Instituto Gulbenkian de Ciência, Portugal
Coarse graining structural changes of protein assemblies
The function of proteins is determined by changes in their atomic structure. At the same time, biophysical experiments demonstrate that few variables (rotation angles, pulling forces, etc.) can account for dominant features of protein function. However, it is not clear how to connect these dominant features to the atomistic changes. I will present a systematic method to quantify the structural changes of protein assemblies based on finite strain theory. I will apply this method to the case of ATP synthase, and show that the spatial distribution of the dominant mode of strain is in-plane and delocalized in two disjoint regions. I will show that this conclusion is robust to all known structures of ATP synthases. The possibility of identifying a strain-mode whose large-scale features are evolutionary preserved suggests that our method can be used to coarse grain the structural changes of proteins.