Molecular basis of ssDNA recognition by RBM45 protein of neurodegenerative disease from multiple molecular dynamics simulations and energy predictions

Neurodegenerative diseases (NDD) are a group of cognitive and behavioral disorders characterized by progressive loss of neuronal structure and function. As the population ages, the incidence is getting higher and higher, but there is currently no effective treatment. The details of RNA/DNA recognition by the RNA-binding protein RBM45 closely related to neurodegenerative diseases through its two tandem RNA-recognition domains at its N-terminus have important implications for structure-based drug discovery against degenerative diseases. To explore the key characteristics of interaction between ssDNA and RBM45, we performed multiple molecular dynamics (MD) simulations along with MM-PBSA energy prediction on the complexes of wild type (WT) and three mutant RBM45s (K100A, F124A/Y165A, and F29A/F70A/F124A/Y165A) with ssDNA, respectively. The findings suggest that these mutated residues of RBM45 modify the interaction of their surrounding residues with ssDNA, thereby affecting RBM45 protein binding to ssDNA. In contrast with WT RBM45 protein, variations in van der Waals and electrostatic interactions with ssDNA caused by these three RBM45 mutants are critical to affect binding between them. In addition, energy analysis showed that RBM45 is a specific ssDNA-binding protein. The results of our work provide valuable theoretical guidance for the design effective drugs of NDD.