Modeling Structural Flexibility of Proteins with Go-Models

Abstract

Structure-based models are an efficient tool for folding studies of proteins since by construction their energy landscape is only minimal frustrated. However, their intrinsic drawback is a lack of structural flexibility as usually only one target structure is employed to construct the potentials. Hence, a Go-model may not capture differences in mutation-induced protein dynamics, if - as in the case of the disease-related A629P mutant of the Menkes protein ATP7A - the structural differences between mutant and wild type are small. In this work, we introduced three implementations of Go-models that take into account the flexibility of proteins in the NMR ensemble. Comparing the wild type and the mutant A629P of the 75-residue large 6th domain Menkes protein, we find that these new Go-potentials lead to broader distributions than Go-models relying on a single member of the NMR-ensemble. This allows us to detect the transient unfolding of a loosely formed β1β4-sheet in the mutant protein. Our results are consistent with previous simulations using physical force field and an explicit solvent, and suggests a mechanism by which these mutations cause Menkes disease. In addition, the improved Go-models suggest differences in the folding pathway between wild type and mutant, an observation that was not accessible to simulations of this 75-residue protein with a physical all-atom force field and explicit solvent.