Simulation of pH-dependent edge strand rearrangement in human beta-2 microglobulin

Abstract

Amyloid fibrils formed from unrelated proteins often share morphological similarities, suggesting common biophysical mechanisms for amyloidogenesis. Biochemical studies of human beta-2 microglobulin (beta2M) have shown that its transition from a water-soluble protein to insoluble aggregates can be triggered by low pH. Additionally, biophysical measurements of beta2M using NMR have identified residues of the protein that participate in the formation of amyloid fibrils. The crystal structure of monomeric human beta2M determined at pH 5.7 shows that one of its edge beta-strands (strand D) adopts a conformation that differs from other structures of the same protein obtained at higher pH. This alternate beta-strand arrangement lacks a beta-bulge, which may facilitate protein aggregation through intermolecular beta-sheet association. To explore whether the pH change may yield the observed conformational difference, molecular dynamics simulations of beta2M were performed. The effects of pH were modeled by specifying the protonation states of Asp, Glu, and His, as well as the C terminus of the main chain. The bulged conformation of strand D is preferred at medium pH (pH 5-7), whereas at low pH (pH < 4) the straight conformation is observed. Therefore, low pH may stabilize the straight conformation of edge strand D and thus increase the amyloidogenicity of beta2M.

Figure 1.

Two crystal structures of β₂M. (Left) β₂M_HLA corresponds to the structure of β₂M in the HLA complex determined to 1.8 Å resolution (PDB 1DUZ). (Right) β₂M_X-Ray was determined as a monomer, also to 1.8 Å (PDB 1LDS).

Figure 2.

The RMS deviation of main-chain atoms at the end of 3 nsec simulations started from either β₂M_X-ray (▪) or β₂M_HLA (○). Bars indicate secondary structure in β₂M_X-ray corresponding to the strands A, B, C, C′, D (black), E, F, and G.

Figure 3.

β₂M_X-ray was simulated at medium pH with 100 mM NaCl and snapshots were obtained at different time points: (i) 38 psec, (ii) 638 psec, (iii) 750 psec, (iv) 1.55 nsec, (v) 2.48 nsec, (vi) 3.0 nsec.

Figure 4.

A detailed view of frame vi from Figure 3, illustrating the bulge in strand D.

Figure 5.

Two 6-nsec simulations were performed with the intermediate conformation β₂M^‡ (middle) corresponding to frame iii of Figure 3. The simulated pH values were set to either low by protonating Asp, Glu, and His, or medium by protonating His only. (Left) The structure obtained after 6 nsec at low pH was superimposed with the frame i of Figure 3 (two trajectories); (right) the structure obtained after 6 nsec at medium pH was superimposed with β₂M_HLA.

Figure 6.

The side chain of H51 can form a H-bond with the side chain of D53, forcing the two residues on the same side of a β-strand and constraining the geometry of the backbone (left), or with the main-chain carbonyl of S52, thus allowing D53 to rotate toward the solvent (right).