Conformational dynamics of superoxide dismutase (SOD1) in osmolytes: a molecular dynamics simulation study

Abstract

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease caused by the misfolding of Cu, Zn superoxide dismutase (SOD1). Several earlier studies have shown that monomeric apo SOD1 undergoes significant local unfolding dynamics and is the predecessor for aggregation. Here, we have employed atomistic molecular dynamics (MD) simulations to study the structure and dynamics of monomeric apo and holo SOD1 in water, aqueous urea and aqueous urea-TMAO (trimethylamine oxide) solutions. Loop IV (zinc-binding loop) and loop VII (electrostatic loop) of holo SOD1 are considered as functionally important loops as they are responsible for the structural stability of holo SOD1. We found larger local unfolding of loop IV and VII of apo SOD1 as compared to holo SOD1 in water. Urea induced more unfolding in holo SOD1 than apo SOD1, whereas the stabilization of both the form of SOD1 was observed in ternary solution (i.e. water/urea/TMAO solution) but the extent of stabilization was higher in holo SOD1 than apo SOD1. The partially unfolded structures of apo SOD1 in water, urea and holo SOD1 in urea were identified by the exposure of the hydrophobic cores, which are highly dynamic and these may be the initial events of aggregation in SOD1. Our simulation studies support the formation of aggregates by means of the local unfolding of monomeric apo SOD1 as compared to holo SOD1 in water.

Fig. 1. Crystal structures of apo and holo SOD1 used in the simulations, along with the structures of urea and TMAO, which are used as osmolytes (red, blue, black and white colours indicate oxygen, nitrogen, carbon and hydrogen, respectively).

Fig. 2. RMSD of the backbone atoms of the whole (A) apo and holo SOD1 in water, (B and C) apo and holo SOD1 in water, urea and urea–TMAO. RMSD of loop IV and VII (D, E and F) of apo SOD1 in water, urea and urea–TMAO and (G, H and I) of holo SOD1 in water, urea and urea–TMAO solutions, respectively.

Fig. 3. Probability distribution of the radius of gyration (R_g) of apo and holo SOD1 in water, urea and urea–TMAO solution.

Fig. 4. Fractions of the native contact of apo and holo SOD1 in (A) water, (B) urea and (C) urea–TMAO solution.

Fig. 5. The initial structure of the monomer holo SOD1, which consists of eight β-sheet, seven loops and two α-helixes present in loop IV and loop VII. Snapshots of a few representative structures of apo SOD1 in (A–C) water, (D–F) urea, (G–I) urea–TMAO and holo SOD1 in (J–L) water, (M–O) urea and (P–R) urea–TMAO solution at 100 ns, 150 ns and 200 ns of the simulations, respectively.

Fig. 6. The difference between the SASA per residue of apo and holo SOD1 containing (A) urea and (B) urea–TMAO w.r.t apo and holo SOD1 in water, respectively.

Fig. 7. Probability distribution of the SASA of loop V of apo and holo SOD1 in (A) water, (B) urea and (C) urea–TMAO solutions.

Fig. 8. Potential surfaces of apo SOD1 in (A) water, (B) urea, (C) urea–TMAO solution and holo SOD1 in (D) water, (E) urea and (F) urea–TMAO solutions at the end of the simulation along with the initial structure generated using chimera (red, blue and white colours show the negatively charged, positively charged and neutral hydrophobic residues, respectively).

Fig. 9. Hydrophobic contact map of apo and holo SOD1 barrels in water (A & D), urea (B & E) and in urea–TMAO solution (C & F).

Fig. 10. Cumulative configuration entropies (per atom) of the backbone (A and B) and sidechain (C and D) of apo and holo SOD1 in water, urea and urea–TMAO solutions, respectively.

Fig. 11. Probability distribution of the number of intramolecular hydrogen bonds present in apo and holo SOD1 in (A) water, (B) urea and (C) TMAO.

Fig. 12. 2D and 3D free energy landscape (FEL) plot of the first two eigenvectors PC1 and PC2 of apo SOD1 in (A and A′) water, (B and B′) urea, (C and C′) urea–TMAO, and holo SOD1 in (D and D′) water, (E and E′) urea and (F and F′) urea–TMAO solutions (energy in kJ mol⁻¹).

Fig. 13. Radial distribution function of the oxygens of urea (OU) around loops IV & VII of apo and holo SOD1 in urea (A &C) and in urea–TMAO (B & D) solutions.

Fig. 14. Spatial distribution function (SDF) of the oxygens of urea (OU) molecules around loops IV (L4) & VII (L7) of apo SOD1 (A and C) and holo SOD1 (B and D) in urea. The SDF of OU around L4 and L7 of apo SOD1 (E and G) and holo SOD1 (F and H) in ternary solution (loops are shown in the VDW method (C, O and N are in khaki, red and blue, respectively), the distribution of OU is shown in the meshed surface (purple)). Iso-surfaces of SDF's are drawn in purple in the first solvation shell corresponding to RDF.