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DNA molecular dynamics

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https://www.readbyqxmd.com/read/29656601/culture-independent-analysis-of-hydrocarbonoclastic-bacterial-communities-in-environmental-samples-during-oil-bioremediation
#1
Narjes Dashti, Nedaa Ali, Samar Salamah, Majida Khanafer, Ghada Al-Shamy, Husain Al-Awadhi, Samir S Radwan
To analyze microbial communities in environmental samples, this study combined Denaturing Gradient Gel Electrophoresis of amplified 16S rRNA-genes in total genomic DNA extracts from those samples with gene sequencing. The environmental samples studied were oily seawater and soil samples, that had been bioaugmented with natural materials rich in hydrocarbonoclastic bacteria. This molecular approach revealed much more diverse bacterial taxa than the culture-dependent method we had used in an earlier study for the analysis of the same samples...
April 15, 2018: MicrobiologyOpen
https://www.readbyqxmd.com/read/29652261/structural-and-functional-roles-of-dynamically-correlated-residues-in-thymidylate-kinase
#2
Santosh Kumar Chaudhary, Jeyaraman Jeyakanthan, Kanagaraj Sekar
Thymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, with ATP as the preferred phosphoryl donor, in the presence of Mg2+ . In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase from Thermus thermophilus. Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of the enzyme...
April 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29650553/enduring-epigenetic-landmarks-define-the-cancer-microenvironment
#3
Ruth Pidsley, Mitchell G Lawrence, Elena Zotenko, Birunthi Niranjan, Aaron Statham, Jenny Song, Roman M Chabanon, Wenjia Qu, Hong Wang, Michelle Richards, Shalima S Nair, Nicola J Armstrong, Hieu T Nim, Melissa Papargiris, Preetika Balanathan, Hugh French, Timothy Peters, Sam Norden, Andrew Ryan, John Pedersen, James Kench, Roger J Daly, Lisa G Horvath, Phillip Stricker, Mark Frydenberg, Renea A Taylor, Clare Stirzaker, Gail P Risbridger, Susan J Clark
The growth and progression of solid tumors involves dynamic cross-talk between cancer epithelium and the surrounding microenvironment. To date, molecular profiling has largely been restricted to the epithelial component of tumors; therefore, features underpinning the persistent protumorigenic phenotype of the tumor microenvironment are unknown. Using whole-genome bisulfite sequencing, we show for the first time that cancer-associated fibroblasts (CAFs) from localized prostate cancer display remarkably distinct and enduring genome-wide changes in DNA methylation, significantly at enhancers and promoters, compared to nonmalignant prostate fibroblasts (NPFs)...
April 12, 2018: Genome Research
https://www.readbyqxmd.com/read/29650370/open-boundary-molecular-dynamics-of-a-dna-molecule-in-a-hybrid-explicit-implicit-salt-solution
#4
Julija Zavadlav, Jurij Sablić, Rudolf Podgornik, Matej Praprotnik
The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system's electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions...
April 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29649876/biomolecular-simulations-under-realistic-macroscopic-salt-conditions
#5
Gregory A Ross, Ariën S Rustenburg, Patrick B Grinaway, Josh Fass, John Damon Chodera
Biomolecular simulations are typically performed in an aqueous environment where the number of ions remains fixed for the duration of the simulation, generally with either a minimally neutralizing ion environment or a number of salt pairs intended to match the macroscopic salt concentration. In contrast, real biomolecules experience local ion environments where the salt concentration is dynamic and may differ from bulk. The degree of salt concentration variability and average deviation from the macroscopic concentration remains, as yet, unknown...
April 13, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29648440/spontaneous-transport-of-single-stranded-dna-through-graphene-mos-2-heterostructure-nanopores
#6
Binquan Luan, Ruhong Zhou
The effective transport of a single-stranded DNA (ssDNA) molecule through a solid-state nanopore is essential to the future success of high-throughput and low-cost DNA sequencing. Compatible with current electric sensing technologies, here, we propose and demonstrate by molecular dynamics simulations the ssDNA transport through a quasi-two-dimensional nanopore in a heterostructure stacked together with different 2D materials, such as graphene and molybdenum disulfide (MoS2 ). Due to different chemical potentials, U, of DNA bases on different 2D materials, it is energetically favorable for a ssDNA molecule to move from the low- U MoS2 surface to the high- U graphene surface through a nanopore...
April 12, 2018: ACS Nano
https://www.readbyqxmd.com/read/29625198/rela-containing-nf%C3%AE%C2%BAb-dimers-have-strikingly-different-dna-binding-cavities-in-the-absence-of-dna
#7
Dominic Narang, Wei Chen, Clarisse G Ricci, Elizabeth A Komives
The main NFκB transcription factor family members RelA-p50 heterodimer and RelA homodimer have different biological functions and show different transcriptional activation profiles. To investigate whether the two family members adopt a similar conformation in their free states, we performed hydrogen-deuterium exchange mass spectrometry (HDXMS), all-atom molecular dynamics (MD) simulations and stopped-flow binding kinetics experiments. Surprisingly, the N-terminal DNA binding domains adopt an open conformation in RelA-p50 but a closed conformation in RelA homodimer...
April 3, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29624374/ph-responsive-nanoparticle-superlattices-with-tunable-dna-bonds
#8
Jinghan Zhu, Youngeun Kim, Haixin Lin, Shunzhi Wang, Chad A Mirkin
Stimuli-responsive nanomaterials with reconfigurable structures and properties have garnered significant interest in the fields of optics, electronics, magnetics, and therapeutics. DNA is a powerful and versatile building material that provides programmable structural and dynamic properties, and indeed, sequence-dependent changes in DNA have already been exploited in creating switchable DNA-based architectures. However, rather than designing a new DNA input sequence for each intended dynamic change, it would be useful to have one simple, generalized stimulus design that could provide multiple different structural outputs...
April 6, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29621315/molecular-evolution-of-dnmt1-in-vertebrates-duplications-in-marsupials-followed-by-positive-selection
#9
David Alvarez-Ponce, María Torres-Sánchez, Felix Feyertag, Asmita Kulkarni, Taylen Nappi
DNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes three active Dnmts (Dnmt1, Dnmt3a and Dnmt3b), the tRNA methyltransferase Dnmt2, and the regulatory protein Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates...
2018: PloS One
https://www.readbyqxmd.com/read/29620943/epigenome-wide-analysis-reveals-specific-dna-hypermethylation-of-t-cells-during-human-hematopoietic-differentiation
#10
J Ramón Tejedor, Clara Bueno, Isabel Cobo, Gustavo F Bayón, Cristina Prieto, Cristina Mangas, Raúl F Pérez, Pablo Santamarina, Rocío G Urdinguio, Pablo Menéndez, Mario F Fraga, Agustín F Fernández
AIM: Epigenetic regulation plays an important role in cellular development and differentiation. A detailed map of the DNA methylation dynamics that occur during cell differentiation would contribute to decipher the molecular networks governing cell fate commitment. METHODS: Illumina MethylationEPIC BeadChip platform was used to describe the genome-wide DNA methylation changes observed throughout hematopoietic maturation by analyzing multiple myeloid and lymphoid hematopoietic cell types...
April 5, 2018: Epigenomics
https://www.readbyqxmd.com/read/29620482/capecitabine-as-a-minor-groove-binder-of-dna-molecular-docking-molecular-dynamics-and-multi-spectroscopic-studies
#11
Shuangshuang Zhang, Hongqin Yang, Ludan Zhao, Ruixue Gan, Peixiao Tang, Qiaomei Sun, Xinnuo Xiong, Hui Li
The interaction mechanism and binding mode of capecitabine with ctDNA was extensively investigated using docking and molecular dynamics (MD) simulations, fluorescence and circular dichroism (CD) spectroscopy, DNA thermal denaturation studies, and viscosity measurements. The possible binding mode and acting forces on the combination between capecitabine and DNA had been predicted through molecular simulation. Results indicated that capecitabine could relatively locate stably in the G-C base-pairs-rich DNA minor groove by hydrogen bond and several weaker nonbonding forces...
April 5, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29617661/integrated-genomic-analysis-of-the-ubiquitin-pathway-across-cancer-types
#12
Zhongqi Ge, Jake S Leighton, Yumeng Wang, Xinxin Peng, Zhongyuan Chen, Hu Chen, Yutong Sun, Fan Yao, Jun Li, Huiwen Zhang, Jianfang Liu, Craig D Shriver, Hai Hu, Helen Piwnica-Worms, Li Ma, Han Liang
Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atlas, we perform comprehensive molecular characterization of 929 ubiquitin-related genes and 95 deubiquitinase genes. Among them, we systematically identify top somatic driver candidates, including mutated FBXW7 with cancer-type-specific patterns and amplified MDM2 showing a mutually exclusive pattern with BRAF mutations...
April 3, 2018: Cell Reports
https://www.readbyqxmd.com/read/29617130/structure-and-dynamics-of-dna-and-rna-double-helices-obtained-from-the-ccg-and-ggc-trinucleotide-repeats
#13
Feng Pan, Viet Hoang Man, Christopher Roland, Celeste Sagui
Expansions of both GGC and CCG sequences lead to a number of expandable, trinucleotide repeat (TR) neurodegenerative diseases. Understanding of these diseases involves, among other things, the structural characterization of the atypical DNA and RNA secondary structures. We have performed molecular dynamics simulations of (GCC)_n and (GGC)_n homoduplexes in order to characterize their conformations, stability and dynamics. Each TR has two reading frames, which results in eight non-equivalent RNA/DNA homoduplexes, characterized by CpG or GpC steps between the Watson-Crick basepairs...
April 4, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29610944/imaging-the-dynamics-of-transcription-loops-in-living-chromosomes
#14
Garry T Morgan
When in the lampbrush configuration, chromosomes display thousands of visible DNA loops that are transcribed at exceptionally high rates by RNA polymerase II (pol II). These transcription loops provide unique opportunities to investigate not only the detailed architecture of pol II transcription sites but also the structural dynamics of chromosome looping, which is receiving fresh attention as the organizational principle underpinning the higher-order structure of all chromosome states. The approach described here allows for extended imaging of individual transcription loops and transcription units under conditions in which loop RNA synthesis continues...
April 3, 2018: Chromosoma
https://www.readbyqxmd.com/read/29609544/detection-of-ctx-m-15-harboring-escherichia-coli-isolated-from-wild-birds-in-tunisia
#15
Houssem Ben Yahia, Rym Ben Sallem, Ghassan Tayh, Naouel Klibi, Insaf Ben Amor, Haythem Gharsa, Abdellatif Boudabbous, Karim Ben Slama
BACKGROUND: The spreading of antibiotic resistant bacteria is becoming nowadays an alarming threat to human and animal health. There is increasing evidence showing that wild birds could significantly contribute to the transmission and spreading of drug-resistant bacteria. However, data for antimicrobial resistance in wild birds remain scarce, especially throughout Africa. The aims of this investigation were to analyze the prevalence of ESBL-producing E. coli in faecal samples of wild birds in Tunisia and to characterize the recovered isolates...
April 2, 2018: BMC Microbiology
https://www.readbyqxmd.com/read/29608918/a-new-multiplex-pcr-protocol-to-detect-mixed-trypanosomatid-infections-in-species-of-apis-and-bombus
#16
Carolina Bartolomé, María Buendía, María Benito, Pilar De la Rúa, Concepción Ornosa, Raquel Martín-Hernández, Mariano Higes, Xulio Maside
Trypanosomatids are highly prevalent pathogens of Hymenoptera; however, most molecular methods used to detect them in Apis and Bombus spp. do not allow the identification of the infecting species, which then becomes expensive and time consuming. To overcome this drawback, we developed a multiplex PCR protocol to readily identify in a single reaction the main trypanosomatids present in these hymenopterans (Lotmaria passim, Crithidia mellificae and Crithidia bombi), which will facilitate the study of their epidemiology and transmission dynamics...
March 30, 2018: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/29608908/cinpa1-binds-directly-to-constitutive-androstane-receptor-and-inhibits-its-activity
#17
Milu T Cherian, Sergio C Chai, William C Wright, Aman Singh, Morgan Alexandra Casal, Jie Zheng, Jing Wu, Richard E Lee, Patrick R Griffin, Taosheng Chen
The constitutive androstane receptor (CAR) and pregnane X receptor (PXR) are xenobiotic sensors that regulate the expression of drug-metabolizing enzymes and efflux transporters. CAR activation promotes drug elimination, thereby reducing therapeutic effectiveness, or causes adverse drug effects via toxic metabolites. CAR inhibitors could be used to attenuate these adverse drug effects. CAR and PXR share ligands and target genes, confounding the understanding of the regulation of receptor-specific activity. We previously identified a small-molecule inhibitor, CINPA1, that inhibits CAR (without activating PXR at lower concentrations) by altering CAR-coregulator interactions and reducing CAR recruitment to DNA response elements of regulated genes...
March 30, 2018: Biochemical Pharmacology
https://www.readbyqxmd.com/read/29605933/modeling-structure-and-dynamics-of-protein-complexes-with-saxs-profiles
#18
Dina Schneidman-Duhovny, Michal Hammel
Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29605844/cpg-islands-a-historical-perspective
#19
Francisco Antequera, Adrian Bird
The discovery of CpG islands (CGIs) and the study of their structure and properties run parallel to the development of molecular biology in the last two decades of the twentieth century and to the development of high-throughput genomic technologies at the turn of the millennium. First identified as discrete G + C-rich regions of unmethylated DNA in several vertebrates, CGIs were soon found to display additional distinctive chromatin features from the rest of the genome in terms of accessibility and of the epigenetic modifications of their histones...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29604840/detection-of-kinetic-change-points-in-piece-wise-linear-single-molecule-motion
#20
Flynn R Hill, Antoine M van Oijen, Karl E Duderstadt
Single-molecule approaches present a powerful way to obtain detailed kinetic information at the molecular level. However, the identification of small rate changes is often hindered by the considerable noise present in such single-molecule kinetic data. We present a general method to detect such kinetic change points in trajectories of motion of processive single molecules having Gaussian noise, with a minimum number of parameters and without the need of an assumed kinetic model beyond piece-wise linearity of motion...
March 28, 2018: Journal of Chemical Physics
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