Prediction of the structure of symmetrical protein assemblies

Abstract

Biological supramolecular systems are commonly built up by the self-assembly of identical protein subunits to produce symmetrical oligomers with cyclical, icosahedral, or helical symmetry that play roles in processes ranging from allosteric control and molecular transport to motor action. The large size of these systems often makes them difficult to structurally characterize using experimental techniques. We have developed a computational protocol to predict the structure of symmetrical protein assemblies based on the structure of a single subunit. The method carries out simultaneous optimization of backbone, side chain, and rigid-body degrees of freedom, while restricting the search space to symmetrical conformations. Using this protocol, we can reconstruct, starting from the structure of a single subunit, the structure of cyclic oligomers and the icosahedral virus capsid of satellite panicum virus using a rigid backbone approximation. We predict the oligomeric state of EscJ from the type III secretion system both in its proposed cyclical and crystallized helical form. Finally, we show that the method can recapitulate the structure of an amyloid-like fibril formed by the peptide NNQQNY from the yeast prion protein Sup35 starting from the amino acid sequence alone and searching the complete space of backbone, side chain, and rigid-body degrees of freedom.

Fig. 1.

Energy versus rmsd distribution after global sampling (Left) and local refinement (Right). x axis, rmsd over the studied subsystem versus the crystal structure; y axis, Rosetta fullatom energy.

Fig. 2.

Comparison of the lowest energy models after refinement to the complete native structures. Native structures are in red and models are in blue.

Fig. 3.

Side chain prediction of selected residues at a subunit interface of 1ejb. The backbone and side chains for the crystal structure subunits A and B are shown in yellow and green, respectively. Side chains for subunits A and B for the lowest-energy models are shown in magenta and blue, respectively.

Fig. 4.

Reconstruction of the helical model of 1yj7 and the capsid model of 1stm. Subunits around a fivefold axis or four consecutive monomers are shown in blue, red, magenta, green, and cyan for the virus (Upper) and helix (Lower), respectively. (Left) Lowest energy models. (Right) Crystal structures.

Fig. 5.

Amyloid fibril modeling. (a) The green arrows indicate the degrees of freedom sampled during the conformational search: side chain and backbone torsional degrees of freedom; three rotations of the peptide; distance from the peptide to the twofold screw axis; spacing along the axis between peptides. (b and c) Superposition of the lowest-energy model (gray) and the crystal structure of the NNQQNY steric zipper (cyan), showing good agreement over the core side chains. (d) Scatter plot of all-atom rmsd to the crystal structure (x axis) versus energy for the fibril modeling simulations.