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Protein & Peptide Letters

Editor-in-Chief

ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

Letter Article

The Residual Structure of Unfolded Proteins was Elucidated from the Standard Deviation of NMR Intensity Differences

Author(s): Fuko Mizuno, Saeko Aoki, Akimasa Matsugami, Fumiaki Hayashi and Chiaki Nishimura*

Volume 30, Issue 2, 2023

Published on: 25 January, 2023

Page: [103 - 107] Pages: 5

DOI: 10.2174/0929866530666230104140830

open access plus

Abstract

Introduction: Sensitive methods are necessary to identify the residual structure in an unfolded protein, which may be similar to the functionally native structure. Signal intensity in NMR experiments is useful for analyzing the line width for a dynamic structure; however, another contribution is contained.

Methods: Here, the signal-intensity difference along the sequence was used for probability to calculate the standard deviation.

Results: The relative values of the standard deviations were 0.57, 0.57, and 0.66 for alpha-synuclein wild-type, A53T, and A30P, respectively. This revealed that the flexible region was mainly in the Cterminal region of alpha-synuclein at higher temperatures as observed by the amide-proton exchange studies.

Conclusion: In particular, the flexible structure was induced by the A30P mutation.

Keywords: α-synuclein, standard deviation, unfolding, signal intensity, NMR, C-terminal.

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[1]
Fink, A.L. The aggregation and fibrillation of alpha-synuclein. Acc. Chem. Res., 2006, 39(9), 628-634.
[http://dx.doi.org/10.1021/ar050073t] [PMID: 16981679]
[2]
Wright, P.E.; Dyson, H.J. Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm. J. Mol. Biol., 1999, 293(2), 321-331.
[http://dx.doi.org/10.1006/jmbi.1999.3110] [PMID: 10550212]
[3]
Sugase, K.; Dyson, H.J.; Wright, P.E. Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature, 2007, 447(7147), 1021-1025.
[http://dx.doi.org/10.1038/nature05858] [PMID: 17522630]
[4]
Bussell, R., Jr; Eliezer, D. Residual structure and dynamics in Parkinson’s disease-associated mutants of alpha-synuclein. J. Biol. Chem., 2001, 276(49), 45996-46003.
[http://dx.doi.org/10.1074/jbc.M106777200] [PMID: 11590151]
[5]
Rospigliosi, C.C.; McClendon, S.; Schmid, A.W.; Ramlall, T.F.; Barré, P.; Lashuel, H.A.; Eliezer, D. E46K Parkinson’s-linked mutation enhances C-terminal-to-N-terminal contacts in alpha-synuclein. J. Mol. Biol., 2009, 388(5), 1022-1032.
[http://dx.doi.org/10.1016/j.jmb.2009.03.065] [PMID: 19345692]
[6]
Cho, M.K.; Nodet, G.; Kim, H.Y.; Jensen, M.R.; Bernado, P.; Fernandez, C.O.; Becker, S.; Blackledge, M.; Zweckstetter, M. Structural characterization of α-synuclein in an aggregation prone state. Protein Sci., 2009, 18(9), 1840-1846.
[http://dx.doi.org/10.1002/pro.194] [PMID: 19554627]
[7]
Dedmon, M.M.; Lindorff-Larsen, K.; Christodoulou, J.; Vendruscolo, M.; Dobson, C.M. Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations. J. Am. Chem. Soc., 2005, 127(2), 476-477.
[http://dx.doi.org/10.1021/ja044834j] [PMID: 15643843]
[8]
Wu, K.P.; Baum, J. Detection of transient interchain interactions in the intrinsically disordered protein alpha-synuclein by NMR paramagnetic relaxation enhancement. J. Am. Chem. Soc., 2010, 132(16), 5546-5547.
[http://dx.doi.org/10.1021/ja9105495] [PMID: 20359221]
[9]
Croke, R.L.; Sallum, C.O.; Watson, E.; Watt, E.D.; Alexandrescu, A.T. Hydrogen exchange of monomeric α-synuclein shows unfolded structure persists at physiological temperature and is independent of molecular crowding in Escherichia coli. Protein Sci., 2008, 17(8), 1434-1445.
[http://dx.doi.org/10.1110/ps.033803.107] [PMID: 18493022]
[10]
Okuwaki, R.; Shinmura, I.; Morita, S.; Matsugami, A.; Hayashi, F.; Goto, Y.; Nishimura, C. Distinct residual and disordered structures of alpha-synuclein analyzed by amide-proton exchange and NMR signal intensity. Biochim. Biophys. Acta. Proteins Proteomics, 2020, 1868(9), 140464.
[http://dx.doi.org/10.1016/j.bbapap.2020.140464] [PMID: 32497661]
[11]
Okazaki, H.; Ohori, Y.; Komoto, M.; Lee, Y.H.; Goto, Y.; Tochio, N.; Nishimura, C. Remaining structures at the N- and C-terminal regions of alpha-synuclein accurately elucidated by amide-proton exchange NMR with fitting. FEBS Lett., 2013, 587(22), 3709-3714.
[http://dx.doi.org/10.1016/j.febslet.2013.09.039] [PMID: 24113654]
[12]
Edrington, T.C. V; Lapointe, R.; Yeagle, P.L.; Gretzula, C.L.; Boesze-Battaglia, K. Peripherin-2: An intracellular analogy to viral fusion proteins. Biochemistry, 2007, 46(12), 3605-3613.
[http://dx.doi.org/10.1021/bi061820c] [PMID: 17323921]
[13]
Jensen, M.R.; Communie, G.; Ribeiro, E.A., Jr; Martinez, N.; Desfosses, A.; Salmon, L.; Mollica, L.; Gabel, F.; Jamin, M.; Longhi, S.; Ruigrok, R.W.H.; Blackledge, M. Intrinsic disorder in measles virus nucleocapsids. Proc. Natl. Acad. Sci. USA, 2011, 108(24), 9839-9844.
[http://dx.doi.org/10.1073/pnas.1103270108] [PMID: 21613569]
[14]
Ono, Y.; Miyashita, M.; Ono, Y.; Okazaki, H.; Watanabe, S.; Tochio, N.; Kigawa, T.; Nishimura, C. Comparison of residual alpha- and beta-structures between two intrinsically disordered proteins by using NMR. Biochim. Biophys. Acta. Proteins Proteomics, 2015, 1854(3), 229-238.
[http://dx.doi.org/10.1016/j.bbapap.2014.12.007] [PMID: 25523747]
[15]
Delaglio, F.; Grzesiek, S.; Vuister, G.; Zhu, G.; Pfeifer, J.; Bax, A. NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR, 1995, 6(3), 277-293.
[http://dx.doi.org/10.1007/BF00197809] [PMID: 8520220]
[16]
Johnson, B.A.; Blevins, R.A. NMR View: A computer program for the visualization and analysis of NMR data. J. Biomol. NMR, 1994, 4(5), 603-614.
[http://dx.doi.org/10.1007/BF00404272] [PMID: 22911360]

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