We present a top-down hierarchical computational framework for mechanobiology problems, the molecular dynamics decorated finite element method (MDeFEM). The MscL in Escherichia coli was given as an example with its continuum model built under the instruction of MDeFEM framework.  Its gating pathways under various external perturbations were investigated, which are in good agreement with current experimental data and all-atom simulation results. The MDeFEM method showed its advantages and great potential in solving the mechanical responses of large biomolecules with complex geometries, which often involves multiple temporal and spatial scales.