Modeling Structural Flexibility of Proteins with Go-Models

Structure-based models are an efficient tool for folding studies of proteins since by construction their energy landscape is only minimally 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 sixth 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 beta 1 beta 4 sheet in the mutant protein. Our results are consistent with previous simulations using a physical force field and an explicit solvent and suggest a mechanism by which these mutations cause Menkes disease. In addition, the improved Go-models suggest differences in the folding pathway between the 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.