Varieties of charge distributions in coat proteins of ssRNA+ viruses

TL;DR

This study analyzes the charge distributions in coat proteins of ssRNA+ viruses, revealing persistent positive charges on N-terminal tails across pH levels and exploring their relationship with genome length and virus stability.

Contribution

It introduces two definitions for N-terminal tails, systematically extracts their sequences, and investigates their charge properties and implications for viral assembly.

Findings

N-terminal tails maintain positive charge even at high pH

Viruses with charged tails have shorter genomes compared to similar viruses without tails

No direct correlation between tail charge and genome length

Abstract

A major part of the interactions involved in the assembly and stability of icosahedral, positive-sense single-stranded RNA (ssRNA+) viruses is electrostatic in nature, as can be inferred from the strong $pH$- and salt-dependence of their assembly phase diagrams. Electrostatic interactions do not act only between the capsid coat proteins (CPs), but just as often provide a significant contribution to the interactions of the CPs with the genomic RNA, mediated to a large extent by positively charged, flexible N-terminal tails of the CPs. In this work, we provide two clear and complementary definitions of an N-terminal tail of a protein, and use them to extract the tail sequences of a large number of CPs of ssRNA+ viruses. We examine the $pH$-dependent interplay of charge on both tails and CPs alike, and show that -- in contrast to the charge on the CPs -- the net positive charge on the N-tails persists even to very basic $pH$ values. In addition, we note a limit to the length of the wild-type genomes of those viruses which utilize positively charged tails, when compared to viruses without charged tails and similar capsid size. At the same time, we observe no clear connection between the charge on the N-tails and the genome lengths of the viruses included in our study.