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Relevant bibliographies by topics / Protein-DNA

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Academic literature on the topic 'Protein-DNA'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 May 2024

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Journal articles on the topic "Protein-DNA"

1

Culard, Françoise, Serge Bouffard, and Michel Charlier. "High-LET Irradiation of a DNA-Binding Protein: Protein-Protein and DNA-Protein Crosslinks." Radiation Research 164, no. 6 (December 2005): 774–80. http://dx.doi.org/10.1667/rr3456.1.

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Chen, Stefanie H., and Carlos C. Goller. "Harnessing single‐stranded DNA binding protein to explore protein–protein and protein–DNA interactions." Biochemistry and Molecular Biology Education 48, no. 2 (December 18, 2019): 181–90. http://dx.doi.org/10.1002/bmb.21324.

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Jones, Susan, Paul van Heyningen, Helen M. Berman, and Janet M. Thornton. "Protein-DNA Interactions." Biochemical Society Transactions 27, no. 3 (June 1, 1999): A88. http://dx.doi.org/10.1042/bst027a088a.

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Gololobov, G. V., S. V. Mikhalap, A. V. Starov, A. F. Kolesnikov, and A. G. Gabibov. "DNA-protein complexes." Applied Biochemistry and Biotechnology 47, no. 2-3 (May 1994): 305–15. http://dx.doi.org/10.1007/bf02787942.

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Luisl, Ben. "DNA-protein interactions." Trends in Genetics 9, no. 11 (November 1993): 401. http://dx.doi.org/10.1016/0168-9525(93)90144-7.

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Corrie, Andrew R. "DNA-protein interactions." Trends in Cell Biology 3, no. 9 (September 1993): 322–23. http://dx.doi.org/10.1016/0962-8924(93)90020-2.

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Suck, Dietrich. "DNA-protein interactions." Trends in Biochemical Sciences 19, no. 1 (January 1994): 48. http://dx.doi.org/10.1016/0968-0004(94)90176-7.

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Wu, X., and M. R. Lieber. "Protein-protein and protein-DNA interaction regions within the DNA end-binding protein Ku70-Ku86." Molecular and Cellular Biology 16, no. 9 (September 1996): 5186–93. http://dx.doi.org/10.1128/mcb.16.9.5186.

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DNA ends are generated during double-strand-break repair and recombination. A p70-p86 heterodimer, Ku, accounts for the DNA end binding activity in eukaryotic cell extracts. When one or both subunits of Ku are missing, mammalian cells are deficient in double-strand-break repair and in specialized recombination, such as V(D)J recombination. Little is known of which regions of Ku70 and Ku86 bind to each other to form the heterodimeric complex or of which regions are important for DNA end binding. We have done genetic and biochemical studies to examine the domains within the two subunits important for protein assembly and for DNA end binding. We found that the C-terminal 20-kDa region of Ku70 and the C-terminal 32-kDa region of Ku86 are important for subunit-subunit interaction. For DNA binding, full-length individual subunits are inactive, indicating that heterodimer assembly precedes DNA binding. DNA end binding activity by the heterodimer requires the C-terminal 40-kDa region of Ku70 and the C-terminal 45-kDa region of Ku86. Leucine zipper-like motifs in both subunits that have been suggested as the Ku70-Ku86 interaction domains do not appear to be the sites of such interaction because these are dispensable for both assembly and DNA end binding. On the basis of these studies, we have organized Ku70 into nine sequence regions conserved between Saccharomyces cerevisiae, Drosophila melanogaster, mice, and humans; only the C-terminal three regions are essential for assembly (amino acids [aa] 439 to 609), and the C-terminal four regions appear to be essential for DNA end binding (aa 254 to 609). Within the minimal active fragment of Ku86 necessary for subunit interaction (aa 449 to 732) and DNA binding (aa 334 to 732), a proline-rich region is the only defined motif.

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Calladine, C. R. "DNA structure and protein–DNA interactions." Acta Crystallographica Section A Foundations of Crystallography 52, a1 (August 8, 1996): C152. http://dx.doi.org/10.1107/s0108767396093154.

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Sexton, Daniel J., Theodore E. Carver, Anthony J. Berdis, and Stephen J. Benkovic. "Protein-Protein and Protein-DNA Interactions at the Bacteriophage T4 DNA Replication Fork." Journal of Biological Chemistry 271, no. 45 (November 8, 1996): 28045–51. http://dx.doi.org/10.1074/jbc.271.45.28045.

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Dissertations / Theses on the topic "Protein-DNA"

1

Slayton, Mark D. "Protein-DNA Interactions of pUL34, an Essential Human Cytomegalovirus DNA-Binding Protein." Ohio University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1533638730703166.

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Moont, Gidon. "Computational modelling of protein/protein and protein/DNA docking." Thesis, University College London (University of London), 2005. http://discovery.ucl.ac.uk/1445703/.

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The docking problem is to start with unbound conformations for the components of a complex, and computationally model a near-native structure for the complex. This thesis describes work in developing computer programs to tackle both protein/protein and protein/DNA docking. Empirical pair potential functions are generated from datasets of residue/residue interactions. A scoring function was parameterised and then used to screen possible complexes, generated by the global search computer algorithm FTDOCK using shape complementarity and electrostatics, for 9 systems. A correct docking (RMSD < 2.5A) is placed within the top 12% of the pair potential score ranked complexes for all systems. The computer software FTDOCK is modified for the docking of proteins to DNA, starting from the unbound protein and DNA coordinates modelled computationally. Complexes are then ranked by protein/DNA pair potentials derived from a database of 20 protein/DNA complexes. A correct docking (at least 65% of correct contacts) was identified at rank < 4 for 3 of the 8 complexes. This improved to 4 out of 8 when the complexes were filtered using experimental data defining the DNA footprint. The FTDOCK program was rewritten, and improved pair potential functions were developed from a set of non-homologous protein/protein interfaces. The algorithms were tested on a non-homologous set of 18 protein/protein complexes, starting with unbound conformations. Us ing cross-validated pair potential functions and the energy rninimisation software MultiDock, a correct docking ( RMSD of CQ interface 25% correct contacts) is found in the top 10 ranks in 6 out of 18 systems. The current best computational docking algorithms are discussed, and strategies for improvement are suggested.

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Dikic, Jasmina, Georgij Kostiuk, Virginijus Siksnys, and Ralf Seidel. "Protein diffusion on DNA." Diffusion fundamentals 20 82013) 73, S. 1, 2013. https://ul.qucosa.de/id/qucosa%3A13660.

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Dikic, Jasmina, Georgij Kostiuk, Virginijus Siksnys, and Ralf Seidel. "Protein diffusion on DNA." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-183614.

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Cao, Zehui. "Designer oligonucleotides for probing dna-protein and protein-protein interactions." [Gainesville, Fla.] : University of Florida, 2004. http://purl.fcla.edu/fcla/etd/UFE0008333.

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Fekete, Richard Alfred. "Characterizing the protein and DNA interactions of the F plasmid DNA binding protein, TraM." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ60291.pdf.

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Seibert, Mark Marvin. "Protein Folding and DNA Origami." Doctoral thesis, Uppsala universitet, Molekylär biofysik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-121549.

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In this thesis, the folding process of the de novo designed polypeptide chignolin was elucidated through atomic-scale Molecular Dynamics (MD) computer simulations. In a series of long timescale and replica exchange MD simulations, chignolin’s folding and unfolding was observed numerous times and the native state was identified from the computed Gibbs free-energy landscape. The rate of the self-assembly process was predicted from the replica exchange data through a novel algorithm and the structural fluctuations of an enzyme, lysozyme, were analyzed. DNA’s structural flexibility was investigated through experimental structure determination methods in the liquid and gas phase. DNA nanostructures could be maintained in a flat geometry when attached to an electrostatically charged, atomically flat surface and imaged in solution with an Atomic Force Microscope. Free in solution under otherwise identical conditions, the origami exhibited substantial compaction, as revealed by small angle X-ray scattering. This condensation was even more extensive in the gas phase. Protein folding is highly reproducible. It can rapidly lead to a stable state, which undergoes moderate fluctuations, at least for small structures. DNA maintains extensive structural flexibility, even when folded into large DNA origami. One may reflect upon the functional roles of proteins and DNA as a consequence of their atomic-level structural flexibility. DNA, biology’s information carrier, is very flexible and malleable, adopting to ever new conformations. Proteins, nature’s machines, faithfully adopt highly reproducible shapes to perform life’s functions robotically.

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Williams, Nicola Louise. "Protein gates in DNA gyrase." Thesis, University of Leicester, 1999. http://hdl.handle.net/2381/29641.

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DNA gyrase is a molecular machine comprising a series of protein gates. The opening and closing of these gates enables the passage of one segment of double-stranded DNA (the T segment) through a transient break in another (the G segment). We have blocked the passage of DNA through each of three dimer interfaces within gyrase and investigated the effects on gyrase mechanism. This has been achieved by cross-linking novel cysteine residues on either side of the dimer interface, or trapping the dimer interface in a closed conformation using a non-hydrolysable ATP analogue. Cross-linking a pair of novel cysteine residues on either side of the bottom dimer interface of DNA gyrase blocks catalytic supercoiling. Limited strand passage is allowed, but T-segment release is prevented. In contrast, ATP-independent relaxation of negatively supercoiled DNA is completely abolished, suggesting that T-segment entry via the bottom gate is blocked. These findings support a two-gate model for supercoiling in by DNA gyrase and suggest that relaxation by gyrase is the reversal of supercoiling. Cross-linking a truncated version of gyrase, (A642B2) that lacks the DNA wrapping domains, does not block ATP-dependent relaxation. This indicates that passage of DNA through the bottom dimer interface is not essential for this reaction. Using a similar approach, we have locked the DNA gate of gyrase using cysteine cross-linking. We show that this locked-gate mutant can bind quinolone drugs and perform DNA cleavage. However, locking the DNA gate prevents strand passage and the ability of DNA to stimulate ATP hydrolysis.

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Stafford, Ryan Leonard Grubbs Robert H. "Design of protein-DNA dimerizers /." Diss., Pasadena, Calif. : Caltech, 2008. http://resolver.caltech.edu/CaltechETD:etd-08232007-154048.

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Neaves, Kelly Jane. "Atomic force microscopy of DNA and DNA-protein constructs." Thesis, University of Cambridge, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.608615.

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Books on the topic "Protein-DNA"

1

Kneale, G. Geoff. DNA-Protein Interactions. New Jersey: Humana Press, 1994. http://dx.doi.org/10.1385/0896032566.

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Moss, Tom. DNA-Protein Interactions. New Jersey: Humana Press, 2001. http://dx.doi.org/10.1385/1592592082.

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Leblanc, Benoît, and Tom Moss, eds. DNA-Protein Interactions. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-015-1.

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Travers, Andrew. DNA-Protein Interactions. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1480-6.

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Leblanc, Benoît P., and Sébastien Rodrigue, eds. DNA-Protein Interactions. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2877-4.

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Simoes-Costa, Marcos, ed. DNA-Protein Interactions. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2847-8.

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Travers, A. A. DNA-protein interactions. London: Chapman & Hall, 1993.

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Lilley, David M. J. 1948-, ed. DNA-protein: Structural interactions. Oxford: IRL Press at Oxford University Press, 1995.

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9

Williams, Mark C., and L. James Maher, eds. Biophysics of DNA-Protein Interactions. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-0-387-92808-1.

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S, Wallace Susan, Houten Bennett van, and Kow Yoke Wah, eds. DNA damage: Effects on DNA structure and protein recognition. New York, N.Y: New York Academy of Sciences, 1994.

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Book chapters on the topic "Protein-DNA"

1

Travers, Andrew. "DNA structure." In DNA-Protein Interactions, 1–27. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1480-6_1.

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Travers, Andrew. "DNA—protein interactions: The three-dimensional architecture of DNA—protein complexes." In DNA-Protein Interactions, 28–51. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1480-6_2.

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Travers, Andrew. "DNA-protein interactions: sequence specific recognition." In DNA-Protein Interactions, 52–86. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1480-6_3.

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Travers, Andrew. "The mechanism of RNA chain initiation." In DNA-Protein Interactions, 87–108. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1480-6_4.

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Travers, Andrew. "The regulation of promoter selectivity in eubacteria." In DNA-Protein Interactions, 109–29. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1480-6_5.

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Travers, Andrew. "The mechanism of eukaryotic transcription." In DNA-Protein Interactions, 130–57. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1480-6_6.

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Travers, Andrew. "Chromatin and transcription." In DNA-Protein Interactions, 158–75. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1480-6_7.

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Kovačič, Lidija, and Rolf Boelens. "Protein-DNA Interactions." In NMR of Biomolecules, 238–52. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527644506.ch13.

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Rhodes, Daniela. "Protein-DNA Recognition." In RNA Biochemistry and Biotechnology, 123–26. Dordrecht: Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4485-8_8.

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Sawada, Jun-ichi, Fumihiko Suzuki, Hiroshi Morioka, Hiroyuki Kobayashi, and Eiko Ohtsuka. "DNA-Protein Interactions." In Real-Time Analysis of Biomolecular Interactions, 127–39. Tokyo: Springer Japan, 2000. http://dx.doi.org/10.1007/978-4-431-66970-8_13.

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Conference papers on the topic "Protein-DNA"

1

Baldi, P. F., and R. H. Lathrop. "DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2000. http://dx.doi.org/10.1142/9789814447362_0011.

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Eikje, Natalja Skrebova. "DNA-RNA, DNA-DNA, DNA-protein and protein-protein interactions in diagnosis of skin cancers by FT-IR microspectroscopy." In SPIE BiOS. SPIE, 2011. http://dx.doi.org/10.1117/12.874692.

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Walhout, A. J. Marian. "GENE-CENTERED PROTEIN-DNA INTERACTOME MAPPING." In Proceedings of the CSB 2007 Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2007. http://dx.doi.org/10.1142/9781860948732_0006.

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Withey, Gary, Jin Ho Kim, and Jimmy Xu. "DNA-programmed protein-nanoelectronic transducer array." In NanoScience + Engineering, edited by Manijeh Razeghi and Hooman Mohseni. SPIE, 2008. http://dx.doi.org/10.1117/12.797219.

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Chang Ming Li. "Polypyrrole Based Reporterless DNA/Protein Sensors." In 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference. IEEE, 2005. http://dx.doi.org/10.1109/iembs.2005.1616828.

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"Classification of families of DNA-recognizing protein domains based on structural features of DNA-protein complexes." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-176.

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Sachanka, A. B., V. V. Shchur, Y. U. Dzichenka, S. A. Usanov, and A. V. Yantsevich. "THERMAL STABILITY OF FUSION PROTEINS OF B. BOVIS DNA-EXOTRANSFERASE AND E. COLI DNA-BINDING PROTEIN." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-371.

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As revealed by dynamic light scattering (DLS) and fluorescent detection fusion of E. coli DNA binding protein (EcSSB) domain to bovine DNA exotransferase (TdT) result in thermal stability increase of the whole protein.

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Millar, David P., and Theodore E. Carver. "Fluorescence studies with DNA probes: dynamic aspects of DNA structure and DNA-protein interactions." In OE/LASE '94, edited by Joseph R. Lakowicz. SPIE, 1994. http://dx.doi.org/10.1117/12.182777.

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Niu, Luming, Wenling Shaiu, James Vesenka, Drena D. Larson, and Eric Henderson. "Atomic force microscopy of DNA-colloidal gold and DNA-protein complexes." In OE/LASE'93: Optics, Electro-Optics, & Laser Applications in Science& Engineering, edited by Richard A. Keller. SPIE, 1993. http://dx.doi.org/10.1117/12.146706.

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Lillian, Todd D. "An Elastic Rod Representation for the LacI-DNA Loop Complex." In ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/detc2011-47407.

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The well-recognized Lac repressor protein (LacI) regulates transcription by bending DNA into a loop. In addition to the known role of DNA flexibility, there is accumulating evidence suggesting that the flexibility of LacI also plays a role in this gene regulation. Here we extend our elastic rod model for DNA (previously used to model DNA only) to represent LacI. Specifically, we represent sites of concentrated flexibility in the protein with flexible elastic rod domains; and we represent relatively rigid domains of the protein with stiff elastic rod domains. Our analysis shows the sensitivity of looping energetics to the degree of flexibility within the protein over a large range of DNA lengths. In addition, we show that the predicted energetically dominant binding topology (A) remains upon introducing protein flexibility.

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Reports on the topic "Protein-DNA"

1

Blackwell, T. K. C-Myc Protein-Protein and Protein-DNA Interactions: Targets for Therapeutic Intervention. Fort Belvoir, VA: Defense Technical Information Center, September 1998. http://dx.doi.org/10.21236/ada371161.

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Blackwell, T. K. C-Myc Protein-Protein and Protein-DNA Interactions: Targets for Therapeutic Intervention. Fort Belvoir, VA: Defense Technical Information Center, September 1997. http://dx.doi.org/10.21236/ada344737.

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Blackwell, T. K. C-MYC Protein-Protein and Protein-DNA Interactions: Targets for Therapeutic Intervention. Fort Belvoir, VA: Defense Technical Information Center, September 1999. http://dx.doi.org/10.21236/ada381686.

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Hanke, Andreas. DNA Conforming Dynamics and Protein Binding. Fort Belvoir, VA: Defense Technical Information Center, December 2006. http://dx.doi.org/10.21236/ada461014.

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Anderson, C. W., M. A. Connelly, H. Zhang, J. A. Sipley, S. P. Lees-Miller, L. G. Lintott, Kazuyasu Sakaguchi, and E. Appella. The human DNA-activated protein kinase, DNA-PK: Substrate specificity. Office of Scientific and Technical Information (OSTI), November 1994. http://dx.doi.org/10.2172/113929.

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Friddle, R. W., J. E. Klare, A. Noy, M. Corzett, R. Balhorn, R. J. Baskin, S. S. Martin, and E. P. Baldwin. DNA Compaction by Yeast Mitochondrial Protein ABF2p. Office of Scientific and Technical Information (OSTI), May 2003. http://dx.doi.org/10.2172/15007313.

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Sarkisian, Christopher J., and Lewis A. Chodosh. Impact of Disrupted BRCA2 Protein-Protein Interactions on DNA Repair and Tumorigenesis. Fort Belvoir, VA: Defense Technical Information Center, July 2001. http://dx.doi.org/10.21236/ada400189.

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Sarkisian, Christopher J., and Lewis A. Chodosh. Impact of Disrupted Brca2 Protein-Protein Interactions on DNA Repair and Tumorigenesis. Fort Belvoir, VA: Defense Technical Information Center, July 2002. http://dx.doi.org/10.21236/ada413006.

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Gupta, G., S. V. Santhana Mariappan, X. Chen, P. Catasti, L. A. III Silks, R. K. Moyzis, E. M. Bradbury, and A. E. Garcia. Structural biology of disease-associated repetitive DNA sequences and protein-DNA complexes involved in DNA damage and repair. Office of Scientific and Technical Information (OSTI), July 1997. http://dx.doi.org/10.2172/505319.

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Boxer, Robert B., and Lewis A. Chodosh. Role of Murine BRCA1 Protein Interactions in DNA Repair. Fort Belvoir, VA: Defense Technical Information Center, July 2001. http://dx.doi.org/10.21236/ada400472.

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