Predicting assembly/disassembly orders of protein complexes using coarse-grained simulations

Abstract

Assembly of a protein complex is very important to its biological function, which can be investigated by determining assembly/disassembly order 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 assembly/disassembly orders of protein complexes using coarse-grained simulations. The protocols were illustrated using two protein complexes, and the predicted assembly/disassembly orders are consistent with available experimental data.