Yu-Sheng Lin
National Sun Yat-Sen University, Taiwan
Title: Predicting the most stable EpB/target molecule complex by stochastic tunneling-basin Hopping- Discrete Molecular Dynamics method
Biography
Biography: Yu-Sheng Lin
Abstract
The global minimum search method (STUN-BH-DMD method for abbreviation) combining the strengths of the Stochastic
Tunneling, Basin Hopping and Discrete Molecular Dynamics method was used to predict the most stable AptEpB/EpCAM
complex. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as a target molecule for the EpCAM
aptamer EpA (AptEpB). For the most stable AptEpB/EpCAM complex predicted by the STUN-BH-DMD method, the AptEpB
is attached to the entangling loop fragments of two EpCAM molecules with most AptEpB residues. After the AptEpB/EpCAM
complex equilibrated with the water environment by the MD simulation at 300 K for 10 ns, the stable hydrogen bonds formed
between the bases of AptEpB and EpCAM residues of the secondary structures including the alpha helix and beta sheet become
less stable in the water environment.