Predicting stable binding modes from simulated dimers of the D76N mutant ofβ2-microglobulin

Abstract

The D76N mutant of the beta-2-microgobulin 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.

Interfacial dynamics and growth modes ofβ2-microglobulin dimers

“…Here, we extend our previous study 13 of β 2 m self-association and investigate how the growth mode is modulated by the geometric changes occurring at the dimer’s interface in the ns– μ s timescale. To achieve this, we developed a method that determines the growth mode based on just two angles, which constitute a minimal representation the dimer’s interfacial geometry.…”

“…As the RMSD reference structure, we used the initial structure, which corresponded to the relaxed structure obtained in our previous work. 13…”

“…We used a dielectric constant of 4, a grid scaling factor ( scale ) of 2, and a convergence criterion ( convergence ) of 0.01 kT/e. 13 Additionally, the Poisson–Boltzmann (PB) calculations used 500 and 50 linear ( nlit ) and non-linear ( nonit ) iterations, respectively. The grid size was calculated as double the maximum value of the 3 atomic spatial coordinates, plus 1 if the final number is even, while the center was located in the geometric center of all the atomic coordinates of the system.…”

“…In our previous study 13 we deployed a simple replication protocol that allows predicting the three-dimensional structure of a polymerized chain of β 2 m dimers forming in the absence of structural rearrangement. In particular, we used PyMOL to visualize the structure of a polymerised chain that was created by the repeated addition of dimers following a simple geometric protocol (Fig 2).…”

“…9,10 Computational modelling covering different resolutions and timescales has been playing a pivotal role in helping understand the nature of protein aggregation 11 and in providing predictions for the structure of the oligomeric species formed along the amyloid pathway. 7,12,13…”