5/9/2023 0 Comments Definition of chaperoneWe find that NCD facilitates the folding of nucleic acids by acting as a macromolecular counterion that locally screens charge repulsion with extreme efficiency. Therefore, we use an integrative combination of single-molecule Förster resonance energy transfer (FRET) spectroscopy and molecular simulations to elucidate the mechanism of chaperone-assisted folding. We note that the tendency for NCD to form nucleocapsid-like particles in the presence of nucleic acids 19, 22 prevents investigation of this process at the high sample concentrations required for many ensemble techniques, such as circular dichroism or NMR spectroscopy. To understand how intrinsically disordered RNA chaperones function, we study NCD’s ability to alter the folding kinetics of a ubiquitous nucleic acid structural motif-a stem-loop hairpin (Fig. In addition to forming the nucleocapsid enclosing the viral RNA, NCD also acts as an RNA chaperone and facilitates many nucleic-acid conformational transitions 15, including dimerization of the viral genome (Supplementary Fig. NCD is intrinsically disordered as a monomer 18, 19 and has many important roles in the life cycle of this virus, which infects one in 50 people worldwide 20. 1a), using a variety of single-molecule fluorescence experiments. We address this question by studying NCD, the nucleocapsid domain of the hepatitis C virus core protein (Fig. These findings give rise to a question of fundamental importance: How do RNA chaperones function without a well-defined structure? Their chaperone activity is present both in vitro and in vivo 3, 5, 8, 12, 13, and the intrinsically disordered regions are both necessary and sufficient for this function 15. ![]() Comparisons among these chaperones reveal very few structural similarities, but many of them are enriched in positively charged and polar residues, resulting in proteins that are known or predicted to be disordered 13, 16, 17. RNA chaperones are a class of proteins that alleviate this problem by helping nucleic acids navigate their rugged energy landscape towards compact and thermodynamically stable conformations 3, 4, 5, 6, 7, 8, 9, 10, 11.Īn important group of RNA chaperones are viral nucleocapsid proteins, which facilitate many nucleic-acid-dependent processes in viral life cycles 12, 13, 14, 15. ![]() As a result, oligonucleotides often adopt long-lived non-native conformations with impaired function. ![]() The folding problem for nucleic acids is exacerbated by their small set of monomeric building blocks, which form strong interactions with each other, making it difficult for a given sequence to specify a unique structure 3. Additionally, as in the case of proteins, non-native interactions can impede the molecular search for biologically active conformations and result in kinetic traps 2. Due to the poly-anionic nature of nucleic acids, formation of these structures is strongly influenced by electrostatics. ![]() Ever since the discovery of transfer RNA and ribosomal RNA, the number of functions attributed to structured nucleic acids has continuously increased 1.
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