Structural Prediction of Neuronal Arhgap21/23 Interactors by Computational Analysis

RhoGAPs, RhoGTPase-activating proteins, have multiple roles in neuronal development, however, their substrate recognition system remains elusive. Both ArhGAP21 and ArhGAP23 RhoGAPs contain N-terminal PDZ domain and pleckstrin homology domain. In this study, the RhoGAP domain of these ArhGAPs was computationally modeled by template-based methods; and their intrinsic RhoGTPase recognition mechanism was analyzed from the domain structures using the protein docking programs, HADDOCK and HDOCK. ArhGAP21 RhoGAP was predicted to preferentially catalyze Cdc42, RhoA, RhoC and RhoG, and downregulate RhoD and Tc10 activities. As for ArhGAP23 RhoGAP RhoA, Cdc42 and RhoB were deduced to be its substrates. The PDZ domains of ArhGAP21/23 possess FTLRXXXVY sequence and similar globular folding conserved with PDZ domains of MAST-family proteins. Peptide docking analysis and molecular dynamics simulation revealed the specific interaction of ArhGAP23 PDZ domain with PTEN C-terminus. The pleckstrin homology domain structure of ArhGAP23 was also predicted, and functional selectivity for the interactors regulated by the folding and disordered domains in ArhGAP21 and ArhGAP23, was examined by in silico analysis. Interaction analysis of these RhoGAPs revealed mammalian ArhGAP21/23-specific typeI and typeIII Arf- and RhoGTPase-regulated signaling. These may form the basis of the functional core signaling necessary for synaptic homeostasis and axon/dendritic transport regulated by RhoGAP localization and activities.