Allosteric Pathways of the Dengue NS3 Helicase Enzyme During the NTP Hydrolysis Cycle

Research Seminar Abstract

The Flaviviridae non-structural 3 (NS3) protein is a viral helicase that plays a pivotal role during the replication of the viral genome. Specifically, this enzyme uses energy released during the hydrolysis of nucleotide triphosphates (NTPs, e.g. adenosine triphosphate, ATP) to translocate and cause the unwinding of a double stranded RNA substrate, thereby preparing the RNA for the replication machinery. Microsecond-long molecular dynamic simulations of the dengue NS3 helicase have been performed on seven structures, five of which represent important RNA-bound structures that model the NTP hydrolysis cycle (no ATP, pre-hydrolysis, post-hydrolysis, and product release states). This set of simulations is used to investigate the structural and dynamic couplings (aka allosteric pathways) between the RNA binding site and the hydrolysis active site. For example, experimental studies have observed an RNA-enhanced ATP hydrolysis activity for the dengue NS3 helicase.1 Comparisons between the reported simulations with RNA absent and bound demonstrate that an RNA substrate influences water dynamics and positioning within the hydrolysis active site, thereby providing an atomic-resolution explanation for the observed activity enhancement. Also, these simulations suggest that the RNA binding site is affected by the different ATP substrates states, thus providing novel details into the RNA-translocation mechanism. The biophysical importance of these allosteric pathways will be presented as well as how these results are being tested using experimental and computational methods.

(1) Wang, C.-C., et. al. Analysis of the nucleoside triphosphatase, RNA triphosphatase, and unwinding activities of the helicase domain of dengue virus NS3 protein. FEBS Letters, 2009, 583(4), 691–6.

Division(s): Physical

Speaker: Russell Davidson

Speaker Institution: Colorado State University

Event Date: 04-13-2017

Event Time: 4:00 PM

Event Location: Chemistry A101

Mixer Time: 3:45 PM

Mixer Location: Chemistry B101E

Host: M. McCullagh