Predicting stable binding modes from simulated dimers of the D76N mutant of β2-microglobulin

Abstract

AbstractThe D76N mutant of the β2m protein is a biologically motivated model system to study protein aggregation. There is strong experimental evidence, supported by molecular simulations, that D76N populates a highly dynamic conformation (which we originally named I2) that exposes aggregation-prone patches as a result of the detachment of the two terminal regions. Here, we use Molecular Dynamics simulations to study the stability of an ensemble of dimers of I2 generated via protein-protein docking. MM-PBSA calculations indicate that within the ensemble of investigated dimers the major contribution to interface stabilization at physiological pH comes from hydrophobic interactions between apolar residues. Our structural analysis also reveals that the interfacial region associated with the most stable binding modes are particularly rich in residues pertaining to both the N- and C-terminus, as well residues from the BC- and DE-loops. On the other hand, the less stable interfaces are stabilized by intermolecular interactions involving residues from the CD- and EF-loops. By focusing on the most stable binding modes, we used a simple geometric rule to propagate the corresponding dimer interfaces. We found that, in the absence of any kind of structural rearrangement occurring at an early stage of the oligomerization pathway, some interfaces drive a self-limited growth process, while others can be propagated indefinitely allowing the formation of long, polymerized chains. In particular, the interfacial region of the most stable binding mode reported here falls in the class of self-limited growth.Graphical AbstractHighlightsThe D76N mutant of protein β2m populates an aggregation-prone monomer (I2) with unstructured terminal regionsMolecular Dynamics simulations and MM-PBSA calculations indicate that dimers of I2 are stabilized by hydrophobic interactionsThe N- and C-terminal regions, together with the BC- and DE-loops are prevalent in the most stable dimer interfaces, while the CD- and EF-loop appear in the less stable onesThe most stable dimer interface has a limited potential to oligomerize in the absence of structural rearrangement