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Journal articles on the topic 'Protein-DNA'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 May 2024

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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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2

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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3

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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4

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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5

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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6

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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7

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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8

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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9

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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10

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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11

Arauzo-Bravo, Marcos, H. Kono, S. Fujii, and A. Sarai. "2P145 Molecular Dynamics Simulations of DNA : Application to the Specificity of Protein-DNA Recognition." Seibutsu Butsuri 45, supplement (2005): S156. http://dx.doi.org/10.2142/biophys.45.s156_1.

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12

Weiss, Michael A., Robert Stearman, Anna Jeitler-Nilsson, Martin Karplus, and Robert T. Sauer. "Protein-Protein Interactions in DNA Recognition." Biophysical Journal 49, no. 1 (January 1986): 29–33. http://dx.doi.org/10.1016/s0006-3495(86)83581-0.

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13

Hang, Bo, and B. Singer. "Protein−Protein Interactions Involving DNA Glycosylases." Chemical Research in Toxicology 16, no. 10 (October 2003): 1181–95. http://dx.doi.org/10.1021/tx030020p.

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14

Manke, Thomas, Ricardo Bringas, and Martin Vingron. "Correlating Protein–DNA and Protein–Protein Interaction Networks." Journal of Molecular Biology 333, no. 1 (October 2003): 75–85. http://dx.doi.org/10.1016/j.jmb.2003.08.004.

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15

Pröpper, K., K. Meindl, D. Rodríguez, M. Sammito, B. Dittrich, G. M. Sheldrick, E. Pohl, and I. Usón. "DNA–protein complex structure prediction:ARCIMBOLDOstructure solution with DNA–protein fragment subsets." Acta Crystallographica Section A Foundations of Crystallography 68, a1 (August 7, 2012): s121. http://dx.doi.org/10.1107/s0108767312097656.

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16

Brand, Luise H., Carsten Henneges, Axel Schüssler, H. Üner Kolukisaoglu, Grit Koch, Niklas Wallmeroth, Andreas Hecker, et al. "Screening for Protein-DNA Interactions by Automatable DNA-Protein Interaction ELISA." PLoS ONE 8, no. 10 (October 11, 2013): e75177. http://dx.doi.org/10.1371/journal.pone.0075177.

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17

III, William L. Perry. "JavaScript DNA Translator: DNA-Aligned Protein Translations." BioTechniques 33, no. 6 (December 2002): 1318–20. http://dx.doi.org/10.2144/02336bc01.

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18

Schmidt, Brian D., and Claude F. Meares. "Proteolytic DNA for Mapping Protein−DNA Interactions†." Biochemistry 41, no. 13 (April 2002): 4186–92. http://dx.doi.org/10.1021/bi015582r.

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19

Parada, C. A., and K. J. Marians. "Mechanism of DNA A protein-dependent pBR322 DNA replication. DNA A protein-mediated trans-strand loading of the DNA B protein at the origin of pBR322 DNA." Journal of Biological Chemistry 266, no. 28 (October 1991): 18895–906. http://dx.doi.org/10.1016/s0021-9258(18)55148-6.

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20

SARAI, Akinori. "Thermodynamics of DNA-protein." Seibutsu Butsuri 35, no. 1 (1995): 20–24. http://dx.doi.org/10.2142/biophys.35.20.

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21

Kamashev, Dimitrii E., Anna V. Balandina, and Vadim L. Karpov. "Tramtrack Protein-DNA Interactions." Journal of Biological Chemistry 275, no. 46 (August 29, 2000): 36056–61. http://dx.doi.org/10.1074/jbc.m001691200.

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22

Stingele, Julian, and Stefan Jentsch. "DNA–protein crosslink repair." Nature Reviews Molecular Cell Biology 16, no. 8 (July 1, 2015): 455–60. http://dx.doi.org/10.1038/nrm4015.

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23

Szuromi, Phil. "Protein-folded DNA nanostructures." Science 355, no. 6331 (March 23, 2017): 1277.13–1279. http://dx.doi.org/10.1126/science.355.6331.1277-m.

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24

GUMPORT, RICHARD I. "Protein binding to DNA." Nature 328, no. 6125 (July 1987): 21. http://dx.doi.org/10.1038/328021b0.

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25

Jackson, Stephen P. "DNA-dependent protein kinase." International Journal of Biochemistry & Cell Biology 29, no. 7 (July 1997): 935–38. http://dx.doi.org/10.1016/s1357-2725(97)00006-x.

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26

Hemminki, Karl, Herman Autrup, and Aage Haugen. "DNA and protein adducts." Toxicology 101, no. 1-2 (July 1995): 41–53. http://dx.doi.org/10.1016/0300-483x(95)03015-8.

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27

Schwabe, John W. R. "How protein handles DNA." Nature Structural & Molecular Biology 3, no. 6 (June 1996): 495–96. http://dx.doi.org/10.1038/nsb0696-495.

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28

Chisti, Yusuf. "Protein and DNA biopharmaceuticals." Biotechnology Advances 24, no. 3 (May 2006): 353. http://dx.doi.org/10.1016/j.biotechadv.2006.01.008.

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29

Mao, Chunhong, Noel G. Carlson, and John W. Little. "Cooperative DNA-Protein Interactions." Journal of Molecular Biology 235, no. 2 (January 1994): 532–44. http://dx.doi.org/10.1006/jmbi.1994.1011.

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30

Golshani, Maryam, Sima Rafati, Mehdi Nejati-Moheimani, Somaye Pourabdi, Amin Arsang, and Saeid Bouzari. "Protein/Protein, DNA/DNA and DNA/Protein based vaccination strategies using truncated Omp2b against Brucella infection in BALB/c Mice." International Journal of Medical Microbiology 307, no. 4-5 (June 2017): 249–56. http://dx.doi.org/10.1016/j.ijmm.2017.03.004.

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31

Friedhoff, Peter, Pingping Li, and Julia Gotthardt. "Protein-protein interactions in DNA mismatch repair." DNA Repair 38 (February 2016): 50–57. http://dx.doi.org/10.1016/j.dnarep.2015.11.013.

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32

Yoo, Jejoong, David Winogradoff, and Aleksei Aksimentiev. "Molecular dynamics simulations of DNA–DNA and DNA–protein interactions." Current Opinion in Structural Biology 64 (October 2020): 88–96. http://dx.doi.org/10.1016/j.sbi.2020.06.007.

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33

Sternberg, Michael JE, Henry A. Gabb, and Richard M. Jackson. "Predictive docking of protein—protein and protein—DNA complexes." Current Opinion in Structural Biology 8, no. 2 (April 1998): 250–56. http://dx.doi.org/10.1016/s0959-440x(98)80047-x.

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34

Nakai, H., and C. C. Richardson. "Interactions of the DNA polymerase and gene 4 protein of bacteriophage T7. Protein-protein and protein-DNA interactions involved in RNA-primed DNA synthesis." Journal of Biological Chemistry 261, no. 32 (November 1986): 15208–16. http://dx.doi.org/10.1016/s0021-9258(18)66855-3.

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35

Tachiki, Hidehisa, Ryuichi Kato, and Seiki Kuramitsu. "DNA Binding and Protein-Protein Interaction Sites in MutS, a Mismatched DNA Recognition Protein fromThermus thermophilusHB8." Journal of Biological Chemistry 275, no. 52 (October 9, 2000): 40703–9. http://dx.doi.org/10.1074/jbc.m007124200.

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36

Constans, J. "DNA and protein polymorphism: Application to anthropology and human genetics." Anthropologischer Anzeiger 46, no. 2 (June 13, 1988): 97–117. http://dx.doi.org/10.1127/anthranz/46/1988/97.

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37

Harrington, Rodney E. "DNA curving and bending in protein?DNA recognition." Molecular Microbiology 6, no. 18 (September 1992): 2549–55. http://dx.doi.org/10.1111/j.1365-2958.1992.tb01431.x.

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38

Price, C. M., and T. R. Cech. "Telomeric DNA-protein interactions of Oxytricha macronuclear DNA." Genes & Development 1, no. 8 (October 1, 1987): 783–93. http://dx.doi.org/10.1101/gad.1.8.783.

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39

Sen, Taner Z., Andrzej Kloczkowski, and Robert L. Jernigan. "A DNA-Centric Look at Protein-DNA Complexes." Structure 14, no. 9 (September 2006): 1341–42. http://dx.doi.org/10.1016/j.str.2006.08.003.

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40

Spotheim-Maurizot, M., and M. Davídková. "Radiation damage to DNA in DNA–protein complexes." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 711, no. 1-2 (June 2011): 41–48. http://dx.doi.org/10.1016/j.mrfmmm.2011.02.003.

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41

Gromiha, M. Michael. "Influence of DNA stiffness in protein–DNA recognition." Journal of Biotechnology 117, no. 2 (May 2005): 137–45. http://dx.doi.org/10.1016/j.jbiotec.2004.12.016.

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42

Anderson, Carl W. "DNA damage and the DNA-activated protein kinase." Trends in Biochemical Sciences 18, no. 11 (November 1993): 433–37. http://dx.doi.org/10.1016/0968-0004(93)90144-c.

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43

Štěpánek, Josef, Vladimír Kopecký, Pierre-Yves Turpin, Zhenlin Li, Bernard Alpert, and Christian Zentz. "DNA Electric Charge Oscillations Govern Protein–DNA Recognition." PLOS ONE 10, no. 4 (April 29, 2015): e0124444. http://dx.doi.org/10.1371/journal.pone.0124444.

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44

Bonincontro, A., R. Caneva, and F. Pedone. "Hydration of aminoacid-DNA and protein-DNA systems." Biochemical Pharmacology 37, no. 9 (May 1988): 1839–40. http://dx.doi.org/10.1016/0006-2952(88)90472-8.

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45

Enderle, Janina, Annika Dorn, and Holger Puchta. "DNA- and DNA-Protein-Crosslink Repair in Plants." International Journal of Molecular Sciences 20, no. 17 (September 3, 2019): 4304. http://dx.doi.org/10.3390/ijms20174304.

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DNA-crosslinks are one of the most severe types of DNA lesions. Crosslinks (CLs) can be subdivided into DNA-intrastrand CLs, DNA-interstrand CLs (ICLs) and DNA-protein crosslinks (DPCs), and arise by various exogenous and endogenous sources. If left unrepaired before the cell enters S-phase, ICLs and DPCs pose a major threat to genomic integrity by blocking replication. In order to prevent the collapse of replication forks and impairment of cell division, complex repair pathways have emerged. In mammals, ICLs are repaired by the so-called Fanconi anemia (FA) pathway, which includes 22 different FANC genes, while in plants only a few of these genes are conserved. In this context, two pathways of ICL repair have been defined, each requiring the interaction of a helicase (FANCJB/RTEL1) and a nuclease (FAN1/MUS81). Moreover, homologous recombination (HR) as well as postreplicative repair factors are also involved. Although DPCs possess a comparable toxic potential to cells, it has only recently been shown that at least three parallel pathways for DPC repair exist in plants, defined by the protease WSS1A, the endonuclease MUS81 and tyrosyl-DNA phosphodiesterase 1 (TDP1). The importance of crosslink repair processes are highlighted by the fact that deficiencies in the respective pathways are associated with diverse hereditary disorders.

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46

Boryskina, O. P., M. Yu Tkachenko, and A. V. Shestopalova. "Protein-DNA complexes: specificity and DNA readout mechanisms." Biopolymers and Cell 27, no. 1 (January 20, 2011): 3–16. http://dx.doi.org/10.7124/bc.00007c.

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47

Bulyk, Martha L. "DNA microarray technologies for measuring protein–DNA interactions." Current Opinion in Biotechnology 17, no. 4 (August 2006): 422–30. http://dx.doi.org/10.1016/j.copbio.2006.06.015.

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48

Travers, Andrew A. "DNA conformation and configuration in protein-DNA complexes." Current Opinion in Structural Biology 2, no. 1 (February 1992): 71–77. http://dx.doi.org/10.1016/0959-440x(92)90180-f.

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49

Krajewski, Wladyslaw A., and Sergey V. Razin. "DNA-protein interactions and spatial organization of DNA." Molecular Biology Reports 18, no. 3 (October 1993): 167–75. http://dx.doi.org/10.1007/bf01674427.

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50

Gao, Mu, and Jeffrey Skolnick. "From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions." PLoS Computational Biology 5, no. 3 (April 3, 2009): e1000341. http://dx.doi.org/10.1371/journal.pcbi.1000341.

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