Ordered LIM domains tune association rates of disordered partners to regulate transcription factor complex formation

Robertson NO1, Smith NC1, Manakas A1, Mahjuob M1, McDonald G2, Kwan AH1 and Matthews JM1

  1. School of Life and Environmental Sciences, University of Sydney, Australia.
  2. Centre for Translational Data Science, University of Sydney, Australia.

Intrinsically disordered regions (IDRs) are overrepresented among transcription factors, where they often act as protein-protein interaction motifs. Despite the importance of IDR interactions there is little quantitative information about the role disorder plays in the thermodynamic and kinetic parameters of binding. We have used LIM domain transcription factors to understand the role disorder can play in complex formation. Transcription factors containing disordered LIM interacting domains (LIDs) interact with the ordered tandem LIM domains (LIM1+2) of LIM-only (LMO) and LIM-homeodomain (LIM-HD) proteins. The resulting complexes regulate gene expression and are important mediators of cell specification, proliferation and differentiation. We have used FRET-based assays to study the binding affinities and kinetics of different LID:LIM1+2 interactions. LDB1LID association rate constants can vary by up to 3-orders of magnitude depending on the interacting LIM1+2 domains. These disparate kinetics are not accounted for by differences in electrostatic attractions; rather they reflect differences in binding mechanisms of LDB1LID. LDB1LIDcan bind single LIM domains with high association rate constants, indicating that the differences in LIM1+2 association occur after the initial encounter. We have used our equilibrium and kinetic data to model LID:LIM1+2 transcription factor complex as it occurs in motor neuron development, showing that the disparate kinetics facilitate the exchange of high affinity binding partners over time. Together, our studies suggest that ordered domains can use the inherent flexibility of IDRs generate highly differential binding kinetics, which may provide a mechanism for temporally regulating transcriptional complex formation during development.