Human FoxP Transcription Factors as Tractable Models of the Evolution and Functional Outcomes of Three-Dimensional Domain Swapping

Abstract

The association of two or more proteins to adopt a quaternary complex is one of the most widespread mechanisms by which protein function is modulated. In this scenario, three-dimensional domain swapping (3D-DS) constitutes one plausible pathway for the evolution of protein oligomerization that exploits readily available intramolecular contacts to be established in an intermolecular fashion. However, analysis of the oligomerization kinetics and thermodynamics of most extant 3D-DS proteins shows its dependence on protein unfolding, obscuring the elucidation of the emergence of 3D-DS during evolution, its occurrence under physiological conditions, and its biological relevance. Here, we describe the human FoxP subfamily of transcription factors as a feasible model to study the evolution of 3D-DS, due to their significantly faster dissociation and dimerization kinetics and lower dissociation constants in comparison to most 3D-DS models. Through the biophysical and functional characterization of FoxP proteins, relevant structural aspects highlighting the evolutionary adaptations of these proteins to enable efficient 3D-DS have been ascertained. Most biophysical studies on FoxP suggest that the dynamics of the polypeptide chain are crucial to decrease the energy barrier of 3D-DS, enabling its fast oligomerization under physiological conditions. Moreover, comparison of biophysical parameters between human FoxP proteins in the context of their minute sequence differences suggests differential evolutionary strategies to favor homoassociation and presages the possibility of heteroassociations, with direct impacts in their gene regulation function.

Unraveling the folding and dimerization properties of the human FoxP subfamily of transcription factors

“…Despite their high sequence identity, FoxP4 possesses a higher energy barrier in the association process, corroborating that the dimerization ability relies on the association rather than the dissociation energy barrier. Interestingly, considering the low energy barrier of FoxP proteins compared with other 3D-DS proteins [8,20,24], these results reinforce the observed feasibility to also form 3D-DS heterooligomers [25], suggesting that FoxP proteins could undergo 3D-DS to form heterodimers under physiological conditions [17].…”

“…The crystal structure of FoxP4 revealed a monomer similar to FoxP1 and FoxP2 (root mean square deviations [RMSD] after structural alignment of 1.79 and 0.96 Å, respectively), with high conservation of the characteristic forkhead fold of the Fox family [17] (Fig. 2A).…”

Special Issue: Structure, Function and Evolution of Protein Domains

“…Villalobos et al [ 8 ] reviewed another transcription factor, namely human FoxP, and showed that it can serve as a tractable model for the evolution and function of three-dimensional (3D) domain swapping (DS), a common theme in the formation of multimeric protein complexes. Biophysical studies on FoxP have suggested that the dynamics of the polypeptide chain are crucial to decrease the energy barrier of 3D-DS, enabling fast oligomerization.…”