Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication. Issue 18 (30th September 2022)

• Record Type: Journal Article
• Authors: Olenginski, Lukasz T.; Kasprzak, Wojciech K.; Bergonzo, Christina; Shapiro, Bruce A.; Dayie, Theodore K.
• Is Part Of: Journal of molecular biology. Volume 434:Issue 18(2022)
• Publication Date: 2022-09-30
• Subjects: hepatitis B virus -- viral replication -- dynamics -- NMR spectroscopy -- conformational selection; HBV hepatitis B virus -- pgRNA pre-genomic RNA -- C HBV core protein -- P HBV polymerase protein -- RT reverse transcriptase -- RH RNase H -- TP terminal protein -- ε epsilon -- nt nucleotide -- PL priming loop -- DR1 direct repeat 1 -- HSPs heat shock proteins -- HFs host factors -- LH lower helix -- UH upper helix -- PTL pseudo-triloop -- NMR nuclear magnetic resonance -- AL apical loop -- SELEX Systematic Evolution of Ligands by Exponential Enrichment -- MD molecular dynamics -- R1 longitudinal relaxation rate -- R2 transverse relaxation rate -- hNOE {1H}-13C heteronuclear Overhauser effect -- CSA chemical shift anisotropy -- SD standard deviation -- PDB Protein Data Bank -- R1ρ rotating-frame relaxation rate -- Rex chemical exchange contribution to R2 -- CPMG Carr-Purcell-Meiboom-Gill -- R2, eff effective R2 rate -- νCPMG frequency of 180° refocusing pulse in CPMG experiment -- kex exchange rate -- pa population of major state -- pb population of minor state -- δω chemical shift difference between major and minor state -- R2, 0 R2 auto-relaxation -- δppmmin δω that would be present if the pa and pb were equal -- AIC Akaike Information Criterion -- τex exchange lifetime -- RMSD root-mean-square-deviation -- norm normalized -- 2D two-dimensional -- CEST chemical exchange saturation transfer (CEST) -- TROSY transverse relaxation optimized spectroscopy -- J(0) spectral density component at ω = 0 -- J(ωC) spectral density component at ω = ωC -- HF1 high frequency component 1 of the spectral density -- HF2 high frequency component 2 of the spectral density; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2022.167633
• Languages: English
• ISSNs: 0022-2836

Abstract

Graphical abstract: Highlights: HBV polymerase binds ε RNA to initiate HBV genome replication. Previous NMR studies hint that ε dynamics may be functional. NMR demonstrates motion on multiple time scales in mainly conserved nucleotides critical for function. MD simulations suggest that ε undergoes structural rearrangements that may be controlled by its priming loop. RNA dynamics are likely an integral part of HBV replication. Abstract: Human hepatitis B virus (HBV) replication is initiated by the binding of the viral polymerase (P) to epsilon (ε), an ≈85-nucleotide (nt) cis -acting regulatory stem-loop RNA located at the 5′-end of the pre-genomic RNA (pgRNA). This interaction triggers P and pgRNA packaging and protein-primed reverse transcription and is therefore an attractive therapeutic target. Our recent nuclear magnetic resonance (NMR) structure of ε provides a useful starting point toward a detailed understanding of HBV replication, and hints at the functional importance of ε dynamics. Here, we present a detailed description of ε motions on the ps to ns and μs to ms time scales by NMR spin relaxation and relaxation dispersion, respectively. We also carried out molecular dynamics simulations to provide additional insight into ε conformational dynamics. These data outline a series of complex motions on multiple time scales within ε. Moreover, these motions occur in mostly conserved nucleotides from structural regions (i.e., priming loop, pseudo-triloop, and U43 bulge) that biochemical and mutational studies have shown to be essential for P binding, P-pgRNA packaging, protein-priming, and DNA synthesis. Taken together, our work implicates RNA dynamics as an integral feature that governs HBV replication.