Protein fusion is a ubiquitous engineering method in synthetic and chemical biology. Two or more natural or engineered proteins are expressed as a single recombinant protein, incorporating so-called linker peptides to connect the constituent domains. The resulting constructs retain the functions of all their components and often feature new emergent behaviours brought about by their proximity and dynamics. Despite overwhelming evidence that the sequence, length, structure and other properties of these linkers have an enormous impact on the performance of the final product, very little is known about their structure and dynamics. The application of efficient and accurate biophysical modelling techniques developed in the last few years alongside single molecule fluorescence experiments promises to provide new insight into the design and use of linkers in fusion proteins.