Measurements of the Self-Assembly Kinetics of Individual Viral Capsids Around Their RNA Genome

Abstract

The formation of a viral capsid-the highly—ordered protein shell that surrounds the genome of a virus—is the canonical example of self-assembly1. The capsids of many positive-sense RNA viruses spontaneously assemble from in vitro mixtures of the coat protein and RNA2. The high yield of proper capsids that assemble is remarkable, given their structural complexity: 180 identical proteins must arrange into three distinct local configurations to form an icosahedral capsid with a triangulation number of 3 (T = 3)1. Despite a wealth of data from structural studies3–5 and simulations6–10, even the most fundamental questions about how these structures assemble remain unresolved. Experiments have not determined whether the assembly pathway involves aggregation or nucleation, or how the RNA controls the process. Here we use interferometric scattering microscopy11,12 to directly observe the in vitro assembly kinetics of individual, unlabeled capsids of bacteriophage MS2. By measuring how many coat proteins bind to each of many individual MS2 RNA strands on time scales from 1 ms to 900 s, we find that the start of assembly is broadly distributed in time and is followed by a rapid increase in the number of bound proteins. These measurements provide strong evidence for a nucleation-and-growth pathway. We also find that malformed structures assemble when multiple nuclei appear on the same RNA before the first nucleus has finished growing. Our measurements reveal the complex assembly pathways for viral capsids around RNA in quantitative detail, including the nucleation threshold, nucleation time, growth time, and constraints on the critical nucleus size. These results may inform strategies for engineering synthetic capsids13 or for derailing the assembly of pathogenic viruses14.