title: Binding of Disordered Peptides to Kelch: Insights from Enhanced Sampling Simulations.
abstract: Keap1 protein plays an essential role in regulating cellular oxidative stress response and is a crucial binding hub for multiple proteins, several of which are intrinsically disordered proteins (IDP). Among Kelch's IDP binding partners, NRF2 and PTMA are the two most interesting cases. They share a highly similar binding motif; however, NRF2 binds to Kelch with a binding affinity of approximately 100-fold higher than that of PTMA. In this study, we perform an exhaustive sampling composed of 6 μs well-tempered metadynamics and 2 μs unbiased molecular dynamics (MD) simulations aiming at characterizing the binding mechanisms and structural properties of these two peptides. Our results agree with previous experimental observations that PTMA is remarkably more disordered than NRF2 in both the free and bound states. This explains PTMA's lower binding affinity. Our extensive sampling also provides valuable insights into the vast conformational ensembles of both NRF2 and PTMA, supports the hypothesis of coupled folding-binding, and confirms the essential role of linear motifs in IDP binding.
authors.affiliation: Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, ON, Canada N2L 3G1.
authors.forename: Trang Nhu
authors.initials: TN
authors.lastname: Do
authors.affiliation: Department of Biochemistry, University of Western Ontario , 1151 Richmond Street, London, ON, Canada N6A 3K7.
authors.forename: Wing-Yiu
authors.initials: WY
authors.lastname: Choy
authors.affiliation: Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, MetaForum, 5600 MB, Eindhoven, The Netherlands.
authors.forename: Mikko
authors.initials: M
authors.lastname: Karttunen
mesh_terms: D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000737:chemistry / Q000378:metabolism*; D000072019:Kelch-Like ECH-Associated Protein 1; D056004:Molecular Dynamics Simulation; D051267:NF-E2-Related Factor 2 / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D011498:Protein Precursors / Q000737:chemistry; D017434:Protein Structure, Tertiary; D013947:Thymosin / Q000031:analogs & derivatives / Q000737:chemistry
chemical_list: D047908:Intracellular Signaling Peptides and Proteins; C431364:KEAP1 protein, human; D000072019:Kelch-Like ECH-Associated Protein 1; D051267:NF-E2-Related Factor 2; C495635:NFE2L2 protein, human; D011498:Protein Precursors; C040782:prothymosin alpha; D013947:Thymosin