Steered molecular dynamics simulations on the binding of the appendant structure and helix-β2 in domain-swapped human cystatin C dimer.
We have performed steered molecular dynamics (SMD) simulations to investigate the dissociation process between the appendant structure (AS) and helix-β2 in human cystatin C dimer. Energy change during SMD showed that electrostatic interactions, including hydrogen bonds and salt bridges, were the dominant interactions to stabilize the two parts of the dimer. Furthermore, our data indicated that residues, Asn35, Asp40, Ser44, Lys75, and Arg93 play significant roles in the formation of these electrostatic interactions. Docking studies suggested that the interactions between AS and β2-helix were formed following domain swapping and were responsible for stabilizing the structure of the domain-swapped dimer.
Province Key Laboratory of Animal Resource and Epidemic Disease Prevention, Liaoning University, Shenyang, 110036, China.
Manli
M
Shen
Jing
J
Guan
Linan
L
Xu
Yuanyuan
Y
Yu
Jianwei
J
He
Gary W
GW
Jones
Youtao
Y
Song
D000682:Amyloid / Q000737:chemistry; D055316:Cystatin C / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D000682:Amyloid; C525030:CST3 protein, human; D055316:Cystatin C