title: Semiclosed Conformations of the Ligand-Binding Domains of NMDA Receptors during Stationary Gating.
abstract: NMDA receptors are tetrameric ligand-gated ion channels. In the continuous presence of saturating agonists, NMDA receptors undergo stationary gating, in which the channel stochastically switches between an open state that permits ion conductance and a closed state that prevents permeation. The ligand-binding domains (LBDs) of the four subunits are expected to have closed clefts in the channel-open state. On the other hand, there is little knowledge about the conformational status of the LBDs in the channel-closed state during stationary gating. To probe the latter conformational status, Kussius and Popescu engineered interlobe disulfide cross-links in NMDA receptors and found that the cross-linking produced stationary gating kinetics that differed only subtly from that produced by agonist binding. These authors assumed that the cross-linking immobilized the LBDs in cleft-closed conformations, and consequently concluded that throughout stationary gating, agonist-bound LBDs also stayed predominantly in cleft-closed conformations and made only infrequent excursions to cleft-open conformations. Here, by calculating the conformational free energies of cross-linked and agonist-bound LBDs, we assess whether cross-linking actually traps the LBDs in cleft-closed conformations and delineate semiclosed conformations of agonist-bound LBDs that may potentially be thermodynamically and kinetically important during stationary gating. Our free-energy results show that the cross-linked LBDs are not locked in the fully closed form; rather, they sample semiclosed conformations almost as readily as the agonist-bound LBDs. Several lines of reasoning suggest that LBDs are semiclosed in the channel-closed state during stationary gating. Our free-energy simulations suggest possible structural details of such semiclosed LBD conformations, including intra- and intermolecular interactions that serve as alternatives to those in the cleft-closed conformations.
authors.affiliation: Department of Physics, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida.
authors.forename: Jian
authors.initials: J
authors.lastname: Dai
authors.affiliation: Department of Physics, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida. Electronic address: hzhou4@fsu.edu.
authors.forename: Huan-Xiang
authors.initials: HX
authors.lastname: Zhou
mesh_terms: D000818:Animals; D003198:Computer Simulation; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D016194:Receptors, N-Methyl-D-Aspartate / Q000819:agonists / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D016194:Receptors, N-Methyl-D-Aspartate