Probing ubiquitin topology

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Ubiquitin is a small protein found in organisms as diverse as yeast and man. It is responsible for the regulation of a host of processes within the cell, including targeting proteins for destruction, gene transcription, cell signalling, and controlling traffic through the cell membrane. Ubiquitin is attached to one or more sites on a target protein by the action of a set of enzymes in a process known as ubiquitination. Ubiquitin is coupled to the amino acid lysine within the target protein structure and, because ubiquitin itself contains lysine residues, it is possible for polymeric ubiquitin chains to build up during ubiquitination / through linkage at any of seven lysines. Thus, poly-ubiquitin can form defined shapes, or topologies, depending upon its linkage pattern. It is believed that different topologies and chain lengths maybe responsible for different functions within the cell, but probing the complete topology of a poly-ubiquitin chain has not previously been possible. Here we propose methods to map poly-ubiquitin linkage, and determine the binding of different topologies with ubiquitin-interacting proteins to allow us to tackle the key question 'does poly-ubiquitin shape and size matter?' in the context of some important biological processes.