Unbinding of glucose from human pulmonary surfactant protein D studied by steered molecular dynamics simulations

Abstract

Steered molecular dynamics (SMD) simulations were performed to investigate the dynamic characteristics in the unbinding process of α- d-glucose from human pulmonary surfactant protein D (SP-D). The result shows that the residues Glu321, Asp325, Glu329 and Arg343 are responsible for the different dynamic strength from the affinity in the stable state of thermodynamics. Especially the hydrogen bonds between the residues Glu321, Glu329 and glucose increase their interaction and contribute the counteraction to the external force. The change of the directions of the hydroxyl groups in the C2 and C6 atoms of α- d-glucose also affects the dynamic strength in the pulling procedure.