Functional regulation of an intrinsically disordered protein via a conformationally excited state

Abstract

A longstanding goal in the field of intrinsically disordered proteins (IDP) is to characterize their structural heterogeneity and pinpoint the role of this heterogeneity in IDP function. Here, we use multinuclear chemical exchange saturation (CEST) NMR to determine the structure of a thermally accessible globally folded excited state in equilibrium with the intrinsically disordered native ensemble of a bacterial transcriptional regulator CytR. We further provide evidence from double resonance CEST experiments that the excited state, which structurally resembles the DNA-bound form of CytR, recognizes DNA by means of a folding-before-binding conformational selection pathway. The disorder-to-order regulatory switch in DNA recognition by natively disordered CytR therefore operates through a dynamical variant of the lock-and-key mechanism where the structurally complementary conformation is transiently accessed via thermal fluctuations.

Machine Learning Subtle Conformational Change due to Phosphorylation in Intrinsically Disordered Proteins

“…78 These states have very distinct composition and location of secondary structure which might be crucial in its binding to Cdc4. 65 From a conformational selection perspective, 79 it is important to consider the fact that distinct conformations can either catalyze or inhibit binding process and thereby modify the binding affinities and subsequent cellular activities. Since phosphorylation of Sic1 is essential for binding to the WD40 domain of Cdc4, 26 we hypothesize that significant modifications in the minor states may underlie this phenomenon, given the substantial structural similarity between the major state of Sic1 and pSic1.…”

Increasing the accuracy of exchange parameters reporting on slow dynamics by performing CEST experiments with highB1fields

“…CEST experiments, originally devised to study slow exchange between visible states (21), are now routinely used to study protein and nucleic acid conformational exchange between a visible major state and invisible minor state(s) occurring over a wide range of time-scales (22)(23)(24). CEST methods have been developed to characterize the exchange at various backbone and side-chain sites (25)(26)(27)(28)(29)(30)(31) and have been used to study various processes, including protein folding (24,32), ligand binding (33,34) and several other processes involving protein and nucleic acid conformational fluctuations (35)(36)(37).…”