id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-355397-y69bk5jc	Caruso, Ícaro P.	Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism	2020-09-06		.txt	text/plain	5105	297	55	Here, we used molecular dynamics (MD) simulations to study the binding of SARS-CoV-2 N-NTD to non-specific (NS) and TRS dsRNAs. We probed dsRNAs' Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. We calculated the structural model of the N-NTD:dsTRS complex based on the experimental data for the N-NTD interaction with a non-specific dsRNA (5'-CACUGAC-3') (dsNS) (16) using the HADDOCK 2.2 server (20) . In contrast to the decrease in the number of intramolecular hydrogen bonds between the sense and anti-sense strands of dsRNAs (WC base-pairing) due to N-NTD binding, we observed an increase in the average number of intermolecular hydrogen bonds formed between the nitrogenous bases of dsTRS and N-NTD (protein-RNA interaction) along the 100 ns MD simulation, whereas for dsNS, this average value was constant ( Figure 3B top).	./cache/cord-355397-y69bk5jc.txt	./txt/cord-355397-y69bk5jc.txt