Protein dynamics are considered significant for many physiological processes, such as metabolism, biomolecular recognition, and the regulation of several vital cellular processes. Due to their flexibility, proteins may stay in different substates with or without the existence of the cognate substrates. To describe thee phenomena, two models have been proposed: the "induced fit" and the "conformational selection" mechanisms. In this study, we used MalK(2), the subunits that mainly include the nucleotide-binding domains (NBDs) of the maltose transporter from Escherichia coli, as a target to understand the NBD dimerization mechanism. Accelerated and conventional molecular dynamics have been performed. The results revealed that Mg-ATP binding to MalK(2) led to a significant change in the free energy profile and thus stabilized the closed conformation. On the contrary, when Mg-ATP was removed, the open conformation would be favored. The fact that ligand binding induces a drastic free energy change leads to a significant inference: MalK(2) dimerization would occur through the induced-fit mechanism rather than the conformational selection mechanism. This study sheds new light on the NBD dimerization mechanism and would be of wide applicability to other ABC transporters.