Viral genome structures are optimal for capsid assembly

RESEARCH ARTICLE elife.elifesciences.org Viral genome structures are optimal for capsid assembly Jason D Perlmutter, Cong Qiao, Michael F Hagan* Martin A Fisher School of Physics, Brandeis University, Waltham, United States Abstract Understanding how virus capsids assemble around their nucleic acid (NA) genomes could promote efforts to block viral propagation or to reengineer capsids for gene therapy applications. We develop a coarse-grained model of capsid proteins and NAs with which we investigate assembly dynamics and thermodynamics. In contrast to recent theoretical models, we find that capsids spontaneously ‘overcharge’; that is, the negative charge of the NA exceeds the positive charge on capsid. When applied to specific viruses, the optimal NA lengths closely correspond to the natural genome lengths. Calculations based on linear polyelectrolytes rather than base-paired NAs underpredict the optimal length, demonstrating the importance of NA structure to capsid assembly. These results suggest that electrostatics, excluded volume, and NA tertiary structure are sufficient to predict assembly thermodynamics and that the ability of viruses to selectively encapsidate their genomic NAs can be explained, at least in part, on a thermodynamic basis. DOI: 10.7554/eLife.00632.001 Introduction *For correspondence: hagan@ brandeis.edu Competing interests: The authors declare that no competing interests exist. Funding: See page 18 Received: 12 February 2013 Accepted: 14 May 2013 Published: 14 June 2013 Reviewing editor: Benoit Roux, University of Chicago, United States Copyright Perlmutter et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. For many viruses the spontaneous assembly of a protein shell, or capsid, around the viral nucleic acid (NA) is an essential step in the viral lifecycle. Identifying the factors which enable capsids to efficiently and selectively assemble around the viral genome could identify targets for new antiviral drugs that block or derail the formation of infectious virions. Conversely, understanding how assembly depends on the NA and protein structure would guide efforts to reengineer capsid proteins and human NAs for gene therapy applications. From a fundamental perspective, high-order complexes that assemble from protein and/or NAs abound in biology. Learning how the properties of viral components determine their co-assembly can shed light on assembly mechanisms of a broad array of structures and the associated selective pressures on their components. In this article, we use GPU computing (Anderson et al., 2008; Nguyen et al., 2011; LeBard et al., 2012) and a simplified, but quantitatively testable, model to elucidate the effects of electrostatics, capsid geometry, and NA tertiary structure on assembly. Assembly around NAs is predominately driven by electrostatic interactions between NA phosphate groups and basic amino acids, often located in flexible tails known as arginine rich motifs (ARMs) (e.g., Schneemann, 2006). There is a correlation between the net charge of these protein motifs and the genome length for many ssRNA viruses (Belyi and Muthukumar, 2006; Hu et al., 2008), with a ‘charge ratio’ of negative charge on NAs to positive charge on proteins typically of order 2:1 (i.e., viruses are ‘overcharged’). Electrophoresis measurements confirm that viral particles are negatively charged (e.g., [Serwer et al., 1995; Serwer and Griess, 1999; Porterfield et al., 2010]), though these measurements include contributions from the capsid exteriors (Bozic et al., 2012; Zlotnick et al., 2013). Based on these observations, it has been proposed that viral genome lengths are thermodynamically optimal for assembly, meaning that their lengths minimize the free energy of the assembled nucleocapsids. However, while estimates of optimal lengths have varied (van der Schoot and Bruinsma, 2005; Angelescu et al., 2006; Belyi and Muthukumar, 2006; Hu et al., 2008; Siber and Podgornik, 2008; Ting et al., 2011; Ni et al., 2012; Siber et al., 2012), recent theoretical models based on linear polyelectrolytes (Siber and Podgornik, 2008; Ting et al., 2011; Ni et al., 2012) have consistently predicted that optimal NA lengths correspond to ‘undercharging’ Perlmutter et al. eLife 2013;2:e00632. DOI: 10.7554/eLife.00632 1 of 21 Research article Biophysics and structural biology eLife digest Viruses are infectious agents made up of proteins and a genome made of DNA or RNA. Upon infecting a host cell, viruses hijack the cell’s gene expression machinery and force it to produce copies of the viral genome and proteins, which then assemble into new viruses that can eventually infect other host cells. Because assembly is an essential step in the viral life cycle, understanding how this process occurs could significantly advance the fight against viral diseases. In many viral families, a protein shell called a capsid forms around the viral genome during the assembly process. However, capsids can also assemble around nucleic acids in solution, indicating that a host cell is not required for their formation. Since capsid proteins are positively charged, and nucleic acids are negatively charged, electrostatic interactions between the two are thought to have an important role in capsid assembly. However, it is unclear how structural features of the viral genome affect assembly, and why the negative charge on viral genomes is actually far greater than the positive charge on capsids. These questions are difficult to address experimentally because most of the intermediates that form during virus assembly are too short-lived to be imaged. Here, Perlmutter et al. have used state of the art computational methods and advances in graphical processing units (GPUs) to produce the most realistic model of capsid assembly to date. They showed that the stability of the complex formed between the nucleic acid and the capsid depends on the length of the viral genome. Yield was highest for genomes within a certain range of lengths, and capsids that assembled around longer or shorter genomes tended to be malformed. Perlmutter et al. also explored how structural features of the virus—including base-pairing between viral nucleic acids, and the size and charge of the capsid—determine the optimal length of the viral genome. When they included structural data from real viruses in their simulations and predicted the optimal lengths for the viral genome, the results were very similar to those seen in existing viruses. This indicates that the structure of the viral genome has been optimized to promote packaging into capsids. Understanding this relationship between structure and packaging will make it easier to develop antiviral agents that thwart or misdirect virus assembly, and could aid the redesign of viruses for use in gene therapy and drug deliver (...truncated)