Sequence-structure Signals of 3D Domain Swapping in Proteins

Three-dimensional domain swapping occurs when two or more identical proteins exchange identical parts of their structure to generate an oligomeric unit. It affects proteins with diverse sequences and structures, and is expected to play important roles in evolution, functional regulation and even conformational diseases. Here, we search for traces of domain swapping in the protein sequence, by means of algorithms that predict the structure and stability of proteins using database-derived potentials. Regions whose sequences are not optimal with regard to the stability of the native structure, or showing marked intrinsic preferences for non-native conformations in absence of tertiary interactions are detected in most domain-swapping proteins. These regions are often located in areas crucial in the swapping process and are likely to influence it on a kinetic or thermodynamic level. In addition, cation–π interactions are frequently observed to zip up the edges of the interface between intertwined chains or to involve hinge loop residues, thereby modulating stability. We end by proposing a set of mutations altering the swapping propensities, whose experimental characterization would contribute to refine our in silico derived hypotheses.