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Model and Methods Energy Hamiltonian.To extend a structure-based model to systems with multiple basins, we modified the contact map and the dihedral angles. Note that all the residue indexes are rearranged from 1 to 366 in the model. To include the side chain dynamics on the conformational change of enzyme, we developed a coarse-grained model in which each amino acid is represented by one or two beads dependent of its location. One bead (named CA in our model), representing the backbone, is located on the Cα atom, and one bead (name CB), representing the side chain, is located on the center of mass or the farthest heavy atom of the side chain, depending on its residue characterize (see details in section of Side-chain Interactions). Based on the fact that the interface between the NTD and CTD is lined by negatively charged residues, that are responsible for an array of hydrogen bonds with the sugar substrate in holo-close form of MBP, we introduced the electrostatic interactions into the two-bead model to study the effect of charged residues on the conformational change of MBP. The two-bead structure-based hamiltonian is given by the expression: