Paper Citing NAMD - Abstract
Jin, Hao-Bai; Kang, Yu; Zhang, Jin; Wu, Tao; Wang, Qi
Interaction between tissue-type plasminogen activator and ligands grafted onto hydrogel
MOLECULAR SIMULATION, 39:513-520, MAY 1 2013
Tissue-type plasminogen activator (t-PA) has shown significant effects on the treatment of common thrombosis. In this work, molecular dynamics simulations are used in proteinligand interaction analysis to investigate the affinity of ligands for affinity chromatography. A hydrogel matrix grafted with amine (positively charged), carboxyl (negatively charged) and hydroxyl (neutral) ligands separately is designed, and its adsorptiondesorption dynamics are studied in detail. The residues on the surface of t-PA, on which the S1 pocket is located, could be more easily adsorbed by charged ligands grafted onto the hydrogel matrix than neutral ligands. The findings offer new insights into the affinity of various ligands for t-PA, and could be of potential use in t-PA purification.
