from-different-geographical-regions-of-colombia
#6
Juan David Ramírez, Carolina Flórez, Mario Olivera, María Consuelo Bernal, Julio Cesar Giraldo
Blastocystis is a common enteric protist colonizing probably more than 1 billion people with a large variety of non-human hosts. Remarkable genetic diversity has been observed, leading to the subdivision of the genus into multiple subtypes (ST), some of which are exclusively found in non-human hosts. The aim of this study was to determine the distribution of Blastocystis STs/18S alleles in symptomatic (abdominal pain, anal pruritus, diarrhea, headache, nauseas and/or vomit) and asymptomatic children from nine geographical regions of Colombia...
2017: PloS One
https://www.readbyqxmd.com/read/28220432/genome-wide-analysis-of-chromatin-accessibility-in-arabidopsis-infected-with-pseudomonas-syringae
#7
Yogendra Bordiya, Hong-Gu Kang
Changes in chromatin accessibility are an important aspect of the molecular changes that occur in eukaryotic cells responding to stress, and they appear to play a critical role in stress-induced transcriptional activation/reprogramming and epigenetic changes. In plants, pathogen infection has been shown to induce rapid and drastic transcriptional reprogramming; growing evidence suggests that chromatin remodeling plays an essential role in this phenomenon. The recent development of genomic tools to assess chromatin accessibility presents a significant opportunity to investigate the relationship between chromatin dynamicity and gene expression...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28220131/plant-stress-responses-and-phenotypic-plasticity-in-the-epigenomics-era-perspectives-on-the-grapevine-scenario-a-model-for-perennial-crop-plants
#8
Ana M Fortes, Philippe Gallusci
Epigenetic marks include Histone Post-Translational Modifications and DNA methylation which are known to participate in the programming of gene expression in plants and animals. These epigenetic marks may be subjected to dynamic changes in response to endogenous and/or external stimuli and can have an impact on phenotypic plasticity. Studying how plant genomes can be epigenetically shaped under stressed conditions has become an essential issue in order to better understand the molecular mechanisms underlying plant stress responses and enabling epigenetic in addition to genetic factors to be considered when breeding crop plants...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28218791/development-and-validation-of-the-first-ssr-markers-for-mimosa-scabrella-benth
#9
F A Saiki, A P Bernardi, M S Reis, H Faoro, E M Souza, F O Pedrosa, A Mantovani, A F Guidolin
Mimosa scabrella Benth., popularly known as ''bracatinga'', is a pioneer and endemic species of Brazil, occurring in Mixed Ombrophilous Forest associated with Brazilian Atlantic Rainforest biomes. It is a fast-growing tree of the Fabaceae family that facilitates the dynamics of ecological succession. SSR development, when there is no genome sequence, is time and labor intensive and there are no molecular markers for M. scabrella. We developed and validated the first microsatellite markers for this tetraploid species, evaluating mother trees and progenies...
February 16, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28218519/probing-the-dynamic-interaction-between-damaged-dna-and-a-cellular-responsive-protein-using-a-piezoelectric-mass-biosensor
#10
Yulong Jin, Yunfeng Xie, Kui Wu, Yanyan Huang, Fuyi Wang, Rui Zhao
The binding events between damaged DNA and recognition biomolecules are of great interest for understanding of the activity of DNA-damaging drugs and the related DNA repair networks. Herein, a simple and sensitive sensor system was tailored for real-time probing the dynamic molecular recognition between cisplatin-damaged DNA (cisPt-DNA) and a cellular responsive protein, high mobility group box 1 (HMGB1). By integrating of flow injection analysis (FIA) with quartz crystal microbalance (QCM), the interaction time-course of cisPt-DNA and HMGB1 domain A (HMGB1a) was investigated...
February 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28218463/closed-reference-metatranscriptomics-enables-in-planta-profiling-of-putative-virulence-activities-in-the-grapevine-trunk-disease-complex
#11
Abraham Morales-Cruz, Gabrielle Allenbeck, Rosa Figueroa-Balderas, Vanessa E Ashworth, Daniel P Lawrence, Renaud Travadon, Rhonda J Smith, Kendra Baumgartner, Philippe E Rolshausen, Dario Cantu
Grapevines, like other perennial crops, are affected by so-called 'trunk diseases', which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i...
February 20, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28216791/molecular-processes-leading-to-necking-in-extensional-flow-of-polymer-solutions-using-microfluidics-and-single-dna-imaging
#12
Shaurya Sachdev, Aswin Muralidharan, Pouyan E Boukany
We study the necking and pinch-off dynamics of liquid droplets that contain a semidilute polymer solution of polyacrylamide close to overlap concentration by combining microfluidics and single DNA observation. Polymeric droplets are stretched by passing them through the stagnation point of a T-shaped microfluidic junction. In contrast with the sudden breakup of Newtonian droplets, a stable neck is formed between the separating ends of the droplet which delays the breakup process. Initially, polymeric filaments experience exponential thinning by forming a stable neck with extensional flow within the filament...
December 27, 2016: Macromolecules
https://www.readbyqxmd.com/read/28215227/elucidating-the-mutational-landscape-in-hepatocyte-nuclear-factor-1%C3%AE-hnf1b-by-computational-approach
#13
P Sneha, C G P Doss
Transcription factors are the major gene-regulatory proteins that recognize specific nucleotide sequences and bind to them. Missense mutations in transcription factors play a significant role in misregulation of gene expression contributing to various diseases and disorders. Understanding their structural and functional impact of the disease-causing mutations becomes prime importance in treating a disease. Commonly associated defect with the mutations of hepatocyte nuclear factor 1 beta (HNF1B) protein, a transcription factor results in maturity-onset diabetes of the young-5 (MODY-5) leading to loss of function...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28211525/focus-on-pna-flexibility-and-rna-binding-using-molecular-dynamics-and-metadynamics
#14
Massimiliano Donato Verona, Vincenzo Verdolino, Ferruccio Palazzesi, Roberto Corradini
Peptide Nucleic Acids (PNAs) can efficiently target DNA or RNA acting as chemical tools for gene regulation. Their backbone modification and functionalization is often used to increase the affinity for a particular sequence improving selectivity. The understanding of the trading forces that lead the single strand PNA to bind the DNA or RNA sequence is preparatory for any further rational design, but a clear and unique description of this process is still not complete. In this paper we report further insights into this subject, by a computational investigation aiming at the characterization of the conformations of a single strand PNA and how these can be correlated to its capability in binding DNA/RNA...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28209181/de-novo-sequencing-and-comparative-transcriptome-analysis-of-adventitious-root-development-induced-by-exogenous-indole-3-butyric-acid-in-cuttings-of-tetraploid-black-locust
#15
Jine Quan, Seng Meng, Erhui Guo, Sheng Zhang, Zhong Zhao, Xitian Yang
BACKGROUND: Indole-3-butyric acid (IBA) is applied to the cuttings of various plant species to induce formation of adventitious roots (ARs) in commercial settings. Tetraploid black locust is an attractive ornamental tree that is drought resistant, sand tolerant, can prevent sand erosion and has various commercial uses. To further elucidate the mechanisms of AR formation, we used Illumina sequencing to analyze transcriptome dynamics and differential gene expression at four developmental stages in control (CK) and IBA-treated groups...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28207811/accelerated-flexible-protein-ligand-docking-using-hamiltonian-replica-exchange-with-a-repulsive-biasing-potential
#16
Katja Ostermeir, Martin Zacharias
A molecular dynamics replica exchange based method has been developed that allows rapid identification of putative ligand binding sites on the surface of biomolecules. The approach employs a set of ambiguity restraints in replica simulations between receptor and ligand that allow close contacts in the reference replica but promotes transient dissociation in higher replicas. This avoids long-lived trapping of the ligand or partner proteins at nonspecific, sticky, sites on the receptor molecule and results in accelerated exploration of the possible binding regions...
2017: PloS One
https://www.readbyqxmd.com/read/28207277/proton-dynamics-in-protein-mass-spectrometry
#17
Jinyu Li, Wenping Lyu, Giulia Rossetti, Albert Konijnenberg, Antonino Natalello, Emiliano Ippoliti, Modesto Orozco, Frank Sobott, Rita Grandori, Paolo Carloni
Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and its impact on protein structural determinants, have not been investigated so far. Here, we address this issue by a multistep simulation strategy on a pharmacologically relevant peptide, the N-terminal residues of amyloid-β peptide (Aβ(1-16)). Our calculations reproduce the experimental maximum charge state from ESI-MS and are also in fair agreement with collision cross section (CCS) data measured here by ESI/IM-MS...
February 22, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28206745/atomistic-molecular-dynamics-simulations-of-mitochondrial-dna-polymerase-%C3%AE-novel-mechanisms-of-function-and-pathogenesis
#18
Liliya Euro, Outi Haapanen, Tomasz Róg, Ilpo Vattulainen, Anu Suomalainen, Vivek Sharma
DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex...
February 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28203077/biosensing-of-dna-oxidative-damage-a-model-of-using-glucose-meter-for-non-glucose-biomarker-detection
#19
Xuena Zhu, Mehenur Sarwar, Qiaoli Yue, Chunying Chen, Chen-Zhong Li
Non-glucose biomarker-DNA oxidative damage biomarker 8-hydroxy-2'-deoxyguanosine (8-OHdG) has been successfully detected using a smartphone-enabled glucose meter. Through a series of immune reactions and enzymatic reactions on a solid lateral flow platform, 8-OHdG concentration has been converted to a relative amount of glucose, and therefore can be detected by conventional glucose meter directly. The device was able to detect 8-OHdG concentrations in phosphate buffer saline as low as 1.73 ng mL(-1) with a dynamic range of 1-200 ng mL(-1)...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28198806/arrays-of-individual-dna-molecules-on-nanopatterned-substrates
#20
Roland Hager, Alma Halilovic, Jonathan R Burns, Friedrich Schäffler, Stefan Howorka
Arrays of individual molecules can combine the advantages of microarrays and single-molecule studies. They miniaturize assays to reduce sample and reagent consumption and increase throughput, and additionally uncover static and dynamic heterogeneity usually masked in molecular ensembles. However, realizing single-DNA arrays must tackle the challenge of capturing structurally highly dynamic strands onto defined substrate positions. Here, we create single-molecule arrays by electrostatically adhering single-stranded DNA of gene-like length onto positively charged carbon nanoislands...
February 13, 2017: Scientific Reports
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