title: Modeling conformational ensembles of slow functional motions in Pin1-WW.
abstract: Protein-protein interactions are often mediated by flexible loops that experience conformational dynamics on the microsecond to millisecond time scales. NMR relaxation studies can map these dynamics. However, defining the network of inter-converting conformers that underlie the relaxation data remains generally challenging. Here, we combine NMR relaxation experiments with simulation to visualize networks of inter-converting conformers. We demonstrate our approach with the apo Pin1-WW domain, for which NMR has revealed conformational dynamics of a flexible loop in the millisecond range. We sample and cluster the free energy landscape using Markov State Models (MSM) with major and minor exchange states with high correlation with the NMR relaxation data and low NOE violations. These MSM are hierarchical ensembles of slowly interconverting, metastable macrostates and rapidly interconverting microstates. We found a low population state that consists primarily of holo-like conformations and is a "hub" visited by most pathways between macrostates. These results suggest that conformational equilibria between holo-like and alternative conformers pre-exist in the intrinsic dynamics of apo Pin1-WW. Analysis using MutInf, a mutual information method for quantifying correlated motions, reveals that WW dynamics not only play a role in substrate recognition, but also may help couple the substrate binding site on the WW domain to the one on the catalytic domain. Our work represents an important step towards building networks of inter-converting conformational states and is generally applicable.
authors.affiliation: Interdisciplinary Center for Network Science and Applications, Notre Dame, Indiana, United States of America.
authors.forename: Faruck
authors.initials: F
authors.lastname: Morcos
authors.forename: Santanu
authors.initials: S
authors.lastname: Chatterjee
authors.forename: Christopher L
authors.initials: CL
authors.lastname: McClendon
authors.forename: Paul R
authors.initials: PR
authors.lastname: Brenner
authors.forename: Roberto
authors.initials: R
authors.lastname: López-Rendón
authors.forename: John
authors.initials: J
authors.lastname: Zintsmaster
authors.forename: Maria
authors.initials: M
authors.lastname: Ercsey-Ravasz
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Sweet
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Jacobson
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: Peng
authors.forename: Jesús A
authors.initials: JA
authors.lastname: Izaguirre
mesh_terms: D001051:Apoenzymes; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D006860:Hydrogen Bonding; D008390:Markov Chains; D056004:Molecular Dynamics Simulation; D000072340:NIMA-Interacting Peptidylprolyl Isomerase; D019906:Nuclear Magnetic Resonance, Biomolecular; D019696:Peptidylprolyl Isomerase / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D017434:Protein Structure, Tertiary
chemical_list: D001051:Apoenzymes; D000072340:NIMA-Interacting Peptidylprolyl Isomerase; C000606846:PIN1 protein, human; D019696:Peptidylprolyl Isomerase