Fast Association and Slow Transitions in the Interaction between Two Intrinsically Disordered Protein Domains

Abstract

Background: Intrinsically disordered proteins are common regulators of protein-protein interactions, but little is known about their mechanisms of interaction. Results: Two intrinsically disordered protein domains, from ACTR and CREB-binding protein, interact through rapid association and slow conformational changes. Conclusion: Electrostatics governs the fast association, but the overall reaction is multistep. Significance: The slow conformational search may be common among intrinsically disordered proteins with many binding partners.

Distinguishing induced fit from conformational selection

“…(The same conclusion was reached in the original paper [38] on other grounds). Thus, this experiment highlights the potential problem of low amplitude of kinetic phases but also show that protein-protein interactions involving disordered protein domains are amenable to the test.…”

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

“…Our finding of an induced-fit mechanism for NCBD binding to ACTR is confirmed by recent experimental evidence from a protein engineering analysis of the binding transition states, which show that, apart from weak native-like interactions, the transition state is largely disordered, 33,34 with -values for binding in the range 0-0.2. We have also calculated -values for binding of NCBD to ACTR based on the simulations, using a simple contact based analysis, i.e., we define the value of residue i as (i) = (q ‡ (i) − q U (i))/(q F (i) − q U (i)), where q ‡ (i), q U (i) and q F (i) are the fraction of its native contacts formed by residue i in the binding transition state, unfolded state and folded state, respectively.…”

“…40 We have previously 38 used large scale atomistic simulations to investigate structure formation in the unbound state of NCBD, and others have used a multi-scale approach to study unbound NCBD. 41 Here, we study the binding mechanism of NCBD to its partners; this complements recent experimental studies, focussed on the association of NCBD to ACTR, [33][34][35] as we discuss below. Although ACTR also undergoes a disorder to order transition upon binding, we have chosen to restrict our attention here to the mechanism as seen from the point of view of NCBD.…”

“…The most powerful methods are single molecule FRET experiments, which can provide information on the overall dimensions 25 and dynamics 26 of unbound IDPs, and NMR experiments which give more localised and higher resolution structural data 27,28 and also mechanistic insights. 29 Kinetic experiments can yield information on binding mechanism, [30][31][32][33][34][35] in particular when used in conjunction with a protein engineering approach. In general, however, it is challenging to resolve mechanistic scenarios from experiment alone.…”

Role of Intrinsic Protein Disorder in the Function and Interactions of the Transcriptional Coactivators CREB-binding Protein (CBP) and p300

“…Thus, the binding mechanism of c-Myb is complex and involves elements of both conformational selection and induced fit. A similar mechanism has been observed for binding of the intrinsically disordered ACTR to the NCBD of CBP; the N-terminal helix of ACTR folds rapidly and binding involves conformational selection (74), whereas other regions of ACTR fold by a slower, induced-fit process following the initial binding event (75).…”