Proteins as bulding blocks for biological nanomaterials.

Abstract

Within the field of nanoscience there is a growing interest in the use of biological molecules such as proteins, peptides and nucleic acids, to create materials with complex structure and function. These molecules self-assemble to form a huge variety of functional nanoscale structures in biological systems. Through the work of supramolecular chemistry there is now a greater understanding of how to control the assembly of molecules into functional entities. The aim of this thesis is to combine the fields of biology and supramolecular chemistry to increase the repertoire of available protein building blocks for use in bionanotechnology. Three proteins have been selected due to their ability to self assemble in nature, Lsr2, the Nterminal domain of Lsr2 (Nterm-Lsr2) and human peroxiredoxin 3 (H𝑠Prx3). Lsr2 is a small DNA binding protein that has the innate ability to self-assemble in vivo via a number of routes. This makes it an ideal candidate as a biological building block for forming nanomaterials in vitro. The truncated version of Lsr2 (Nterm-Lsr2) oligomerises into linear chains via anti-parallel β-sheet formation between the extended N-termini of neighbouring dimers. This process was facilitated in vitro using low concentrations of trypsin which removed three N-terminal residues, Met¹, Ala² and Lys³, allowing an inter-dimer anti-parallel β-sheet to form. Using trypsin to initiate assembly led to unwanted proteolysis at additional lysine and arginine residues within the polypeptide chain. A novel and more controlled method of initiating assembly was developed by replacing three N-terminal residues with an enteropeptidase recognition site. Enteropeptidase cleaves specifically at Lys⁴ leaving an identical sequence to the native protein when treated with trypsin but without additional fractionation. This allows the formation of an ordered network of “spaghetti-like” fibres. The structures alternate between a tetramer and high molecular weight oligomers in response to variations in pH. Further control is exerted over the system by exploiting the open symmetry of the assemblies. Increasing and decreasing the protein tecton concentration leads to the formation of larger and smaller structures respectively. Wild type H𝑠Prx3 has been shown to assemble into one dimensional tubes at acidic pH (pH 4.2). By incorporating the N-terminal histidine tag and linker sequence (H𝑠Prx3-6his) into the current assembly system, a number of novel oligomerisation routes were developed. The presence of the tag and linker stabilises the dodecameric toroid leaving an ideal tecton from which higher ordered structures can form. The increased pH sensitivity of H𝑠Prx3-6his allows the formation of tubes at pH 7.4. The size of the assembly was further controlled by small changes in pH, with the tube length increasing with decreasing pH values. It is proposed that electrostatic interactions at the ring interface are driving the assembly. Increasing the salt concentration, thereby disrupting these electrostatic interactions, caused the tubes to dissociate into single rings. Increasing the histidine content within the tag led to the formation of longer tubes, suggesting that the presence of the non-native histidine residues is the origin of the pH sensitivity. The metal-binding imidazole side groups of the histidine tag were also utilised to stabilise stacks of H𝑠Prx3-6his through coordination to Ni²⁺. The switch from high molecular weight stacks to low molecular weight rings was achieved with the addition of chelating agents to the solution. Throughout this study, novel protein building blocks have been developed that assemble and disassemble in a controllable manner in response to variations in environmental conditions. The assembly system of an existing protein tecton (H𝑠Prx3-WT) has been enhanced, creating a protein building block that associates within the physiological pH range. These new routes towards controlled protein oligomerisation could be utilised in future work to form protein nanomaterials for specific functions.