Unbiased picture of the ligand docking process for the hevein protein-oligosaccharide complex.

ABSTRACT: The ligand-docking behavior of hevein, the major latex protein from the rubber tree Hevea brasiliensis (Euphorbiaceae), has been investigated by the unguided molecular dynamics (MD) simulation method. An oligosaccharide molecule, initially placed in an arbitrary position, was allowed to move around hevein for a prolonged simulation time, on the order of microseconds, with the expectation of spontaneous ligand docking of the oligosaccharide molecule to the binding site of hevein. In the binary solution system consisting of a hevein molecule and a chito-trisaccharide (GlcNAc₃) molecule, three out of the six separate simulation runs successfully reproduced the complex structure of the observed binding from. It appeared that the surface topology formed by two aromatic side chains of

SUBMITTER: Yui T 

PROVIDER: S-EPMC11772807 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature