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http://dx.doi.org/10.6564/JKMRS.2018.22.1.018

Backbone Dynamics and Model-Free Analysis of N-terminal Domain of Human Replication Protein A 70  

Yoo, Sooji (Department of Chemistry, Gwangju Institute of Science and Technology)
Park, Chin-Ju (Department of Chemistry, Gwangju Institute of Science and Technology)
Publication Information
Journal of the Korean Magnetic Resonance Society / v.22, no.1, 2018 , pp. 18-25 More about this Journal
Abstract
Replication protein A (RPA) is an essential single-stranded DNA binding protein in DNA processing. It is known that N terminal domain of RPA70 (RPA70N) recruits various protein partners including damage-response proteins such as p53, ATRIP, Rad9, and MRE11. Although the common binding residues of RPA70N were revealed, dynamic properties of the protein are not studied yet. In this study, we measured $^{15}N$ relaxation parameters ($T_1,\;T_2$ and heteronuclear NOE) of human RPA70N and analyzed them using model-free analysis. Our data showed that the two loops near the binding site experience fast time scale motion while the binding site does not. It suggests that the protein binding surface of RPA70N is mostly rigid for minimizing entropy cost of binding and the loops can experience conformational changes.
Keywords
RPA70N; NMR; backbone dynamics; model-free analysis; reduced spectral density mapping;
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1 A. Georgaki, B. Strack, V. Podust, and U. Hubscher, FEBS Lett. 308, 240 (1992)   DOI
2 A. Johnson and M. O'Donnell, Annu. Rev. Biochem. 74, 283 (2005)   DOI
3 Y. J. Machida, J. L. Hamlin, and A. Dutta, Cell. 123, 13 (2005)
4 S. K. Binz, A. M. Sheehan, and M. S. Wold, DNA Repair (Amst). 3, 1015 (2004)   DOI
5 M. S. Wold, Annu. Rev. Biochem. 66, 61 (1997)
6 M. E. Stauffer and W. J. Chazin, J. Biol. Chem. 279, 30915 (2004)   DOI
7 A. Bochkarev and E. Bochkareva, Curr. Opin. Struct. Biol. 14, 36 (2004)   DOI
8 L. Zou and S.J. Elledge, Science 300, 1542 (2003)   DOI
9 D. Shechter, V. Costanzo, and J. Gautier, Nat. Cell Biol. 6, 648 (2004)   DOI
10 A. Yuzhakov, Z. Kelman, J. Hurwitz, and M. O'Donnell, EMBO J. 18, 6189 (1999)   DOI
11 M. L. Mayer, Nat. Struct. Mol. Biol. 12, 208 (2005)   DOI
12 E. Bochkareva, L. Kaustov, A. Ayed, G. -S. Yi, Y. Lu, A. P. -Lucena, J. C. C. Liao, A. L. Okorokov, J. Milner, C. H. Arrowsmith, and A. Bochkarev, Proc.Natl. Acad. Sci. 102, 15412 (2005)   DOI
13 X. Xu, S. Vaithiyalingam, G. G. Glick, D. A. Mordes, W. J. Chazin, and D. Cortez, Mol. Cell. Biol. 28, 7345 (2008)   DOI
14 H. L. Ball, M. R. Ehrhardt, D. A. Mordes, G. G. Glick, W. J. Chazin, and D. Cortez, Mol. Cell. Biol. 27, 3367 (2007)   DOI
15 C. Iftode, Y. Daniely, and J. A. Borowiec, Crit. Rev. Biochem. Mol. Biol. 34, 141 (1999)   DOI
16 E. Bochkareva, V. Belegu, S. Korolev, and A. Bochkarev, EMBO J. 20, 612 (2001)   DOI
17 G. Mer, A. Bochkarev, R. Gupta, E. Bochkareva, L. Frappier, C. J. Ingles, A. M. Edwards, and W. J. Chazin, Cell 103, 449 (2000)   DOI
18 D. L. Theobald, R. M. Mitton-Fry, and D. S. Wuttke, Annu. Rev. Biophys. Biomol. Struct. 32, 115 (2003)   DOI
19 E. Bochkareva, S. Korolev, S. P. Lees-Miller, and A. Bochkarev, EMBO J. 21, 1855 (2002)   DOI
20 G. W. Daughdrill, J. Ackerman, N. G. Isern, M. V. Botuyan, C. Arrowsmith, M. S. Wold, and D. F. Lowry, Nucleic Acids Res. 29, 3270 (2001)   DOI
21 D. M. Jacobs, A. S. Lipton, N. G. Isern, G. W. Daughdrill, D. F. Lowry, X. Gomes, and M. S. Wold, J. Biomol. NMR 14, 321(1999)
22 C. A. Brosey, S. E. Soss, S. Brooks, C. Yan, I. Ivanov, K. Dorai, and W. J. Chazin, Struct. Des. 23, 1028 (2015)   DOI
23 D. Kang, S. Lee, K.-S. Ryu, H.-K.Cheong, E.-H. Kim, and C.-J.Park, FEBS Lett. 592, 547 (2018).   DOI
24 J.-J. Yi, W.-J. Kim, J.-K. Rhee, J. Lim, B.-J. Lee, and W.S.Son, J. Kor. Magn. Reson. Soc. 21, 26 (2017)   DOI
25 S. Lee and C.-J. Park, J. Kor. Magn. Reson. Soc. 20, 138 (2016)   DOI
26 O. Davulcu, Y. Peng, R. Bruschweiler, J. J. Skalicky, and M. S. Chapman, J. Struct. Biol. 200, 258 (2017)   DOI
27 K. Berlin, A. Longhini, T. K. Dayie, and D. Fushman, J. Biomol. NMR 57, 333 (2013)   DOI
28 C. Bracken, P. a Carr, J. Cavanagh, and A. G. Palmer, J. Mol. Biol. 285, 2133 (1999)   DOI
29 W. T. Huntress, J. Chem. Phys. 48, 3524 (1968)   DOI
30 D. E. Woessner, J. Chem. Phys. 37, 647 (1962)   DOI
31 P. S. Hubbard, J. Chem. Phys. 53, 985 (1970)   DOI
32 N. A. Farrow, O. Zhang, A. Szabo, D. A. Torchia, and L. E. Kay, J. Biomol. NMR 6, 153 (1995)
33 J.-F. Lefevre, K. T. Dayie, J. W. Peng, and G. Wagner, Biochemistry 35, 2674 (1996)