Abstract
Transcription activator-like effectors (TALEs) form a novel class of DNA-binding proteins with predictable specificity. The TALE protein for avrBs3 is composed of 17.5 repeat domains of 34 amino acid residues, and each repeat domain recognizes one specific base-pair. The specificity is encoded by the repeat-variable diresidue (RVD) of each repeat domain, and this modular nature of DNA base recognition enables useful applications in biotechnology. However, there is very little available structural information about the binding mode and the specificity. In this study, we attempt to generate possible binding modes of the TALE with avrBs3 using protein structure modeling, protein-DNA docking, and molecular dynamics simulation. We discuss the observed binding specificities in terms of the molecular interactions found in the models.
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