Reversible pH-controlled DNA-binding peptide nanotweezers: An in-silico study

Abstract

Abstract:We describe the molecular dynamics (MD)-aided engineering design of mutant peptides based on the α-helical coiled-coil GCN4 leucine zipper peptide (GCN4-p1) in order to obtain environmentally-responsive nanotweezers. The actuation mechanism of the nanotweezers depends on the modifi cation of electrostatic charges on the residues along the length of the coiled coil. Modulating the solution pH between neutral and acidic values results in the reversible movement of helices toward and away from each other and creates a complete closed-open-closed transition cycle between the helices. Our results indicate that the mutants show a reversible opening of up to 15 Å (1.5 nm; approximately 150% of the initial separation) upon pH actuation. Investigation on the physicochemical phenomena that infl uence conformational properties, structural stability, and reversibility of the coiled-coil peptide-based nanotweezers revealed that a rationale-and design-based approach is needed to engineer stable peptide or macromolecules into stimuli-responsive devices. The effi cacy of the mutant that demonstrated the most signifi cant reversible actuation for environmentally responsive modulation of DNA-binding activity was also demonstrated. Our results have signifi cant implications in bioseparations and in the engineering of novel transcription factors.