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Steered molecular dynamics simulations on the binding of the appendant structure and helix-β2 in domain-swapped human cystatin C dimer

Shen, M. and Guan, J. and Xu, L. and He, J. and Jones, G.W. and Song, Y. (2012) Steered molecular dynamics simulations on the binding of the appendant structure and helix-β2 in domain-swapped human cystatin C dimer. Journal of Biomolecular Structure and Dynamics. ISSN 0739-1102

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Abstract

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.

Item Type: Article
Keywords: human cystatin C; steered molecular dynamics; appendant structure; amyloid; domain swapping;
Subjects: Science & Engineering > Biology
Item ID: 3884
Depositing User: Dr. Gary Jones
Date Deposited: 20 Sep 2012 09:42
Journal or Publication Title: Journal of Biomolecular Structure and Dynamics
Publisher: Adenine Press
Refereed: Yes
URI:

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