Driving conformational switching in de novo designed α-helical coiled-coils with novel molecular components

Abstract

This research project is multidisciplinary in nature. It involves the use of biomolecular design –peptide design – and the synthesis of small organic compounds to generate conformational switching in peptide structures.

In this thesis, we demonstrate that we can design and synthesize de novo peptide sequences with the necessary information to assemble as α-helical coiled-coil structures when associated with their corresponding peptide partners. In addition, some of the peptide structures are designed to form both α-helical coiled-coils and fibrous systems.

Since we aim to promote conformational changes in the initial folding states of our peptide assemblies, the design of these individual sequences that we refer to as chassis peptides includes tuneable positions which after being modified will help these changes to happen.

We make use of the Negishi reaction to synthesize unnatural amino acids – pyridyl-alanine analogues – for metal-binding investigations. The insertion of these novel amino acids into our self-assembling peptide systems provides different conformational changes depending on the positions in which these amino acids are inserted. These experiments are an attempt to form novel metal-based chiral biocatalysts. They also allow us to investigate to what extent peptide self-assembly can control metal binding and to what extent the metal binding can control peptide self-assembly.

This research project also includes the synthesis of an azobenzene derivative for trans-to-cis and cis-to-trans photoisomerization. We successfully attached an azobenzene linker to three different coiled-coil forming peptide structures, exhibiting different switching efficiency in each. By using these photoswitches we induce conformational changes in the secondary structure of the peptide structures by the use of light. Some of these are reversible structural changes which makes it a potential power source for protein motors.