Solving a Levinthal's paradox for virus assembly identifies a unique antiviral strategy

Abstract

One of the important puzzles in virology is how viruses assemble the protein containers that package their genomes rapidly and efficiently in vivo while avoiding triggering their hosts' antiviral defenses. Viral assembly appears directed toward a relatively small subset of the vast number of all possible assembly intermediates and pathways, akin to Levinthal's paradox for the folding of polypeptide chains. Using an in silico assembly model, we demonstrate that this reduction in complexity can be understood if aspects of in vivo assembly, which have mostly been neglected in in vitro experimental and theoretical modeling assembly studies, are included in the analysis. In particular, we show that the increasing viral coat protein concentration that occurs in infected cells plays unexpected and vital roles in avoiding potential kinetic assembly traps, significantly reducing the number of assembly pathways and assembly initiation sites, and resulting in enhanced assembly efficiency and genome packaging specificity. Because capsid assembly is a vital determinant of the overall fitness of a virus in the infection process, these insights have important consequences for our understanding of how selection impacts on the evolution of viral quasispecies. These results moreover suggest strategies for optimizing the production of protein nanocontainers for drug delivery and of virus-like particles for vaccination. We demonstrate here in silico that drugs targeting the specific RNA-capsid protein contacts can delay assembly, reduce viral load, and lead to an increase of misencapsidation of cellular RNAs, hence opening up unique avenues for antiviral therapy.

Revealing the density of encoded functions in a viral RNA

“…A hierarchy of PS CP affinities is an essential requirement of the PS-mediated assembly model (9) and is consistent with the sequence/structure variations in PSs PS1-5 on the genomic fragment. PS3 is the highest affinity site and the other PSs contribute to assembly efficiency but cannot trigger VLP formation alone.…”

“…Here we have used smFCS assays to probe the roles of RNA in STNV assembly at nanomolar concentrations, showing that it follows a two-stage PS-mediated mechanism, thus preventing assembly around noncognate RNAs. Even with relatively short PS fragments we have recreated assembly features seen with the intact genome, showing that CP recognition of degenerate PSs, and the latter's relative spacing along the genomic RNA, both contribute to efficient cooperative capsid assembly (9,41). These assays also validate the use of RNA SELEX against viral CPs, combined with theoretical analysis techniques pioneered by us, as a route for identifying PSs (15).…”

“…PSs are bound sequence-specifically by their cognate CPs, increasing the yield, rate and/or fidelity of assembly. PSmediated assembly has many potential advantages for the virus, including solving a viral version of the Levinthal Paradox (9). For the T = 3 MS2, there is a known assembly origin, the 19-nt-long coat protein gene translational operator (TR) stem-loop (10).…”

Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ

“…For Qβ and other ssRNA viruses, there is clearly an evolutionary mandate for efficient and accurate virion assembly (34). After the gRNA is replicated and coat proteins are produced, the rate-limiting step in virion production is encapsidation of the RNA (35).…”

Communication: Free energy of ligand-receptor systems forming multimeric complexes

“…21,22 We envisage applications of our theory to the association of more complex molecules like DNA tiles [23][24][25] or virial caspids. 26 In Sec. II, we derive our theory while in Sec.…”