The mechanism of coupled folding-upon-binding of an intrinsically disordered protein

Abstract

<jats:title>Abstract</jats:title><jats:p>Intrinsically disordered proteins (IDPs), which in isolation do not adopt a well-defined tertiary structure but instead populate a structurally heterogeneous ensemble of interconverting states, play important roles in many biological pathways. IDPs often fold into ordered states upon binding to their physiological interaction partners (a so-called “folding-upon-binding” process), but it has proven difficult to obtain an atomic-level description of the structural mechanisms by which they do so. Here, we describe in atomic detail the folding-upon-binding mechanism of an IDP segment to its binding partner, as observed in unbiased molecular dynamics simulations. In our simulations, we observed over 70 binding and unbinding events between the α-helical molecular recognition element (α-MoRE) of the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N<jats:sub>TAIL</jats:sub>) and the X domain (XD) of the measles virus phosphoprotein complex. We found that folding-upon-binding primarily occurred through induced-folding pathways (in which intermolecular contacts form before or concurrently with the secondary structure of the disordered protein)—an observation supported by previous experiments—and that the transition state ensemble was characterized by the formation of just a few key intermolecular contacts, and was otherwise highly structurally heterogeneous. We found that when a large amount of helical content was present early in a transition path, N<jats:sub>TAIL</jats:sub> typically unfolded, then refolded after additional intermolecular contacts formed. We also found that, among conformations with similar numbers of intermolecular contacts, those with less helical content had a higher probability of ultimately forming the native complex than conformations with more helical content, which were more likely to unbind. These observations suggest that even after intermolecular contacts have formed, disordered regions can have a kinetic advantage over folded regions in the folding-upon-binding process.</jats:p>

Location and Concentration of Aromatic‐Rich Segments Dictates the Percolating Inter‐Molecular Network and Viscoelastic Properties of Ageing Condensates

“…Simulations are performed in explicit water and ions at room temperature and physiological salt concentration using the a99SB-disp force field. [46] By computing the PMF as a function of the center-of-mass (COM) distance between one reference peptide, which we dissociate from the other peptides (see further details of these calculations in Supporting Information), we determine the binding free energy difference between the structured (kinked 𝛽-sheet motif; PDB code 5WHN) and the fully disordered state of a TDP-43 LARKS aggregate (Figure 1a).…”

“…The chosen LARKS distribution across the low-complexity domains is in all cases symmetric and equispaced (as shown in Figure 1c for the "1-Center," "2-Equispaced," and "3-Equispaced" sequences) and the total length using the a99SB-disp force field. [46] Simulations are carried out at room conditions and physiological NaCl concentration. While the solid green curve denotes the interaction strength among peptides with a kinked 𝛽-sheet structure, the dashed red curve accounts for the interaction energy among the same segments when they are fully disordered.…”

“…[41][42][43][44][45] In this work, we use multiscale simulations to investigate the impact of LARKS abundance and patterning in the progressive maturation of biomolecular condensates. Our multiscale approach bridges atomistic force fields [46,47] and coarse-grained models of proteins and nucleic acids. [48,49] Based on structured versus disordered peptide binding interactions predicted from free-energy atomistic calculations, we develop a coarse-grained model for LARKS-containing low-complexity domains that considers the accumulation of local structural transitions over time inside coarse-grained protein condensates.…”

“…Disorder-to-𝛽-sheet structural transitions augments protein binding, and their progressive accumulation within biomolecular condensates increases density. a) Atomistic potential of mean force (PMF) dissociation curves of a 6-amino acid segment (PDB code: 5WHN) of the TDP-43 lowcomplexity domain sequence from a 𝛽-sheet structure formed by six peptides (of the same sequence) as a function of the center-of-mass distance (COM)using the a99SB-disp force field [46]. Simulations are carried out at room conditions and physiological NaCl concentration.…”