Modulation of Enzymatic Activity of Dengue Virus Nonstructural Protein NS3 Nucleoside Triphosphatase/Helicase by Poly(U)

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M. Junaid^1,2, C. Angsuthanasombat¹, J. E. S. Wikberg³, N. Ali⁴, and G. Katzenmeier^1*

¹Laboratory of Molecular and Cellular Microbiology, Institute of Molecular Biosciences, Mahidol University, Salaya, 73170 Thailand; E-mail: katzenmeier.ger@mahidol.ac.th

²Department of Pharmacy, University of Malakand, K. P. K, 18550 Pakistan; E-mail: juniphdr@gmail.com

³Department of Pharmaceutical Biosciences, Division of Pharmacology, Uppsala University, Uppsala, 75124 Sweden

⁴Department of Pharmacology, Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Khyber Pakhtunkhwa, 25000 Pakistan

^* To whom correspondence should be addressed.

Received March 22, 2013; Revision received April 26, 2013

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The nonstructural protein 3 (NS3) appears to be the most promising target for anti-flavivirus therapy because of its multiple enzymatic activities that are indispensable for virus replication. NS3 of dengue virus type 2 (DEN2) is composed of two domains, a serine protease in the N-terminal domain (NS3pro) and RNA-stimulated nucleoside triphosphatase (NTPase)/RNA helicase at the C-terminus (NS3h). NS3 plays an important role in viral replication and the coordinated regulation of all the catalytic activities in the full-length NS3 protein. In this study, a plasmid harboring the NS3 helicase domain (NS3h) was constructed by PCR. The 56.5 kDa NS3h protein was purified by metal-chelate affinity chromatography followed by renaturation, mediated by artificial chaperone-assisted refolding, which yielded the active helicase. NTPase activity was assayed with Malachite Green. The NTPase activity in the presence of poly(U) showed a higher turnover number (k_cat) and a lower K_m value than without poly(U). The activity increased approximately fourfold in the presence of polynucleotides. This indicates that NTPase activity of dengue NS3 can be stimulated by polynucleotides. A helicase assay based on internal fluorescence quenching was conducted using short internally quenched DNA oligonucleotides as substrates. Significant fluorescence signaling increase was observed in the absence of polynucleotides such as poly(U). No unwinding activity was observed with addition of poly(U). The approach we describe here is useful for the further characterization of substrate specificity and for the design of high-throughput assays aimed at discovery of inhibitors against NS3 NTPase/helicase activities.

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KEY WORDS: Dengue virus, NS3 protein, NTPase, helicase, assay, substrate, polynucleotide

DOI: 10.1134/S0006297913080105

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