Assessing the Effect of Loop Mutations in the Folding Space of β2-Microglobulin with Molecular Dynamics Simulations

Abstract

We use molecular dynamics simulations of a full atomistic Gō model to explore the impact of selected DE-loop mutations (D59P and W60C) on the folding space of protein human β2-microglobulin (Hβ2m), the causing agent of dialysis-related amyloidosis, a conformational disorder characterized by the deposition of insoluble amyloid fibrils in the osteoarticular system. Our simulations replicate the effect of mutations on the thermal stability that is observed in experiments in vitro. Furthermore, they predict the population of a partially folded state, with 60% of native internal free energy, which is akin to a molten globule. In the intermediate state, the solvent accessible surface area increases up to 40 times relative to the native state in 38% of the hydrophobic core residues, indicating that the identified species has aggregation potential. The intermediate state preserves the disulfide bond established between residue Cys25 and residue Cys80, which helps maintain the integrity of the core region, and is characterized by having two unstructured termini. The movements of the termini dominate the essential modes of the intermediate state, and exhibit the largest displacements in the D59P mutant, which is the most aggregation prone variant. PROPKA predictions of pKa suggest that the population of the intermediate state may be enhanced at acidic pH explaining the larger amyloidogenic potential observed in vitro at low pH for the WT protein and mutant forms.

A tale of two tails: The importance of unstructured termini in the aggregation pathway of β2‐microglobulin

“…To guarantee equilibrium sampling of the conformational space, we deploy Replica‐Exchange (RE) DMD with a temperature grid calibrated to ensure a high acceptance probability (>90%) for the RE moves and replica “round‐trips.” Further details on the model and RE‐DMD simulations can be found in Refs. .…”

Knotted proteins: A tangled tale of Structural Biology

“…To address the folding process of specific proteins researchers developed another class of models, which use an off-lattice representation of the protein (that can be either full-atomistic or restricted to C α atoms) [42–49] . The folding space of off-lattice models is often explored with Monte Carlo (MC) methods or Molecular Dynamics (MD) schemes (discrete MD, Langevin etc).…”

Computational Investigation of the Missense Mutations in DHCR7 Gene Associated with Smith-Lemli-Opitz Syndrome

“…This was done using the MD trajectories obtained above and computing the residue cross-correlation for each trajectory with Bio3D [ 27 ]. These types of analyses were successfully used to elucidate the effects of a single mutation on the human β2-microglobulin’s protein dynamics [ 28 ]. For each mutation and wild type, we calculated the average cross-correlation from three independent MD runs.…”