Chapter 12. Viruses

12.1. Introduction

A prototypical example of a large-scale system is a virus. Typical viral protein coats range from 0.5 million atoms up; with the addition of viral RNA or DNA, atom counts can easily exceed one million. Understanding the structure of viral protein coats is essential for investigating antigenic sites amenable to recognition by natural or synthetic agents and for understanding the process of coat assembly and disassembly that is critical to the viral life cycle. Much as with large finite simulations improving on small periodic simulations, full atomistic simulations of viruses can improve substantially on current technology, which imposes simplifying assumptions such as symmetry constraints.

As a start towards more sophisticated analyses of viral coat structure, a specific viral structure was simulated: human rhinovirus-14 (RHV). This viral coat is composed of sixty protomers arranged with icosahedral symmetry; each protomer is in turn composed of multiple subunits.

12.2. Procedure

The subunit structure at a resolution of 3.0 Å was obtained from the Brookhaven protein databank (file 4RHV) [1]. The atom types and forcefield parameters were selected from the AMBER forcefield [2], and connectivities were generated to match standard amino acids. Investigation of the fitting of asymmetric units showed that several charged groups on the surface of the protomer appeared to form salt bridges with oppositely-charged groups on the opposing surface of a neighboring protomer. After accounting for these, a net charge of +5 remained, composed of 10 positively charged groups and 15 negatively charged groups. Counterions (sodium or chloride) were positioned near each of these charged residues. Finally, the protein coat, consisting of 60 copies of the asymmetric unit, was then built using the crystallographic symmetry operations from the structure deposited with the protein databank. The final structure contained 512,760 atoms including crystallographic waters and the added counterions.

The structure was then minimized to better position the counterions and to attempt to find the best, symmetry-free, relaxed structure for the coat. This also served to test whether the coat was stable in the absence of the viral genome. Dynamics at 0 K was used to perform the minimization. A CMM level of 6 was used with a bounding cube 360 Å on a side. The farfield was updated every 5 minimization steps.

12.3. Results

After 6000 steps of minimization, the RMS force reached a value of 0.2 kcal/mol. The energy of the final structure was -1.03x10^6 kcal/mol.

The RMS difference in coordinates between the initial and final structures was 0.495 Å, but there was no change in the radius of gyration during the course of the minimization.

Note that the structure remained relatively stable, despite the absence of RNA in the interior. This suggests that the RNA does not play an essential role in maintaining the integrity of the protein coat, though it does undoubtedly affect the structure of the internal portions of the protomer units.

12.4. Conclusions

We have demonstrated that building a symmetry-constraint-free model of a viral protein coat is now practical.

The coat structure is stable with respect to minimization from the X-ray geometry, suggesting that there is sufficient strength in the interactions between protomers to hold the coat together, even in the absence of RNA.

Future work on this project will include studying the pH dependence of the stability of the system, as experiments have suggested that acid-induced changes may be relevant to uncoating for rhinovirus-14 [3], but perhaps not for poliovirus [4]. The temperature dependence of the stability can also be determined.

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Kian-Tat Lim