Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

Abstract

Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as molecular recognition elements (MoREs). They fold into ordered structures upon binding to their partner molecules. Currently, there is still a lack of in-depth understanding of how coupled binding and folding occurs in MoREs. Here, we quantified the unbound ensembles of the α-MoRE within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein. We developed a multiscaled approach by combining a physics-based and an atomic hybrid model to decipher the mechanism by which the α-MoRE interacts with the X domain of the measles virus phosphoprotein. Our multiscaled approach led to remarkable qualitative and quantitative agreements between the theoretical predictions and experimental results (e.g., chemical shifts). We found that the free α-MoRE rapidly interconverts between multiple discrete partially helical conformations and the unfolded state, in accordance with the experimental observations. We quantified the underlying global folding-binding landscape. This leads to a synergistic mechanism in which the recognition event proceeds via (minor) conformational selection, followed by (major) induced folding. We also provided evidence that the α-MoRE is a compact molten globule-like IDP and behaves as a downhill folder in the induced folding process. We further provided a theoretical explanation for the inherent connections between "downhill folding," "molten globule," and "intrinsic disorder" in IDP-related systems. Particularly, we proposed that binding and unbinding of IDPs proceed in a stepwise way through a "kinetic divide-and-conquer" strategy that confers them high specificity without high affinity. multiscale simulation | hybrid structure-based model | free-energy surface | flexible binding | flexible recognition I ntrinsically disordered proteins (IDPs) are a newly recognized class of naturally abundant, functional proteins that are unable to fold into a well-defined secondary or tertiary structure under physiological conditions of pH and salinity in the absence of a partner (1-3). IDPs perform a wide spectrum of biological functions, often related to molecular recognition, signal transduction, and cell regulation (4). In contrast, canonical proteins with ordered structure mainly carry out their functions in catalysis and membrane transport (5). The functional repertoire of ordered proteins and that of IDPs are complementary to each other (2, 4). Earlier bioinformatics studies predicted that more than 50% of eukaryotic proteins have long disordered regions (1, 6), and the proportion further increases up to 70% in signaling proteins (7). Due to their ubiquitous occurrence in the living world and close relationship with human diseases, IDPs have in recent years become a hot topic in protein science (3,8). One of the most interesting characteristics of IDPs is that they often undergo disorder-to-order transitions upon binding to their partner(s), such as proteins or DNA (9-14), even though some IDP-p...

Molecular mechanism of multispecific recognition of Calmodulin through conformational changes

“…In the present work, we have found that skMLCK and CaM have similar properties in their mixturebinding pathways. In addition, we found the skMLCK binding peptide gradually forms α-helical structures binding to CaM, which is in accordance with a "divide-and-conquer" mechanism proposed for the IDP binding-folding (54). In a word, we find many interesting intrinsically disordered properties of skMLCK during its binding process with CaM in our work.…”

“…To extend a SBM to systems with two basins, we integrated information of the open (PDB ID: 1CLL) and closed (PDB ID: 2BBM) structures by a mixed-contact map model (10,13,32,60,61). Because the charged interactions and the hydrophobic interactions play an important role in in CaM recognition (13,15,25,(29)(30)(31)54), we added the electrostatic interactions and hydrophobic interactions in our SBM. The electrostatic potential is represented by the Debye-Huckel model (64).…”

“…By investigating the synchronization of binding and folding, the conventional association mechanism can be classified into cooperative "coupled binding−folding" as well as noncooperative "folding before binding" and "binding before folding" (52,53). A mechanism of conformational selection followed by induced folding has been also proposed for the binding-folding of IDP (54). Accordingly, What is the mechanism for this binding process simultaneously involving both the local conformational changes of receptor and the global conformational changes of peptide?…”

The binding mechanisms of intrinsically disordered proteins

“…Finally, computational studies on IDP-protein interactions, 52 including that between ACTR and NCBD, 67 30 and ACTR/NCBD (ca.…”

Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling

“…The development of atomic-resolution models requires, however, complementation of experimental data by computational simulations. Theoretical approaches have been improved to effectively model disordered conformational ensembles based on structural information derived from native mass spectrometry and other biophysical analyses [28][29][30].…”