Molecular Dynamics Study of Streptavidin Binding to Surface-Immobilized Biotin

We use MD simulations to study the interaction between surface-immobilized biotin and streptavidin. We developed two general models with 10 kcal/mol constraints applied to the whole biotin residue, or alternatively, to one C-terminal oxygen atom of biotin. We evaluated the effect of the constraints on the temperature and energy fluctuations along the simulations. For both the restrained and unrestrained streptavidin/biotin system, we found the lowest energy structures. We conclude that streptavidin binding to the immobilized biotin is diffusion controlled and cannot be fully modeled with a relatively short simulation period. The structural details from the unrestrained streptavidin/biotin system extends the understanding of the streptavidin/biotin docking states, especially for an arrangement in which biotin is immobilized on the surface and has limited access to the streptavidin docking pocket.