Predicting the assembly/disassembly order of protein complexes via coarse-grained simulations

The assembly of a protein complex is very important for its biological function, which can be investigated by determining the order of assembly/disassembly of its protein subunits. Although static structures of many protein complexes are available in the protein data bank, their assembly/disassembly orders of subunits are largely unknown. In addition to experimental techniques for studying subcomplexes in the assembly/disassembly of a protein complex, computational methods can be used to predict the assembly/disassembly order. Since sampling is a nontrivial issue in simulating the assembly/disassembly process, coarse-grained simulations are more efficient than atomic simulations are. In this work, we developed computational protocols for predicting the assembly/disassembly orders of protein complexes via coarse-grained simulations. The protocols were illustrated via two protein complexes, and the predicted assembly/disassembly orders were consistent with the available experimental data.