Abstract
The study of double-stranded RNA unwinding by helicases is a problem of basic scientific interest. One such example is provided by studies on the hepatitis C virus (HCV) NS3 helicase using single molecule mechanical experiments. HCV currently infects nearly 3% of the world population and NS3 is a protein essential for viral genome replication. The objective of this study is to model the RNA unwinding mechanism based on previously published data and study its characteristics and their dependence on force, ATP and NS3 protein concentration. In this work, RNA unwinding by NS3 helicase is hypothesized to occur in a series of discrete steps and the steps themselves occurring in accordance with an underlying point process. A point process driven change point model is employed to model the RNA unwinding mechanism. The results are in large agreement with findings in previous studies. A gamma distribution based renewal process was found to model well the point process that drives the unwinding mechanism. The analysis suggests that the periods of constant extension observed during NS3 activity can indeed be classified into pauses and subpauses and that each depend on the ATP concentration. The step size is independent of external factors and seems to have a median value of 11.37 base pairs. The steps themselves are composed of a number of substeps with an average of about 4 substeps per step and an average substep size of about 3.7 base pairs. An interesting finding pertains to the stepping velocity. Our analysis indicates that stepping velocity may be of two kinds- a low and a high velocity.
Highlights
The study of RNA unwinding by helicases is a problem of basic scientific interest
In [1], Dumont et al proposed the concept of pauses and subpauses, which are periods of constant extension between the discrete steps observed directly from single molecule experiments
Even in identical molecules the number of base pairs that separate as function of time varies as separation requires random thermal activations that differ in different identical molecules
Summary
The study of RNA unwinding by helicases is a problem of basic scientific interest. Recent advances in single molecule techniques have allowed the study of these proteins and their action at an unprecedented detail [1,2]. The results presented here were obtained using the data analysis methods proposed in Arunajadai [6] In this method, RNA unwinding by NS3 is hypothesized to occur in a series of discrete steps. In [1], Dumont et al proposed the concept of pauses and subpauses, which are periods of constant extension between the discrete steps observed directly from single molecule experiments. Such behavior has been observed in single molecular studies involving the separation of double-stranded DNA into two separated single strands at constant force [7,8] which may provide information pertinent to the mechanism of DNA replication. We see that there is reasonable agreement among most of the characteristics of the unwinding mechanism but there are some new inferences which might be worth further investigation
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