Abstract
The C-terminus domain of non-structural 3 (NS3) protein of the Flaviviridae viruses (e.g. HCV, dengue, West Nile, Zika) is a nucleotide triphosphatase (NTPase) -dependent superfamily 2 (SF2) helicase that unwinds double-stranded RNA while translocating along the nucleic polymer. Due to these functions, NS3 is an important target for antiviral development yet the biophysics of this enzyme are poorly understood. Microsecond-long molecular dynamic simulations of the dengue NS3 helicase domain are reported from which allosteric effects of RNA and NTPase substrates are observed. The presence of a bound single-stranded RNA catalytically enhances the phosphate hydrolysis reaction by affecting the dynamics and positioning of waters within the hydrolysis active site. Coupled with results from the simulations, electronic structure calculations of the reaction are used to quantify this enhancement to be a 150-fold increase, in qualitative agreement with the experimental enhancement factor of 10–100. Additionally, protein-RNA interactions exhibit NTPase substrate-induced allostery, where the presence of a nucleotide (e.g. ATP or ADP) structurally perturbs residues in direct contact with the phosphodiester backbone of the RNA. Residue-residue network analyses highlight pathways of short ranged interactions that connect the two active sites. These analyses identify motif V as a highly connected region of protein structure through which energy released from either active site is hypothesized to move, thereby inducing the observed allosteric effects. These results lay the foundation for the design of novel allosteric inhibitors of NS3.
Highlights
IntroductionFlaviviruses (family Flaviviridae) are small (*11 kilobases) positive-sense, single-stranded RNA (ssRNA) viruses that include members such as dengue (serotypes 1-4), Zika, West Nile, yellow fever, and Japanese Encephalitis viruses
Flaviviruses are small (*11 kilobases) positive-sense, single-stranded RNA viruses that include members such as dengue, Zika, West Nile, yellow fever, and Japanese Encephalitis viruses
It is difficult to fully deconvolute the specific influences of these structural allosteries on the water molecules in the active site, we propose that the observed influence of RNA on number and dynamics of water molecules originates from the structural rearrangement of α2, where Val227 and Met231 become more prominent in the hydrolysis active site when RNA is bound
Summary
Flaviviruses (family Flaviviridae) are small (*11 kilobases) positive-sense, single-stranded RNA (ssRNA) viruses that include members such as dengue (serotypes 1-4), Zika, West Nile, yellow fever, and Japanese Encephalitis viruses. The dengue virus (DENV) is a public health threat that causes serious morbidity and mortality globally [1, 2]. Infection with DENV can result in “break-bone” fever, an extraordinarily painful disease with symptoms ranging from a mild fever to a fatal hemorrhagic syndrome [3]. There are approximately 50 million serious infections and 20,000 deaths each year, and dengue infections are a leading cause of mortality in children in a number of Latin and Asian countries [1]. Dengue viruses have re-emerged in the United States, and a growing number of locally acquired infections in Florida, Texas, and Hawaii have been reported over the last decade. Despite a reinvigorated effort due to the recent Zika epidemic [4], there are currently no approved small molecule antivirals to treat Flavivirus-induced diseases
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
