Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers

Abstract

Intermediates of the self-assembly process of the salt stable cowpea chlorotic mottle virus (ss-CCMV) capsid can be modelled atomistically on realistic computational timescales either by studying oligomers in equilibrium or by focusing on their dissociation instead of their association. Our previous studies showed that among the three possible dimer interfaces in the icosahedral capsid, two are thermodynamically relevant for capsid formation. The aim of the current study is to evaluate the relative structural stabilities of the three different ss-CCMV dimers and to find and understand the conditions that lead to their dissociation. Long timescale molecular dynamics simulations at 300 K of the various dimers and of the pentamer of dimers underscore the importance of large contact surfaces on stabilizing the capsid subunits within an oligomer. Simulations in implicit solvent show that at higher temperature (350 K), the N-terminal tails of the protein units act as tethers, delaying dissociation for all but the most stable interface. The pentamer of dimers is also found to be stable on long timescales at 300 K, with an inherent flexibility of the outer protein chains.

Figure 1

(a) T1, (b) T2 and (c) T3 dimers from the original capsid; (d) the whole icosahedral ss-CCMV capsid, coloured by chains, showing the positions of the three interface types between the protein monomers.

Figure 2

(a) ${\mathrm{C}}_{\alpha }$ RMSD, (b) interface RMSD, (c) per-residue fluctuation (background colour bars represent the interface residues for T1 (green), T2 (red), T3 (blue), (d) change of the interface surface area during the trajectory for T1 (green), T2 (red) and T3 (blue) dimers.

Figure 3

Binding energy landscape as a function of monomer contacts and center of mass distances, with initial and final structures presented, of the implicit water MD simulations for T1 (a), T2 (b), T3 (c) and TX (d) at 350 K. All frames from the four trajectories per dimer were used to generate these graphs.

Figure 4

(a) ${\mathrm{C}}_{\alpha }$ RMSD, (b) iRMSD and (c) interface surface for T1 (green), T2 (red), T3 (blue) and TX (purple) for 600 ns NPT ensemble in explicit water on 350 K. Structures (d–g) show the lowest frequency motions for T1 (d), T2 (e), T3 (f) and TX (g).

Figure 5

(a) ${\mathrm{C}}_{\alpha }$ RMSD of the PD from two parallel MD simulations starting from different random velocities from the same structure for $2\mathrm{\mu }\text{s}$; (b) residue fluctuation in the PD for the inner chains (red) and outer chains (green); (c) variation in the number of hydrogen bonds for the separated T1 dimers (AB ... IJ), standalone T1 dimer (T1) and separated T2 dimers (AC ... IA), standalone T2 dimer (T2); (d) variation in the angle between the body of monomers in the separated T1 dimers (AB ... IJ), standalone T1 dimer (T1) and separated T2 dimers (AC ... IA), standalone T2 dimer (T2).