Molecular dynamics simulations to investigate the domain swapping mechanism of human cystatin C

Human cystatin C (HCC), one of the amyloidgenic proteins, has been proved to form a dimeric structure via a domain swapping process and then cause amyloid deposits in the brains of patients suffering from Alzheimer's disease. HCC monomer consists of a core with a five-stranded antiparallel β-sheet (β region) wrapped around a central helix. The connectivity of these secondary structures is: (N)-β1-α-β2-L1-β3-AS-β4-L2- β5-(C). In this study, various molecular dynamics simulations were conducted to investigate the conformational changes of the monomeric HCC at different temperatures (300 and 500 K) and pH levels (2, 4, and 7) to gain insight into the domain swapping mechanism. The results show that high temperature (500 K) and low pH (pH 2) will trigger the domain swapping process of HCC. We further proposed that the domain swapping mechanism of HCC follows four steps: (1) the α-helix moves away from the β region; (2) the contacts between β2 and β3-AS disappear; (3) the β2-L1-β3 hairpin unfolds following the so-called "zip-up" mechanism; and finally (4) the HCC dimer is formed. Our study shows that high temperature can accelerate the unfolding of HCC and the departure of the α-helix from the β-region, especially at low pH value. This is attributed to the fact that that low pH results in the protonation of the side chains of Asp, Glu, and His residues, which further disrupts the following four salt-bridge interactions stabilizing the α-β interface of the native structure: Asp15-Arg53 (β1-β2), Glu21/20-Lys54 (helix-β2), Asp40-Arg70 (helix-AS), and His43-Asp81 (β2-AS).