Steered molecular dynamics (SMD), a computer simulation method for studying force-induced reactions in biopolymers, has been applied to investigate the response of protein domains to stretching apart of their terminal ends. The simulations mimic atomic force microscopy and optical tweezer experiment
Steered molecular dynamics simulations of protein-ligand interactions
β Scribed by Yechun Xu; Jianhua Shen; Xiaomin Luo; Xu Shen; Kaixian Chen; Hualiang Jiang
- Publisher
- SP Science China Press
- Year
- 2004
- Tongue
- English
- Weight
- 817 KB
- Volume
- 47
- Category
- Article
- ISSN
- 1674-7291
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## Abstract Molecular dynamics simulations of Ca^+2^ ions near protein were performed with three force fields: GROMOS96, OPLSβAA, and CHARMM22. The simulations reveal major, forceβfield dependent, inconsistencies in the interaction between the Ca^+2^ ions with the protein. The variations are attrib
Atomic force microscopy (AFM) experiments and steered molecular dynamics (SMD) simulations have revealed much about the dynamics of protein-ligand binding and unbinding, as well as the stretching and unfolding of proteins. Both techniques induce ligand unbinding or protein unfolding by applying exte