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Protein sliding dna

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https://www.readbyqxmd.com/read/27926800/interobserver-reproducibility-of-cytologic-p16-ink4a-ki-67-dual-immunostaining-in-human-papillomavirus-positive-women
#1
Maria Benevolo, Elena Allia, Daniela Gustinucci, Francesca Rollo, Simonetta Bulletti, Elena Cesarini, Basilio Passamonti, Maria Rosaria Giovagnoli, Elisabetta Carico, Francesca M Carozzi, Alessandra Mongia, Giulia Fantacci, Massimo Confortini, Teresa Rubino, Cristina Fodero, Sonia Prandi, Natalina Marchi, Angelo Farruggio, Anna Coccia, Luigia Macrì, Bruno Ghiringhello, Guglielmo Ronco, Emma Bragantini, Enzo Polla, Vincenzo Maccallini, Giovanni Negri, Paolo Giorgi Rossi
BACKGROUND: The accumulation of cyclin-dependent kinase inhibitor 2A (p16(ink4a) ) protein in a cell is associated with neoplastic progression in precancerous cervical lesions. Dual staining for p16(ink4a) and Ki-67 has been proposed as a triage test in cervical cancer screening for women who test positive for human papillomavirus DNA. In this study, interobserver reproducibility of the interpretation of this test was assessed. METHODS: Forty-two immunostained, liquid-based cytology slides were divided into 2 sets and were interpreted by 17 to 21 readers from 9 different laboratories, yielding a total of 816 reports...
December 7, 2016: Cancer
https://www.readbyqxmd.com/read/27913731/disentangling-polydispersity-in-the-pcna-p15paf-complex-a-disordered-transient-and-multivalent-macromolecular-assembly
#2
Tiago N Cordeiro, Po-Chia Chen, Alfredo De Biasio, Nathalie Sibille, Francisco J Blanco, Jochen S Hub, Ramon Crehuet, Pau Bernadó
The intrinsically disordered p15(PAF) regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15(PAF) and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27851738/cascading-muts-and-mutl-sliding-clamps-control-dna-diffusion-to-activate-mismatch-repair
#3
Jiaquan Liu, Jeungphill Hanne, Brooke M Britton, Jared Bennett, Daehyung Kim, Jong-Bong Lee, Richard Fishel
Mismatched nucleotides arise from polymerase misincorporation errors, recombination between heteroallelic parents and chemical or physical DNA damage. Highly conserved MutS (MSH) and MutL (MLH/PMS) homologues initiate mismatch repair and, in higher eukaryotes, act as DNA damage sensors that can trigger apoptosis. Defects in human mismatch repair genes cause Lynch syndrome or hereditary non-polyposis colorectal cancer and 10-40% of related sporadic tumours. However, the collaborative mechanics of MSH and MLH/PMS proteins have not been resolved in any organism...
November 16, 2016: Nature
https://www.readbyqxmd.com/read/27815500/a-hidden-active-site-in-the-potential-drug-target-mycobacterium-tuberculosis-dutpase-is-accessible-through-small-amplitude-protein-conformational-changes
#4
Anna Lopata, Ibolya Leveles, Abris A Bendes, Bela Viskolcz, Beata G Vertessy, Balazs Jojart, Judit Toth
dUTPases catalyze the hydrolysis of dUTP into dUMP and pyrophosphate to maintain the proper nucleotide pool for DNA metabolism. Recent evidence suggests dUTPases may also represent a selective drug target in mycobacteria because of these enzymes' crucial role in maintaining DNA integrity. Nucleotide-hydrolyzing enzymes typically harbor a buried ligand-binding pocket at interdomain or intersubunit clefts, facilitating proper solvent shielding for the catalyzed reaction. The mechanism by which substrate binds this hidden pocket and product is released in dUTPases is unresolved due to conflicting crystallographic and spectroscopic data...
November 4, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27813331/sliding-on-dna-from-peptides-to-small-molecules
#5
Kan Xiong, Graham S Erwin, Aseem Z Ansari, Paul C Blainey
Many DNA binding proteins utilize one-dimensional (1D) diffusion along DNA to accelerate their DNA target recognition. Although 1D diffusion of proteins along DNA has been studied for decades, a quantitative understanding is only beginning to emerge and few chemical tools are available to apply 1D diffusion as a design principle. Recently, we discovered that peptides can bind and slide along DNA-even transporting cargo along DNA. Such molecules are known as molecular sleds. Here, to advance our understanding of structure-function relationships governing sequence nonspecific DNA interaction of natural molecular sleds and to explore the potential for controlling sliding activity, we test the DNA binding and sliding activities of chemically modified peptides and analogs, and show that synthetic small molecules can slide on DNA...
November 4, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27738136/dynamic-unwrapping-of-nucleosomes-by-hsrad51-that-includes-sliding-and-rotational-motion-of-histone-octamers
#6
Gayan Senavirathne, Santosh K Mahto, Jeungphill Hanne, Daniel O'Brian, Richard Fishel
Wrapping of genomic DNA into nucleosomes poses thermodynamic and kinetic barriers to biological processes such as replication, transcription, repair and recombination. Previous biochemical studies have demonstrated that in the presence of adenosine triphosphate (ATP) the human RAD51 (HsRAD51) recombinase can form a nucleoprotein filament (NPF) on double-stranded DNA (dsDNA) that is capable of unwrapping the nucleosomal DNA from the histone octamer (HO). Here, we have used single molecule Förster Resonance Energy Transfer (smFRET) to examine the real time nucleosome dynamics in the presence of the HsRAD51 NPF...
October 13, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27694621/single-molecule-fret-studies-of-the-cooperative-and-non-cooperative-binding-kinetics-of-the-bacteriophage-t4-single-stranded-dna-binding-protein-gp32-to-ssdna-lattices-at-replication-fork-junctions
#7
Wonbae Lee, John P Gillies, Davis Jose, Brett A Israels, Peter H von Hippel, Andrew H Marcus
Gene 32 protein (gp32) is the single-stranded (ss) DNA binding protein of the bacteriophage T4. It binds transiently and cooperatively to ssDNA sequences exposed during the DNA replication process and regulates the interactions of the other sub-assemblies of the replication complex during the replication cycle. We here use single-molecule FRET techniques to build on previous thermodynamic studies of gp32 binding to initiate studies of the dynamics of the isolated and cooperative binding of gp32 molecules within the replication complex...
September 30, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27685804/identification-of-%C3%AE-clamp-dna-interaction-regions-that-impair-the-ability-of-e-coli-to-tolerate-specific-classes-of-dna-damage
#8
Michael T Nanfara, Vignesh M P Babu, Mohamed A Ghazy, Mark D Sutton
The E. coli dnaN-encoded β sliding clamp protein plays a pivotal role in managing the actions on DNA of the 5 bacterial DNA polymerases, proteins involved in mismatch repair, as well as several additional proteins involved in DNA replication. Results of in vitro experiments indicate that the loading of β clamp onto DNA relies on both the DnaX clamp loader complex as well as several discrete sliding clamp-DNA interactions. However, the importance of these DNA interactions to E. coli viability, as well as the ability of the β clamp to support the actions of its numerous partner proteins, have not yet been examined...
2016: PloS One
https://www.readbyqxmd.com/read/27651172/sliding-clamp-of-dna-polymerase-iii-as-a-drug-target-for-tb-therapy-comprehensive-conformational-and-binding-analysis-from-molecular-dynamic-simulations
#9
Kgothatso E Machaba, Favorite N Cele, Ndumiso N Mhlongo, Mahmoud E S Soliman
Tuberculosis, caused by Mycobacterium tuberculosis, is one of the most common causes of death in the world. Mycobacterium tuberculosis -sliding clamp is a protein essential for many important DNA transactions including replication and DNA repair proteins, thus, a potential drug target for tuberculosis. Further investigation is needed in understanding DNA polymerase sliding clamp structure, especially from a computational perspective. In this study, we employ a wide-range of comparative molecular dynamic analyses on two systems: Mycobacterium tuberculosis - sliding clamp enzyme in its apo and bound form...
September 20, 2016: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/27635237/how-mcm-loading-and-spreading-specify-eukaryotic-dna-replication-initiation-sites
#10
REVIEW
Olivier Hyrien
DNA replication origins strikingly differ between eukaryotic species and cell types. Origins are localized and can be highly efficient in budding yeast, are randomly located in early fly and frog embryos, which do not transcribe their genomes, and are clustered in broad (10-100 kb) non-transcribed zones, frequently abutting transcribed genes, in mammalian cells. Nonetheless, in all cases, origins are established during the G1-phase of the cell cycle by the loading of double hexamers of the Mcm 2-7 proteins (MCM DHs), the core of the replicative helicase...
2016: F1000Research
https://www.readbyqxmd.com/read/27591891/the-chromatin-remodelling-protein-chd1-contains-a-previously-unrecognised-c-terminal-helical-domain
#11
Biswaranjan Mohanty, Stephanie Helder, Ana P G Silva, Joel P Mackay, Daniel P Ryan
The packaging of eukaryotic DNA into nucleosomes, and the organisation of these nucleosomes into chromatin, plays a critical role in regulating all DNA-associated processes. Chromodomain helicase DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin remodelling protein that is conserved throughout eukaryotes and has an ability to assemble and organise nucleosomes both in vitro and in vivo. This activity is involved in the regulation of transcription and is implicated in mammalian development and stem cell biology...
October 23, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27580107/comparison-of-gene-expression-profiles-of-t-cells-in-porcine-colostrum-and-peripheral-blood
#12
Shohei Ogawa, Mie Okutani, Takamitsu Tsukahara, Nobuo Nakanishi, Yoshihiro Kato, Kikuto Fukuta, Gustavo A Romero-Pérez, Kazunari Ushida, Ryo Inoue
OBJECTIVE To compare gene expression patterns of T cells in porcine colostrum and peripheral blood. ANIMALS 10 multiparous sows. PROCEDURES Cytotoxic and CD4-CD8 double-positive T cells were separated from porcine colostrum and peripheral blood. Total RNA was extracted. The cDNA prepared from RNA was amplified, labeled, fragmented, and competitively hybridized to DNA microarray slides. The DNA microarray data were validated by use of a real-time reverse-transcription PCR assay, and expression of the genes FOS, NFKBI, IFNG, CXCR6, CCR5, ITGB2, CCR7, and SELL was assessed...
September 2016: American Journal of Veterinary Research
https://www.readbyqxmd.com/read/27576706/the-relationship-between-human-nucleolar-organizer-regions-and-nucleoli-probed-by-3d-immunofish
#13
Marjolein van Sluis, Chelly van Vuuren, Brian McStay
3D-immunoFISH is a valuable technique to compare the localization of DNA sequences and proteins in cells where three-dimensional structure has been preserved. As nucleoli contain a multitude of protein factors dedicated to ribosome biogenesis and form around specific chromosomal loci, 3D-immunoFISH is a particularly relevant technique for their study. In human cells, nucleoli form around transcriptionally active ribosomal gene (rDNA) arrays termed nucleolar organizer regions (NORs) positioned on the p-arms of each of the acrocentric chromosomes...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27573245/human-dna-ligase-i-interacts-with-and-is-targeted-for-degradation-by-the-dcaf7-specificity-factor-of-the-cul4-ddb1-ubiquitin-ligase-complex
#14
Zhimin Peng, Zhongping Liao, Yoshihiro Matsumoto, Austin Yang, Alan E Tomkinson
The synthesis, processing, and joining of Okazaki fragments during DNA replication is complex, requiring the sequential action of a large number of proteins. Proliferating cell nuclear antigen, a DNA sliding clamp, interacts with and coordinates the activity of several DNA replication proteins, including the enzymes flap endonuclease 1 (FEN-1) and DNA ligase I that complete the processing and joining of Okazaki fragments, respectively. Although it is evident that maintaining the appropriate relative stoichiometry of FEN-1 and DNA ligase I, which compete for binding to proliferating cell nuclear antigen, is critical to prevent genomic instability, little is known about how the steady state levels of DNA replication proteins are regulated, in particular the proteolytic mechanisms involved in their turnover...
October 14, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27554844/on-the-domains-of-t4-phage-sliding-clamp-gp45-an-intermolecular-crosstalk-governs-structural-stability-and-biological-activity
#15
Manika Indrajit Singh, Bylapudi Ganesh, Vikas Jain
BACKGROUND: DNA polymerase processivity factors are ubiquitously present in all living organisms. Notwithstanding their high significance, the molecular details of clamps pertaining to the factors contributing to their stability are presently lacking. The bacteriophage T4 sliding clamp gp45 forms a homotrimer that besides being involved in DNA replication, moonlights as a transcription factor. Here we have carried out a detailed characterization of gp45 to understand the role of monomer-monomer interface interactions in stability and functioning of the protein...
August 21, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27535137/human-ino80-yy1-chromatin-remodeling-complex-transcriptionally-regulates-the-brca2-and-cdkn1a-interacting-protein-bccip-in-cells
#16
Jiaming Su, Yi Sui, Jian Ding, Fuqiang Li, Shuang Shen, Yang Yang, Zeming Lu, Fei Wang, Lingling Cao, Xiaoxia Liu, Jingji Jin, Yong Cai
The BCCIP (BRCA2- and CDKN1A-interacting protein) is an important cofactor for BRCA2 in tumor suppression. Although the low expression of BCCIP is observed in multiple clinically diagnosed primary tumor tissues such as ovarian cancer, renal cell carcinoma and colorectal carcinoma, the mechanism of how BCCIP is regulated in cells is still unclear. The human INO80/YY1 chromatin remodeling complex composed of 15 subunits catalyzes ATP-dependent sliding of nucleosomes along DNA. Here, we first report that BCCIP is a novel target gene of the INO80/YY1 complex by presenting a series of experimental evidence...
October 2016: Protein & Cell
https://www.readbyqxmd.com/read/27466393/single-strand-transposition-at-the-host-replication-fork
#17
Laure Lavatine, Susu He, Anne Caumont-Sarcos, Catherine Guynet, Brigitte Marty, Mick Chandler, Bao Ton-Hoang
Members of the IS200/IS605 insertion sequence family differ fundamentally from classical IS essentially by their specific single-strand (ss) transposition mechanism, orchestrated by the Y1 transposase, TnpA, a small HuH enzyme which recognizes and processes ss DNA substrates. Transposition occurs by the 'peel and paste' pathway composed of two steps: precise excision of the top strand as a circular ss DNA intermediate; and subsequent integration into a specific ssDNA target. Transposition of family members was experimentally shown or suggested by in silico high-throughput analysis to be intimately coupled to the lagging strand template of the replication fork...
September 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27437582/sliding-sleeves-of-xrcc4-xlf-bridge-dna-and-connect-fragments-of-broken-dna
#18
Ineke Brouwer, Gerrit Sitters, Andrea Candelli, Stephanie J Heerema, Iddo Heller, Abinadabe J de Melo, Hongshan Zhang, Davide Normanno, Mauro Modesti, Erwin J G Peterman, Gijs J L Wuite
Non-homologous end joining (NHEJ) is the primary pathway for repairing DNA double-strand breaks (DSBs) in mammalian cells. Such breaks are formed, for example, during gene-segment rearrangements in the adaptive immune system or by cancer therapeutic agents. Although the core components of the NHEJ machinery are known, it has remained difficult to assess the specific roles of these components and the dynamics of bringing and holding the fragments of broken DNA together. The structurally similar XRCC4 and XLF proteins are proposed to assemble as highly dynamic filaments at (or near) DSBs...
July 28, 2016: Nature
https://www.readbyqxmd.com/read/27417498/dynamics-of-plant-dna-replication-based-on-pcna-visualization
#19
Ryohei Yokoyama, Takeshi Hirakawa, Seri Hayashi, Takuya Sakamoto, Sachihiro Matsunaga
DNA replication is an essential process for the copying of genomic information in living organisms. Imaging of DNA replication in tissues and organs is mainly performed using fixed cells after incorporation of thymidine analogs. To establish a useful marker line to measure the duration of DNA replication and analyze the dynamics of DNA replication, we focused on the proliferating cell nuclear antigen (PCNA), which functions as a DNA sliding clamp for replicative DNA polymerases and is an essential component of replisomes...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27399259/structure-of-chromatin-remodeler-swi2-snf2-in-the-resting-state
#20
Xian Xia, Xiaoyu Liu, Tong Li, Xianyang Fang, Zhucheng Chen
SWI2/SNF2 family proteins regulate a myriad of nucleic acid transactions by sliding, removing and reconstructing nucleosomes in eukaryotic cells. They contain two RecA-like core domains, which couple ATP hydrolysis and DNA translocation to chromatin remodeling. Here we report the crystal structure of Snf2 from the yeast Myceliophthora thermophila. The data show the two RecA-like core domains of Snf2 stacking together and twisting their ATP-binding motifs away from each other, thus explaining the inactivity of the protein in the ground state...
August 2016: Nature Structural & Molecular Biology
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