Structure Prediction of Domain Insertion Proteins from Structures of Individual Domains

Multi-domain proteins continue to be a major challenge in protein structure prediction. Here, we present a Monte Carlo (MC) algorithm, implemented within Rosetta, to predict the structure of proteins in which one domain is inserted into another. Three new MC moves combine rigid-body and loop movements to search the constrained conformation by structure disruption and subsequent repair of chain breaks. Local searches find that the algorithm samples and recovers near-native structures consistently. Further global searches produced top-ranked structures within 5 Å in 31 of 50 cases in low resolution mode, and refinement of top-ranked low-resolution structures produce models within 2 Å in 21 of 50 cases. Rigid-body orientations were often correctly recovered despite errors in the linker conformation. The algorithm is broadly applicable to de novo structure prediction of both naturally occurring and engineered domain insertion proteins.