Predicting stable binding modes from simulated dimers of the D76N mutant of [Formula: see text] 2-microglobulin

Nuno F B Oliveira; Filipe E P Rodrigues; João N M Vitorino; Rui J S Loureiro; Patrícia F N Faísca; Miguel Machuqueiro

doi:10.1016/j.csbj.2021.09.003

Predicting stable binding modes from simulated dimers of the D76N mutant of $β$ 2-microglobulin

Comput Struct Biotechnol J. 2021 Sep 8:19:5160-5169. doi: 10.1016/j.csbj.2021.09.003. eCollection 2021.

Authors

Nuno F B Oliveira^{1

2}, Filipe E P Rodrigues^{1

2}, João N M Vitorino^{1

2}, Rui J S Loureiro¹, Patrícia F N Faísca^{1

3}, Miguel Machuqueiro^{1

2}

Affiliations

¹ BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.
² Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa 1749-016, Portugal.
³ Department of Physics, Faculty of Sciences, University of Lisbon, Lisbon 1749-016, Portugal.

Abstract

The D76N mutant of the $β_{2} m$ 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 $I_{2}$ ) 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 $I_{2}$ 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.

Keywords: 0000; 1111; Configurational clustering; Folding intermediates; MM-PBSA; Molecular Dynamics; Protein oligomerization.