Structural Studies of Peptide Binding Interaction of HCV IRES Domain IV
- Structural Studies of Peptide Binding Interaction of HCV IRES Domain IV
- 김낙균; 방경미; 신지연; 송현규
- HCV IRES; HCV IRES domain IV; RNA structure; RNA binding peptide; NMR
- Issue Date
- Journal of the Korean Magnetic Resonance Society
- VOL 21-113
- The hepatitis C virus (HCV) internal ribosome entry site (IRES) is an RNA structure located in the 5’-UTR of the HCV RNA genome. The HCV IRES consists of four domains I, II, III, and IV, where domains II - IV are recognized by 40S ribosomal subunit and the domain III is bound to eukaryotic initiation factor 3 (eIF3) for translation initiation. Here, we have characterized the tertiary interaction between an L-/K- rich peptide and the HCV IRES domain IV. To probe the peptide binding interface in RNA, we synthesized 13C- and 15N- double labeled RNA and the binding site was identified by using the chemical shift perturbation (CSP) NMR methods. Our results showed that the peptide binds to the upper stem of the IRES domain IV, indicating that the tertiary interaction between the IRES domain IV and the peptide would disrupt the initiation of translation of HCV mRNA by blocking the start codon exposure. This study will provide an insight into the new peptide-based anti-viral drug design targeting HCV IRES RNA.
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