title: Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs.
abstract: Proteins perform their function or interact with partners by exchanging between conformational substates on a wide range of spatiotemporal scales. Structurally characterizing these exchanges is challenging, both experimentally and computationally. Large, diffusional motions are often on timescales that are difficult to access with molecular dynamics simulations, especially for large proteins and their complexes. The low frequency modes of normal mode analysis (NMA) report on molecular fluctuations associated with biological activity. However, NMA is limited to a second order expansion about a minimum of the potential energy function, which limits opportunities to observe diffusional motions. By contrast, kino-geometric conformational sampling (KGS) permits large perturbations while maintaining the exact geometry of explicit conformational constraints, such as hydrogen bonds. Here, we extend KGS and show that a conformational ensemble of the α subunit Gαs of heterotrimeric stimulatory protein Gs exhibits structural features implicated in its activation pathway. Activation of protein Gs by G protein-coupled receptors (GPCRs) is associated with GDP release and large conformational changes of its α-helical domain. Our method reveals a coupled α-helical domain opening motion while, simultaneously, Gαs helix α5 samples an activated conformation. These motions are moderated in the activated state. The motion centers on a dynamic hub near the nucleotide-binding site of Gαs, and radiates to helix α4. We find that comparative NMA-based ensembles underestimate the amplitudes of the motion. Additionally, the ensembles fall short in predicting the accepted direction of the full activation pathway. Taken together, our findings suggest that nullspace sampling with explicit, holonomic constraints yields ensembles that illuminate molecular mechanisms involved in GDP release and protein Gs activation, and further establish conformational coupling between key structural elements of Gαs.
authors.affiliation: Department of Chemistry, Stanford University, Stanford, California, United States of America.
authors.forename: Dimitar V
authors.initials: DV
authors.lastname: Pachov
authors.affiliation: Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, Stanford University, Stanford, California, United States of America.
authors.forename: Henry
authors.initials: H
authors.lastname: van den Bedem
mesh_terms: D001665:Binding Sites; D002864:Chromogranins; D004058:Diffusion; D019205:GTP-Binding Protein alpha Subunits, Gs / Q000737:chemistry* / Q000648:ultrastructure*; D006153:Guanosine Diphosphate / Q000737:chemistry*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D021122:Protein Subunits; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: D002864:Chromogranins; D021122:Protein Subunits; D043562:Receptors, G-Protein-Coupled; D006153:Guanosine Diphosphate; C498642:Gnas protein, mouse; D019205:GTP-Binding Protein alpha Subunits, Gs