Plexins are a family of single pass transmembrane receptors with 9 family members: plexin-A1-4, B1-3, C1 and D1. Plexins receive the guidance cues of semaphoring ligands on the outside of the cell and transmit their signal through the lipid membrane. Because of their function, plexins can regulate cell migration and targeting processes, for example by controlling axon and blood vessel guidance. Misfunction of plexin enables serious diseases, including cancer metastasis.Up to now, it is believed that the binding of small Rho GTPases with the Rho GTPase Binding Domain (RBD) of plexin is necessary to the function of plexin. At the meanwhile, the same RBD can bind with different small Rho GTPases, such as Rac1 and Rnd1 GTPase, and different RBDs such plexin-A1-RBD, plexin-A2-RBD, plexin-B1-RBD, can bind with the same GTPase. Thus understanding the structure and dynamics of the free and bound forms of RBD and GTPases can help to understand the signal transduction processes of plexin.In this project, the complexes of RBDs bound with Rac1/Rnd1 GTPases, and the free form of RBDs and GTPases were investigated using miscrosecond length all atom molecular dynamics simulations. It is found that RBDs experience more structural changes than Rho-GTPases during the binding process. Different RBDs showed different structure fluctuation dependences on regions when binding with small Rho GTPases. Calculating the backbone dihedral angle covariance matrix, all the RBDs in the free states have similar correlations to their bound states, but the Rac1 GTPase in the free states has less correlations than their bound states. Mapping the highly correlated residues to the structure, it was expected that plexin-A1-RBD, plexin-B1-RBD, and plexin-A2-RBD all having similar signal pathways, but different key residues taking the role in the process.