Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics

• Published in: Journal of chemical theory and computation 2021-05, Vol.17 (5), p.3203-3220
• Main Authors: Sieradzan, Adam K, Korneev, Anatolii, Begun, Alexander, Kachlishvili, Khatuna, Scheraga, Harold A, Molochkov, Alexander, Senet, Patrick, Niemi, Antti J, Maisuradze, Gia G
• Format: Article
• Language: English
• Subjects: Biomolecular Systems; Folding; Intrinsically Disordered Proteins - chemistry; Molecular dynamics; Molecular Dynamics Simulation; Phosphorylation; Protein Folding; Proteins; Residues; Schrodinger equation; Standing waves; Thermodynamics
• ISSN: 1549-9618; 1549-9626; 1549-9626
• DOI: 10.1021/acs.jctc.1c00155

Apart from being the most common mechanism of regulating protein function and transmitting signals throughout the cell, phosphorylation has an ability to induce disorder-to-order transition in an intrinsically disordered protein. In particular, it was shown that folding of the intrinsically disordered protein, eIF4E-binding protein isoform 2 (4E-BP2), can be induced by multisite phosphorylation. Here, the principles that govern the folding of phosphorylated 4E-BP2 (pT37pT46 4E-BP218–62) are investigated by analyzing canonical and replica exchange molecular dynamics trajectories, generated with the coarse-grained united-residue force field, in terms of local and global motions and the time dependence of formation of contacts between Cαs of selected pairs of residues. The key residues involved in the folding of the pT37pT46 4E-BP218–62 are elucidated by this analysis. The correlations between local and global motions are identified. Moreover, for a better understanding of the physics of the formation of the folded state, the experimental structure of the pT37pT46 4E-BP218–62 is analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. It is shown that without molecular dynamics simulations the kinks are able to identify not only the phosphorylated sites of protein, the key players in folding, but also the reasons for the weak stability of the pT37pT46 4E-BP218–62.