Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

Abstract

Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform (RPX) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.

Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins

“…Monomers were docked into symmetric three, four, five, and sixfold cyclic assemblies using the Rosetta rpxDock method. , A set of 4618 helical repeat monomers were docked in 4 symmetries, and the top 100 docks of each symmetry were output, resulting in 1.85 million docks. Oligomers were then filtered based on the number of contacts in the interface between subunits and by the predicted quality of the interface interactions, as described in the Materials and Methods.…”

“…Furthermore, these monomers can be easily extended or retracted simply by adding or removing terminal repeats, thus increasing or decreasing pocket size . We anticipated that by combining these curved helical repeat proteins into cyclic homo-oligomers, , we could generate a library of designs encompassing a variety of cavities across the asymmetric oligomeric interface with differing sizes and shapes that can be used as a basis for enzyme or small molecule binding, and built into higher order symmetric assemblies.…”

Accurate Computational Design of 3D Protein Crystals

“…A library of cyclic oligomer scaffolds (C2, C3, C4) from crystal structures deposited in the PDB (http://www.rcsb.org/pdb/) and from previous de novo designs 28,30,35,42 were docked into tetrahedral and octahedral cages (T32, T33, O32, O42 and O43). Cage dockings were carried out by RPXDock, which used hierarchical sampling of residue pair transform scoring to find high designability docking 32 . The top 100 to 500 dockings of each symmetry were sequence designed by Rosetta 24 using a protocol based on two-component protein-protein interface design methods implemented within the RosettaScripts framework 43 .…”

“…10b). The fusions with new backbone were docked by RPXDock 32 in D3 symmetry with only translation DOF along the C3 axes of the dihedral (Extended Data Fig. 10c).…”

“…3, Extended Data Fig. 4) by using RPXDock 32 to dock a wide range of designed oligomers with C2, C3 or C4 symmetry into T33, T32, O43, O42 and O32 assemblies (the two indices indicate the symmetries of the constituent oligomers; O43 indicates an octahedron generated from a designed cyclic tetramer and cyclic trimer) and designing sequences directing assembly using Rosetta 24 . Following experimental validation, the polyhedra were placed into the corresponding Wyckoff sites in the target crystal lattice, the translational spacing sampled finely around 3 Å of close contact (methods, Extended Data Fig.…”