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

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 121; no. 6; p. e2313360121
• Main Authors: Sisk, Thomas R, Robustelli, Paul
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 06.02.2024
• Subjects: Biological Sciences; Intrinsically Disordered Proteins - chemistry; Molecular Dynamics Simulation; Physical Sciences; Protein Binding; Protein Folding; deep learning; Markov state models; protein folding; molecular dynamics; intrinsically disordered proteins
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.2313360121

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 a deep learning-based Markov state modeling approach to characterize the folding-upon-binding pathways observed in a long timescale molecular dynamics simulation of a disordered region of the measles virus nucleoprotein N reversibly binding the X domain of the measles virus phosphoprotein complex. We find that folding-upon-binding predominantly occurs via two distinct encounter complexes that are differentiated by the binding orientation, helical content, and conformational heterogeneity of N . We observe that folding-upon-binding predominantly proceeds through a multi-step induced fit mechanism with several intermediates and do not find evidence for the existence of canonical conformational selection pathways. We observe four kinetically separated native-like bound states that interconvert on timescales of eighty to five hundred nanoseconds. These bound states share a core set of native intermolecular contacts and stable N helices and are differentiated by a sequential formation of native and non-native contacts and additional helical turns. Our analyses provide an atomic resolution structural description of intermediate states in a folding-upon-binding pathway and elucidate the nature of the kinetic barriers between metastable states in a dynamic and heterogenous, or "fuzzy", protein complex.