Theory Meets Experiment: Metal Ion Effects in HCV Genomic RNA Kissing Complex Formation.

Li-Zhen Sun,Xiao Heng,Shi-Jie Chen

doi:10.3389/fmolb.2017.00092

Abstract

The long-range base pairing between the 5BSL3. 2 and 3′X domains in hepatitis C virus (HCV) genomic RNA is essential for viral replication. Experimental evidence points to the critical role of metal ions, especially Mg2+ ions, in the formation of the 5BSL3.2:3′X kissing complex. Furthermore, NMR studies suggested an important ion-dependent conformational switch in the kissing process. However, for a long time, mechanistic understanding of the ion effects for the process has been unclear. Recently, computational modeling based on the Vfold RNA folding model and the partial charge-based tightly bound ion (PCTBI) model, in combination with the NMR data, revealed novel physical insights into the role of metal ions in the 5BSL3.2-3′X system. The use of the PCTBI model, which accounts for the ion correlation and fluctuation, gives reliable predictions for the ion-dependent electrostatic free energy landscape and ion-induced population shift of the 5BSL3.2:3′X kissing complex. Furthermore, the predicted ion binding sites offer insights about how ion-RNA interactions shift the conformational equilibrium. The integrated theory-experiment study shows that Mg2+ ions may be essential for HCV viral replication. Moreover, the observed Mg2+-dependent conformational equilibrium may be an adaptive property of the HCV genomic RNA such that the equilibrium is optimized to the intracellular Mg2+ concentration in liver cells for efficient viral replication.

Highlights

Belonging to the Flaviviridae family, hepatitis C virus (HCV) is the only member of the Hepacivirus genus
Both viral protein translation and minus-strand RNA synthesis occur on the genomic RNA
We focus on the major conclusions and the analysis for the ion binding effects in the 5BSL3.2:3′X HCV kissing complex formation (Kranawetter et al, 2017; Sun et al, 2017a)

Summary

INTRODUCTION

Belonging to the Flaviviridae family, hepatitis C virus (HCV) is the only member of the Hepacivirus genus. It has infected nearly 200 million individuals around the globe. The 5′-untranslated region (UTR) contains a highly structured internal ribosomal entry site (IRES) that initiates translation of the polyprotein encoded in the open reading frame (ORF). The polyprotein translated from the single ORF is processed by host and viral proteases to produce structural proteins and nonstructural proteins. Minus-strand RNA synthesis initiates at the 3′-UTR by viral nonstructural protein 5B (NS5B), which produces positive-strand RNA using the minus-strand RNA as template (Moradpour et al, 2007)

Metal Ions in Viral RNA

COMPUTATIONAL MODELING OF

DISCUSSION AND CONCLUSION