Probing order within intrinsically disordered proteins

Decades have passed since the realisation that a protein’s amino acid sequence can contain all the information required to form a complex three-dimensional fold. Until recently, these encoded structures were thought to be crucial determinants of protein function. Much effort was directed to fully understand the mechanisms behind how and why proteins fold, with natively unfolded proteins thought to be experimental artefacts. Today, the field of natively unfolded – or so-called intrinsically disordered – proteins, is rapidly developing. Protein disorder content has been positively correlated with organismal complexity, with over thirty percent of eukaryotic proteins predicted to contain disordered regions. However, the biophysical consequences of disorder are yet to be fully determined. With the aim of addressing some of the outstanding questions, the work described in this thesis focuses on the relevance of structure within disordered proteins. Whilst populating a variety of conformations in isolation, a subset of disordered proteins can fold upon binding to a partner macromolecule. This folded state may be present within the ensemble of conformations sampled by the unbound protein, opening the question of what comes first: folding or binding? Protein engineering techniques were employed to alter the level of residual ‘bound-like’ structure within the free conformational ensemble, and the consequences on coupled folding and binding reactions were investigated. Resultant changes in the rate of association are easily imaginable; yet, this work demonstrates that the majority of the observed changes in binding affinity were due to alterations in the rate of dissociation, thus altering the lifetime of the bound complex. Promiscuous binding is a touted advantage of being disordered. If many disordered proteins, each with their own conformational ensemble, can bind and fold to the same partner, then where is the folding component encoded? Does the partner protein template the folding reaction? Or, is the folding information contained within the disordered protein sequence? Utilising phi-value analysis on the BCL-2 family of proteins, residues in the disordered sequence were probed to ascertain which form contacts at the transition state of the reaction. Comparison with phi-value analyses of alternative pairs – sharing either the ordered or disordered protein – provides insight into the encoding of these interactions. In the context of a bimolecular reaction, the amino acid sequence of the disordered protein was shown to determine the interactions within the transition state. Thus, analogous to the discovery from decades’ past, it is the sequence of the protein that folds which encodes its pathway, even when binding is a prerequisite.