Steered molecular dynamics simulation of the binding of the β2 and β3 regions in domain-swapped human cystatin C dimer

Abstract

The crystal structure of the human cystatin C (hCC) dimer revealed that a stable twofold-symmetric dimer was formed via 3D domain swapping. Domain swapping with the need for near-complete unfolding has been proposed as a possible route for amyloid fibril initiation. Thus, the interesting interactions that occur between the two molecules may be important for the further aggregation of the protein. In this work, we performed steered molecular dynamics (SMD) simulations to investigate the dissociation of the β2 and β3 strands in the hCC dimer. The energy changes observed during the SMD simulations showed that electrostatic interactions were the dominant interactions involved in stabilizing the two parts of the dimer during the early stages of SMD simulation, whereas van der Waals (VDW) interactions and electrostatic interactions were equally matched during the latter stages. Furthermore, our data indicated that the two parts of the dimer are stabilized by intermolecular hydrogen bonds among the residues Arg51 (β2), Gln48 (β2), Asp65 (β3), and Glu67 (β3), salt bridges among the residues Arg53 (β2), Arg51 (β2), and Asp65 (β3), and VDW interactions among the residues Gln48 (β2), Arg51 (β2), Glu67 (β3), Asp65 (β3), Phe63 (β3), and Asn61 (β3). The residues Gln48 (β2), Arg51 (β2), Asp65 (β3) and Glu67 (β3) appear to be crucial, as they play important roles in both electrostatic and VDW interactions. Thus, the present study determined the key residues involved in the stabilization of the domain-swapped dimer structure, and also provided molecular-level insights into the dissociation process of the hCC dimer.

Human cystatin C monomer, dimer, oligomer, and amyloid structures are related to health and disease

“…Ribbon representation of the hCC dimer. The interacting regions of β2 and β3 strands proposed by He are highlighted in yellow and magenta, respectively, whereas Shen's fragments are marked in red (helix‐β2) and blue (appendant structure). Figure prepared using pymol software using the hCC dimer (PDB code: 1TIJ).…”

“…hCC and some other amyloidogenic proteins, like β‐amyloid, form meta‐stable oligomers in the shape of small rings . These rings of protein molecules can form pores in the cell membrane and thus are considered to be more toxic than fibrils . While the structural mechanism of hCC oligomerization might turn out to be common with better described proteins, the relation of hCC oligomers and other second‐wave fibril forming proteins to individual diseases requires further research.…”

“…The added protein must be similar to the analyzed one that allows comparison of related peaks in a selected ion monitoring (SIM) chromatogram. [49] are highlighted in yellow and magenta, respectively, whereas Shen's [50] fragments are marked in red (helix-b2) and blue (appendant structure). Figure prepared using PYMOL software using the hCC dimer (PDB code: 1TIJ).…”

“…The structural and biochemical studies on the mutant hCC proteins mentioned in the previous section provided clues to the mechanism of the domain swapping process in hCC. The L68V and L68Q mutants, which destabilize the hydrophobic core packing of hCC, have provided further data , as have steered molecular dynamics simulations . The molecular dynamics work has focused on the β2 and β3 strands of the hCC dimer, in particular, identifying specific residues and interactions that contribute to protein stabilization and structural change.…”

The conformational feasibility for the formation of reaching dimer in ASV and HIV integrase: a molecular dynamics study

“…Computational methods such as molecular modeling and molecular dynamics (MD) simulations have gained importance in identifying biomolecular structures and also in understanding their structural as well as functional dynamics (Costantino, Entrena-Guadix, Macchiarulo, Gioiello & Pellicciari 2005; Villa, Wohnert & Stock 2009; Huggins et al 2010; Casoni, Clerici & Contini 2013; He et al 2013). In recent years, molecular dynamics studies have been used to explore the structural dynamics of HIV proteins including protease, reverse transcriptase and IN (Lins et al 1999; Madrid, Jacobo-Molina, Ding & Arnold 1999; Madrid, Lukin, Madura, Ding & Arnold 2001; Hornak, Okur, Rizzo & Simmerling 2006; Liu, Liu & Fu 2008; Kim, Hartley, Curran & Engelman 2009; Yokoyama, Naganawa, Yoshimura, Matsushita & Sato 2012).…”