Emergence and evolution of an interaction between intrinsically disordered proteins

Abstract

Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. However, it is not clear how such interactions emerge and evolve on a molecular level. We performed phylogenetic reconstruction, resurrection and biophysical characterization of two interacting disordered protein domains, CID and NCBD. CID appeared after the divergence of protostomes and deuterostomes 450–600 million years ago, while NCBD was present in the protostome/deuterostome ancestor. The most ancient CID/NCBD formed a relatively weak complex (Kd∼5 µM). At the time of the first vertebrate-specific whole genome duplication, the affinity had increased (Kd∼200 nM) and was maintained in further speciation. Experiments together with molecular modeling using NMR chemical shifts suggest that new interactions involving intrinsically disordered proteins may evolve via a low-affinity complex which is optimized by modulating direct interactions as well as dynamics, while tolerating several potentially disruptive mutations.DOI: http://dx.doi.org/10.7554/eLife.16059.001

Evolution of an interaction between disordered proteins resulted in increased heterogeneity of the binding transition state

“…The f-values for Ca11R were ranging between 0.2-0.3 and were lower, close to 0. To facilitate a direct comparison with the extant human complex, we extended a previously published data set on helix 1 from human CID (Ca1Human) 27 with new Ala®Gly mutations in helix 2 (Ca2Human) and helix 3 (Ca3Human) ( Table 2) We note that according to Brønsted plots, Ca1Human has a slightly higher helical content in the transition state compared to Ca11R, consistent with a higher helical propensity for Ca1Human than for Ca11R, as suggested by predictions using AGADIR 20 . We further note that the A1075G mutation in Ca3Human did not display a large effect on KD, which precluded a reliable estimation of a f-value.…”

“…NCBD is an archetype example of such a disordered protein interaction domain that has evolved to bind several cellular targets, including transcription factors and transcriptional co-regulators 10,11,39 . Every time a new partner was included in the repertoire, NCBD somehow adapted its affinity for the new ligand, while maintaining affinity for already established one(s), as occurred around 450-500 Myr, when the interaction between NCBD and CID was established 20 . On a molecular level, it is intriguing how such multi partner protein domains evolve.…”

“…Previous phylogenetic analyses revealed that while NCBD was present already in the last common ancestor of all bilaterian animals (deuterostomes and protostomes) CID likely emerged later as an interaction domain within the ancestral ACTR/TIF2/SRC protein in the deuterostome lineage (including chordates, echinoderms and hemichordates; Figure 1) 20 . The evolution of the NCBD/CID interaction was previously examined using ancestral sequence reconstruction in combination with several biophysical methods to assess differences in affinity, structure and dynamics between the extant human and ancestral protein complex 20,21 .…”

“…After the emergence of CID in the ancestral ACTR/TIF2/SRC, NCBD increased its affinity for CID while maintaining the affinity for some of its other binding partners 20 . While the overall structure of the ancestral NCBD/CID complex, which we denote as "Cambrian-like", is similar to the modern high affinity human one, there are several differences on the molecular level ( Figure 1) 21 .…”

Divergent evolution of a protein-protein interaction revealed through ancestral sequence reconstruction and resurrection

“…Evolutionary biochemistry, i.e., phylogenetic reconstruction of ancestral sequences followed by expression and experimental characterization of the ancient proteins ( Fig. 2a-b) is a powerful tool for understanding protein function (Hochberg and Thornton 6 2017), including protein-protein interactions (Hultqvist et al 2017;Jemth et al 2018;Wheeler et al 2018). To better understand the evolution and hence function of the PDZ3:CRIPT interaction we reconstructed sequences of ancestral time-matched variants of PDZ3 and CRIPT and compared their binding affinity and stability to PDZ3 and CRIPT from seven extant species.…”