Peptide-based Molecular Motor Design

Abstract

This thesis concerns the use of dimeric coiled-coil peptides as components for synthetic protein motors. Studies of the hub structures of two motor designs are described. Firstly, I discuss experiments on the interactions between peptides designed for use in the Tumbleweed hub, a three-legged motor design containing three dimeric coiled-coil domains. Biophysical characterisation is carried out, including experiments to test the specificity of the interactions, which enable the peptides to be successful potential components for a stable hub structure. Secondly, I discuss the design of another motor hub, with two coiled-coil domains, using similar peptides to those used in the Tumbleweed system. The requirements for this design to produce a progressive motor are discussed. The design requires one peptide spanning the length of the motor hub, which has residues involved in both coiled-coil domains. These two coiled coil-contributing regions are linked by a central span of residues. Inducing a conformational change in this central region, in order to change the dimensions of the hub, is investigated, with the introduction of an azobenzene moiety in its cis and trans isomeric forms, using MD simulations. The ability of various residues to affect the range of conformational states this central region occupies is also investigated. Experimental studies of one of the possible systems are outlined and analysed.