Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model

TR Sisk, P Robustelli - … of the National Academy of Sciences, 2024 - National Acad Sciences
A central challenge in the study of intrinsically disordered proteins is the characterization of
the mechanisms by which they bind their physiological interaction partners. Here, we utilize …

Thermodynamic contribution of backbone conformational entropy in the binding between SH3 domain and proline-rich motif

D Zeng, Q Shen, JH Cho - Biochemical and biophysical research …, 2017 - Elsevier
Biological functions of intrinsically disordered proteins (IDPs), and proteins containing
intrinsically disordered regions (IDRs) are often mediated by short linear motifs, like proline …

Ensemble-based thermodynamics of the fuzzy binding between intrinsically disordered proteins and small-molecule ligands

B Chong, Y Yang, C Zhou, Q Huang… - Journal of Chemical …, 2020 - ACS Publications
In contrast to the “lock-and-key” model underlying the long-term success of structural biology
and rational drug design, intrinsically disordered proteins (IDPs) exist in an ensemble of …

[PDF][PDF] Energetics of a protein disorder–order transition in small molecule recognition

AA Gupta, PN Barlow, J Michel - 2022 - wrap.warwick.ac.uk
Many proteins recognise other proteins via mechanisms that involve the folding of
intrinsically disordered regions upon complex formation. Here we investigate how the …

Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation

J Alston, A Soranno, AS Holehouse - bioRxiv, 2023 - biorxiv.org
Intrinsically disordered regions (IDRs) are critical for cellular function, yet often appear to
lack sequence conservation when assessed by multiple sequence alignments. This raises …

Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation

A Holehouse, J Alston, A Soranno - 2024 - researchsquare.com
Intrinsically disordered regions (IDRs) are critical for cellular function yet often appear to lack
sequence conservation when assessed by multiple sequence alignments. This raises the …

Mechanism of coupled folding-upon-binding of an intrinsically disordered protein

P Robustelli, S Piana, DE Shaw - Journal of the American …, 2020 - ACS Publications
Intrinsically disordered proteins (IDPs), which in isolation do not adopt a well-defined tertiary
structure but instead populate a structurally heterogeneous ensemble of interconverting …

[PDF][PDF] Tuning Free Energy by Backbone Conformational Entropy: A Strategy from Disordered Proteins

AC Chia-en - Biophysical Journal, 2018 - cell.com
Intrinsically disordered proteins (IDPs) or regions (IDRs) exhibit biological activities and play
important roles in cell signaling and regulation, yet they do not form a well-defined three …

Demultiplexing the heterogeneous conformational ensembles of intrinsically disordered proteins into structurally similar clusters

R Appadurai, JK Koneru, M Bonomi, P Robustelli… - bioRxiv, 2022 - biorxiv.org
Intrinsically disordered proteins (IDPs) populate a range of conformations that are best
described by a heterogeneous ensemble. Grouping an IDP ensemble into “structurally …

[HTML][HTML] Binding mechanisms of intrinsically disordered proteins: theory, simulation, and experiment

L Mollica, LM Bessa, X Hanoulle, MR Jensen… - Frontiers in molecular …, 2016 - frontiersin.org
In recent years, protein science has been revolutionized by the discovery of intrinsically
disordered proteins (IDPs). In contrast to the classical paradigm that a given protein …