A Theoretical Study of SRPK Interaction with the Flexible Domains of Hepatitis B Capsids

Abstract

Hepatitis B virus (HBV) controls genome encapsidation and reverse transcription from a single-stranded RNA to a double-stranded DNA through the flexible C-terminal domain (CTD) of the capsid proteins. Although the microscopic structure of the nucleocapsid plays a critical role in the life cycle of HBV, the location of CTD residues at different stages of viral replication remains poorly understood. In this work, we report the radial distributions of individual amino-acid residues of the CTD tails for both empty and RNA-containing HBV capsids by using a coarse-grained model for the key biological components and the classical density functional theory. The density functional theory calculations reveal substantial exposure of the CTD residues outside the capsid, in particular when it is devoid of any nucleic materials. The outermost layer of the capsid surface mainly consists of residues from (170)Ser-(175)Arg of the CTD tails, i.e., the serine-arginine protein kinase binding motif. The theoretical description corroborates recent in vitro studies that show a transient CTD distribution captured by serine-arginine protein kinase binding. We have also investigated the nucleocapsid structural changes due to phosphorylation of serine residues and shown a correlation between the CTD location and the internal distribution of RNA segments.

A Thermodynamic Model for Genome Packaging in Hepatitis B Virus

“…In this work, the intracellular fluid is represented by an aqueous solution of NaCl at the physiological concentration C s ¼ 0.14 M. It has been well documented that thermodynamic properties of the aqueous electrolyte solution can be accurately reproduced with the primitive model, assuming that the cations and the anions are charged hard spheres with diameters s Na þ ¼ 0.39 nm and s Cl À ¼ 0.36 nm, respectively (44). As in our previous publications (36,37), we use a spherical shell model for the HBV T4 capsid with an inner radius R C ¼ 13 nm and a shell thickness d ¼ 2 nm. The symmetric pores on the capsid shell are modeled as a semipermeable membrane that allows transport of monomeric nucleic acids and small ions.…”

“…From in vitro assembly of HBV nucleocapsids in Escherichia coli, it has been noted that the RNA packaging is insensitive to the origin of the genome or the RNA sequence (5,7). The nonspecific nature of RNA encapsidation suggests that the essential features of HBV capsids can be faithfully described with a coarse-grained molecular model (34,36,37).…”

“…The excess free energy is calculated from the classical density functional theory (DFT). We have demonstrated in our earlier works the theoretical performance of the DFT for inhomogeneous polyelectrolyte systems (49,50) and its successful applications to HBV nucleocapsids (34,36,37). The Supporting Material details a self-contained description of the relevant DFT equations used in this work.…”

“…In addition, more detailed capsid features are implemented such that CTD segments are set to be exposable into the outside region. It has been shown that such semipermeable characters are relevant to build the HBV capsid model (36). Fig.…”

Making the invisible visible: fast magic-angle-spinning NMR reveals the evasive hepatitis B virus capsid functional C-terminal domain

“…The NTD is sufficient for selfassembly at high enough concentrations, and has been characterized via cryo-electron microscopy [34,35] , X-ray crystallography [36] , and solid-state NMR [37,38,38] . The CTD has been described as a flexible, disordered domain [39] ; it shows four arginine-rich repeats (Figure 1e) commonly found in RNA-and DNA-binding proteins [40] and interacts with the pgRNA during capsid assembly. Therefore, the phosphorylated CTD is not moving freely, but engages in interactions, likely of electrostatic nature between the arginine side chains and the pgRNA phosphate groups.…”