Probing the relationship between RNA-stimulated ATPase and helicase activities of HCV NS3 using 2'-O-methyl RNA substrates

Protein displacement by DExH/D "RNA helicases" without duplex unwinding

Members of the DExH/D superfamily of nucleic acid-activated nucleotide triphosphatases are essential for virtually all aspects of RNA metabolism, including pre-messenger RNA splicing, RNA interference, translation, and nucleocytoplasmic trafficking. Physiological substrates for these enzymes are thought to be regions of double-stranded RNA, because several DExH/D proteins catalyze strand separation in vitro. These "RNA helicases" can also disrupt RNA-protein interactions, but it is unclear whether this activity is coupled to duplex unwinding. Here we demonstrate that two unrelated DExH/D proteins catalyze protein displacement independently of duplex unwinding. Therefore, the essential functions of DExH/D proteins are not confined to RNA duplexes but can be exerted on a wide range of ribonucleoprotein substrates.

eIF4A: the godfather of the DEAD box helicases

eIF4A has long been considered the "gold standard" for DEAD box helicases. In large measure, this reflected two items: first, the role of eIF4A in protein synthesis initiation was relatively well established. Second, a wide variety of biochemical studies had established the ability of eIF4A to bind nucleic acids in an ATP-dependent manner, to hydrolyze ATP in an RNA-dependent manner, and to unwind RNA duplexes in an ATP-dependent manner. In this article, these basic observations are reviewed for biochemical consistency and also interpreted in light of the available crystal structures for DEAD box proteins. The role of non-processive vs. processive helicase activity in protein synthesis is discussed. Also examined is the influence of ancillary protein factors (eIF4B, eIF4G, and eIF4H) on this activity. Finally, the "real" role(s) for eIF4A helicase activity in protein synthesis is discussed and related to other circumstances that likely also involve the use of non-processive or slightly processive DEAD box helicases (ribosome biosynthesis, RNA splicing).

Nucleotide triphosphatase/helicase of hepatitis C virus as a target for antiviral therapy

The RNA nucleoside triphosphatase (NTPase)/helicases represent a large family of proteins that are detected in almost all biological systems where RNA plays a central role. The enzymes are capable of enzymatically unwinding duplex RNA structures by disrupting the hydrogen bonds that keep the two strands together. The strand separating activity is associated with hydrolysis of nucleoside triphosphate (NTP). Because of this, potential specific inhibitors of NTPase/helicases could act by one or more of the following mechanisms: (i) inhibition of NTPase activity by interference with NTP binding, (ii) inhibition of NTPase activity by an allosteric mechanism and (iii) inhibition of the coupling of NTP hydrolysis at the unwinding reaction. There are also other inhibitory mechanisms conceivable, which may involve a modulation of the interaction of the enzyme with its RNA substrate, for example, (iv) the competitive inhibition of RNA binding and (v) the inhibition of the unwinding by sterical blockade of the translocation of the NTPase/helicase along the polynucleotide chain. NTPase/helicase has also been identified in the viral genome of hepatitis C virus (HCV) which is a member of the Flaviviridae family. It is conceivable that the inhibition of the unwinding activity of the enzyme leads to the inhibition of virus replication and this may represent a novel antiviral strategy. This review updates the current spectrum of inhibitors targeting different mechanisms by which the NTPase and/or helicase activities of the HCV NTPase/helicase are inhibited. Consequently, some of the compounds might be important as antiviral agents against HCV.

Helicase from hepatitis C virus, energetics of DNA binding

The ability of a helicase to bind single-stranded nucleic acid is critical for nucleic acid unwinding. The helicase from the hepatitis C virus, NS3 protein, binds to the 3'-DNA or the RNA strand during unwinding. As a step to understand the mechanism of unwinding, DNA binding properties of the helicase domain of NS3 (NS3h) were investigated by fluorimetric binding equilibrium titrations. The global analysis of the binding data by a combinatorial approach was done using MATLAB. NS3h interactions with single-stranded DNA (ssDNA) are 300-1000-fold tighter relative to duplex DNA. The NS3h protein binds to ssDNA less than 15 nt in length with a stoichiometry of one protein per DNA. The minimal ssDNA binding site of NS3h helicase was determined to be 8 nucleotides with the microscopic K(d) of 2-4 nm or an observed free energy of -50 kJ/mol. These NS3h-DNA interactions are highly sensitive to salt, and the K(d) increases 4 times when the NaCl concentration is doubled. Multiple HCV helicase proteins bind to ssDNA >15 nucleotides in length, with an apparent occluded site of 8-11 nucleotides. The DNA binding data indicate that the interactions of multiple NS3h protein molecules with long ssDNA are both noncooperative and sequence-independent. We discuss the DNA binding properties of HCV helicase in relation to other superfamily 1 and 2 helicases. These studies provide the basis to investigate the DNA binding interactions with the unwinding substrate and their modulation by the ATPase activity of HCV helicase.

Vinylphosphonate internucleotide linkages inhibit the activity of PcrA DNA helicase

During the past 5 years a great deal of structural and biochemical information has given us a detailed insight into the molecular mechanism of action of the PcrA DNA helicase and challenged previous notions about the molecular mechanism of action of helicases in general. Despite this wealth of information the mechanisms of the interaction of helicases with their DNA substrates and their unidirectional translocation along ssDNA are poorly understood. In this study, we synthesized a chemically modified DNA substrate with reduced backbone rotational flexibility and minimal steric hindrance and studied its effect on the activity of the monomeric 3'-5' DNA helicase, PcrA. Our results show that a single modification on the backbone of the translocating strand is sufficient to inhibit the activity of PcrA helicase, suggesting that rotational flexibility of the backbone is important for efficient unwinding.

Characterization of imidazo[4,5-d]pyridazine nucleosides as modulators of unwinding reaction mediated by West Nile virus nucleoside triphosphatase/helicase: evidence for activity on the level of substrate and/or enzyme

Compounds that interact with DNA or RNA generally act as inhibitors of enzymes that unwind DNA or RNA. In the present study we describe the synthesis and properties of some nucleoside analogues that interact with double-stranded DNA but that, in contrast, facilitate the unwinding reaction mediated by West Nile (WN) virus nucleoside triphosphatase (NTPase)/helicase. The nucleoside analogues described, 1-(2'-O-methyl-beta-D-ribofuranosyl)imidazo[4,5-d]pyridazine-4,7(5H,6H)-dione (HMC-HO4), 1-(beta-D-ribofuranosyl)imidazo[4,5-d]pyridazine-4,7(5H,6H)-dione, and 1-(2'-deoxy-alpha-D-ribofuranosyl)imidazo[4,5-d]pyridazine-4,7(5H,6H)dione, all contain the imidazo[4,5-d]pyridazine ring system. The extent of the enhancing effect on helicase activity was found to be dependent on the time of exposure of the DNA substrate to the compounds and their concentrations. The nucleoside analogues were nevertheless found to be capable of uncoupling the ATPase and helicase activities of the enzyme by a mechanism operating on the level of the enzyme. Thus, in the case of HMC-HO4, the direct interaction with the enzyme caused inhibition of its helicase activity, with a half-maximal inhibitory concentration of 30 microM. The similar potency of the compound against replication of WN virus in cell culture suggests that inhibition of the helicase activity of the viral enzyme is responsible for the observed antiviral activity of HMC-HO4 and may indeed represent an important mode of action of antiviral drugs in general. Comparative studies performed with the related NTPase/helicase from hepatitis C virus revealed that the extent of the effects mediated by imidazo[4,5-d]pyridazine nucleosides is enzyme specific. The substances described may represent a starting point for the development of a new class of helicase-specific antivirals.

The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding

The RNA helicase/protease NS3 plays a central role in the RNA replication of hepatitis C virus (HCV), a cytoplasmic RNA virus that represents a major worldwide health problem. NS3 is, therefore, an important drug target in the effort to combat HCV. Most work has focused on the protease, rather than the helicase, activities of the enzyme. In order to further characterize NS3 helicase activity, we evaluated individual stages of duplex unwinding by NS3 alone and in complex with cofactor NS4A. Despite a putative replicative role in RNA unwinding, we found that NS3 alone is a surprisingly poor helicase on RNA, but that RNA activity is promoted by cofactor NS4A. In contrast, NS3 alone is a highly processive helicase on DNA. Phylogenetic analysis suggests that this robust DNA helicase activity is not vestigial and may have specifically evolved in HCV. Given that HCV has no replicative DNA intermediate, these findings suggest that NS3 may have the capacity to affect host DNA.

Structure-based mutational analysis of the hepatitis C virus NS3 helicase

The carboxyl terminus of the hepatitis C virus (HCV) nonstructural protein 3 (NS3) possesses ATP-dependent RNA helicase activity. Based on the conserved sequence motifs and the crystal structures of the helicase domain, 17 mutants of the HCV NS3 helicase were generated. The ATP hydrolysis, RNA binding, and RNA unwinding activities of the mutant proteins were examined in vitro to determine the functional role of the mutated residues. The data revealed that Lys-210 in the Walker A motif and Asp-290, Glu-291, and His-293 in the Walker B motif were crucial to ATPase activity and that Thr-322 and Thr-324 in motif III and Arg-461 in motif VI significantly influenced ATPase activity. When the pairing between His-293 and Gln-460, referred to as gatekeepers, was replaced with the Asp-293/His-460 pair, which makes the NS3 helicase more like the DEAD helicase subgroup, ATPase activity was not restored. It thus indicated that the whole microenvironment surrounding the gatekeepers, rather than the residues per se, was important to the enzymatic activities. Arg-461 and Trp-501 are important residues for RNA binding, while Val-432 may only play a coadjutant role. The data demonstrated that RNA helicase activity was possibly abolished by the loss of ATPase activity or by reduced RNA binding activity. Nevertheless, a low threshold level of ATPase activity was found sufficient for helicase activity. Results in this study provide a valuable reference for efforts under way to develop anti-HCV therapeutic drugs targeting NS3.

Design, high-level expression, purification and characterization of soluble fragments of the hepatitis C virus NS3 RNA helicase suitable for NMR-based drug discovery methods and mechanistic studies

RNA helicases represent a family of enzymes that unwind double-stranded (ds) RNA in a nucleoside triphosphate (NTP)-dependent fashion and which are required in all aspects of cellular RNA metabolism and processing. The hepatitis C virus (HCV) non-structural 3 (NS3) protein possesses a serine protease activity in the N-terminal one-third, whereas RNA-stimulated NTPase and helicase activities reside in the C-terminal portion of the 631 amino acid residue bifunctional enzyme. The HCV NS3 RNA helicase is of key importance in the life cycle of HCV, which makes it a target for the development of therapeutics. However, neither the precise mechanism nor the substrate structure has been defined for this enzyme. For nuclear magnetic resonance (NMR)-based drug discovery methods and for mechanistic studies we engineered, prepared and characterized various truncated constructs of the 451-residue HCV NS3 RNA helicase. Our goal was to produce smaller fragments of the enzyme, which would be amenable to solution NMR techniques while retaining their native NTP and/or nucleic acid binding sites. Solution conditions were optimized to obtain high-quality heteronuclear NMR spectra of nitrogen-15 isotope-labeled constructs, which are typical of well-folded monomeric proteins. Moreover, NMR binding studies and functional data directly support the correct folding of these fragments.

Further characterization of the helicase activity of eIF4A. Substrate specificity

Eukaryotic initiation factor (eIF) 4A is the archetypal member of the DEAD box family of RNA helicases and is proposed to unwind structures in the 5'-untranslated region of mRNA to facilitate binding of the 40 S ribosomal subunit. The helicase activity of eIF4A has been further characterized with respect to substrate specificity and directionality. Results confirm that the initial rate and amplitude of duplex unwinding by eIF4A is dependent on the overall stability, rather than the length or sequence, of the duplex substrate. eIF4A helicase activity is minimally dependent on the length of the single-stranded region adjacent to the double-stranded region of the substrate. Interestingly, eIF4A is able to unwind blunt-ended duplexes. eIF4A helicase activity is also affected by substitution of 2'-OH (RNA) groups with 2'-H (DNA) or 2'-methoxyethyl groups. These observations, taken together with results from competitive inhibition experiments, suggest that eIF4A may interact directly with double-stranded RNA, and recognition of helicase substrates occurs via chemical and/or structural features of the duplex. These results allow for refinement of a previously proposed model for the mechanism of action of eIF4A helicase activity.

Unwinding of nucleic acids by HCV NS3 helicase is sensitive to the structure of the duplex

Hepatitis C virus (HCV) helicase, non-structural protein 3 (NS3), is proposed to aid in HCV genome replication and is considered a target for inhibition of HCV. In order to investigate the substrate requirements for nucleic acid unwinding by NS3, substrates were prepared by annealing a 30mer oligonucleotide to a 15mer. The resulting 15 bp duplex contained a single-stranded DNA overhang of 15 nt referred to as the bound strand. Other substrates were prepared in which the 15mer DNA was replaced by a strand of peptide nucleic acid (PNA). The PNA-DNA substrate was unwound by NS3, but the observed rate of strand separation was at least 25-fold slower than for the equivalent DNA-DNA substrate. Binding of NS3 to the PNA-DNA substrate was similar to the DNA-DNA substrate, due to the fact that NS3 initially binds to the single-stranded overhang, which was identical in each substrate. A PNA-RNA substrate was not unwound by NS3 under similar conditions. In contrast, morpholino-DNA and phosphorothioate-DNA substrates were utilized as efficiently by NS3 as DNA-DNA substrates. These results indicate that the PNA-DNA and PNA-RNA heteroduplexes adopt structures that are unfavorable for unwinding by NS3, suggesting that the unwinding activity of NS3 is sensitive to the structure of the duplex.