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NMR Spectroscopy Reveals that RNase A is Chiefly Denatured in 40% Acetic Acid: Implications for Oligomer Formation by 3D Domain Swapping

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Instituto de Química Física “Rocasolano”, C.S.I.C., Serrano 119, E-28006 Madrid, Spain, and Laboratori d’Enginyeria de Proteïnes, Department de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi s/n, E-17071 Girona, Spain
[email protected]
†Instituto de Química Física “Rocasolano”.
‡Universitat de Girona.
Cite this: J. Am. Chem. Soc. 2010, 132, 5, 1621–1630
Publication Date (Web):January 19, 2010
https://doi.org/10.1021/ja9081638
Copyright © 2010 American Chemical Society
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    Abstract

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    Protein self-recognition is essential in many biochemical processes and its study is of fundamental interest to understand the molecular mechanism of amyloid formation. Ribonuclease A (RNase A) is a monomeric protein that may form several oligomers by 3D domain swapping of its N-terminal α-helix, C-terminal β-strand, or both. RNase A oligomerization is induced by 40% acetic acid, which has been assumed to mildly unfold the protein by detaching the terminal segments and consequently facilitating intersubunit swapping, once the acetic acid is removed by lyophilization and the protein is redissolved in a benign buffer. Using UV difference, near UV circular dichroism, folding kinetics, and multidimensional heteronuclear NMR spectroscopy, the conformation of RNase A in 40% acetic acid and in 8 M urea has been characterized. These studies demonstrate that RNase A is chiefly unfolded in 40% acetic acid; it partially retains the native helices, whereas the β-sheet is fully denatured and all X-Pro peptide bonds are predominantly in the trans conformation. Refolding occurs via an intermediate, IN, with non-native X-Pro peptide bonds. IN is known to be populated during RNase A refolding following denaturation in concentrated solutions of urea or guanidinium chloride, and we find that urea- or GdmCl-denatured RNase A can oligomerize during refolding. By revealing the importance of a chiefly denaturated state and a refolding intermediate with non-native X-Pro peptide bonds, these findings revise the model for RNase A oligomerization via 3D domain swapping and have general implications for amyloid formation.

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    Graphs showing (i) UV difference spectra of RNase A in 40% acetic acid, (ii) regions of NOESY spectra of RNase A in 40% HAc and 8 M urea, (iii) Cβ- and Cγ-edited 1H−15N HSQC spectra, (iv) the conformational chemical shifts of RNase A peptides, (v) representative chromatograms of RNase A oligomers forming after urea and GdmCl denaturation, and (vi) structures of the RNase A N-dimer and RNase 1 PM8 dimer and a table summarizing RNase A oligomer yield following denaturation in 40% HAc, 10 M urea, or 6 M GdmCl. This material is available free of charge via the Internet at http://pubs.acs.org.

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