The actinin family of actin crosslinking proteins: natural functions and potential applications in synthetic biology

Actinin and spectrin proteins are members of the Spectrin Family of Actin Crosslinking Proteins. The importance of these proteins in the cytoskeleton is demonstrated by the fact that they are common targets for disease causing mutations. In their most prominent roles, actinin and spectrin are responsible for stabilising and maintaining the muscle architecture during contraction, and providing shape and elasticity to the red blood cell in circulation, respectively. To carry out such roles, actinin and spectrin must possess important mechanical and physical properties. These attributes are desirable when choosing a building block for protein-based nanoconstruction. In this study, I assess the contribution of several disease-associated mutations in the actinin-1 actin binding domain that have recently been linked to a rare platelet disorder, congenital macrothrombocytopenia. I investigate the suitability of both actinin and spectrin proteins as potential building blocks for nanoscale structures, and I evaluate a fusion-based assembly strategy to bring about self-assembly of protein nanostructures. I report that the actinin-1 mutant proteins display increased actin binding compared to WT actinin-1 proteins. I find that both actinin and spectrin proteins exhibit enormous potential as nano-building blocks in terms of their stability and ability to self-assemble, and I successfully design and create homodimeric and heterodimeric bivalent building blocks using the fusion-based assembly strategy. Overall, this study has gathered helpful information that will contribute to furthering the advancement of actinin and spectrin knowledge in terms of their natural functions, and potential unnatural functions in protein nanotechnology.

Characterisation of an ubiquitin binding CUE domain in presenilin-1

The presenilins are the catalytic component of the gamma-secretase protease complex, involved in the regulated intramembrane proteolysis of numerous type-1 transmembrane proteins, including Amyloid precursor protein (APP) and Notch. In addition to their role in the γ-secretase complex the presenilins are involved in a number of γ-secretase independent functions such as calcium homeostasis, apoptosis, inflammation and protein trafficking. Presenilin function is known to be regulated through posttranslational modifications like endoproteolysis, phosphorylation and ubiquitination. Using a bioinformatics and protein sequence analysis approach this lab has identified a putative ubiquitin binding CUE domain in the presenilins. The aim of this project was to characterise the function of the presenilin CUE domains. Firstly, the presenilins are shown to contain a functional ubiquitin-binding CUE domain that preferentially binds to K63-linked polyubiquitin chains. The PS1 CUE domain is shown to be dispensable for PS1 endoproteolysis and γ-secretase mediated cleavage of APP, Notch and IL-1R1. This suggests the PS1 CUE domain is involved in a γ-secretase independent PS1 function. Our hypothesis is that the PS1 CUE domain is involved in regulating PS1’s intermolecular protein-protein interactions or intramolecular PS1:PS1 interactions. Here the PS1 CUE domain is shown to be dispensable for the interaction of PS1 and the K63-linked polyubiquitinated PS1 interacting proteins P75NTR, IL-1R1, TRAF6, TRAF2 and RIP1. To further investigate PS1 CUE domain function a mass spectrometry proteomics based approach is used to identify PS1 CUE domain interacting proteins. This proteomics approach demonstrated that the PS1 CUE domain is not required for PS1 dimerization. Instead a number of proteins thatinteract with the PS1 CUE domain are identified as well as proteins whose interaction with PS1 is downregulated by the presence of the PS1 CUE domain. Bioinformatic analysis of these proteins suggests possible roles for the PS1 CUE domain in regulating cell signalling, ubiquitination or cellular trafficking.