The flavivirus NS3 protein is a helicase that has pivotal functions during the viral genome replication process, where it unwinds double-stranded RNA and translocates along the nucleic acid polymer in a nucleoside triphosphate hydrolysis-dependent mechanism. An increased interest in this enzyme as a potential target for development of antiviral therapeutics was sparked by the 2015 Zika virus epidemic in the Americas. Crystallographic and computational studies of the flavivirus NS3 helicase have identified the RNA-binding loop as an interesting structural element, which may function as an origin for the RNA-enhanced NTPase activity observed for this family of helicases. Microsecond-long unbiased molecular dynamics as well as extensive replica exchange umbrella sampling simulations of the Zika NS3 helicase have been performed to investigate the RNA-dependence of this loop’s structural conformations. Specifically, the effect of the bound single-stranded RNA (ssRNA) oligomer on the putative “open” and “closed” conformations of this loop are studied. In the Apo substrate state, the two structures are nearly isoergonic (ΔA = -0.22 kcal/mol), explaining the structural ambiguity observed in Apo NS3h crystal structures. The bound ssRNA is seen to stabilize the “open” conformation (ΔA = 1.97 kcal/mol) through direct protein-RNA interactions at the top of the loop. Interestingly, a small ssRNA oligomer bound over 13 Å away from the loop is seen to affect the free energy surface to favor the “open” structure while minimizing barriers between the two states. The mechanism of the transition between “open” and “closed” states is characterized as are residues of importance for the RNA-binding loop structures. From these results, point mutations are posited that are hypothesized to stabilize the “closed” RNA-binding loop and negatively impact RNA-binding and the RNA-enhanced NTPase activity.
October 19, 2014
Risk factors for recurrence of paroxysmal atrial fibrillation after second-generation of cryoballoon ablation.
May 12, 2020
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December 24, 2020
- ACC 2020The American College of Cardiology decided to cancel ACC.20/WCC due to COVID-19, which was scheduled to take place March 28-30 in Chicago. However, ACC.20/WCC Virtual Meeting continues to release cutting edge science and practice changing updates for cardiovascular professionals on demand and free through June 2020.
- CROI 2020Every year, CROI hosts some of the world's leading experts in HIV research, who come to present exciting new data and drive forward the field of HIV/AIDS research. This year, due to COVID-19, CROI held their meeting virtually.