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1. Exploring the Activation Process of the Glycine Receptor

   https://doi.org/10.1021/jacs.4c08489  

   Yan, Junfang; Chen, Luonan; Warshel, Arieh; Bai, Chen (September 2024, Journal of the American Chemical Society)

   Glycine receptors (GlyR) conduct inhibitory glycinergic neurotransmission in the spinal cord and the brainstem. They play an important role in muscle tone, motor coordination, respiration, and pain perception. However, the mechanism underlying GlyR activation remains unclear. There are five potential glycine binding sites in α1 GlyR, and different binding patterns may cause distinct activation or desensitization behaviors. In this study, we investigated the coupling of protein conformational changes and glycine binding events to elucidate the influence of binding patterns on the activation and desensitization processes of α1 GlyRs. Subsequently, we explored the energetic distinctions between the apical and lateral pathways during α1 GlyR conduction to identify the pivotal factors in the ion conduction pathway preference. Moreover, we predicted the mutational effects of the key residues and verified our predictions using electrophysiological experiments. For the mutants that can be activated by glycine, the predictions of the mutational directions were all correct. The strength of the mutational effects was assessed using Pearson’s correlation coefficient, yielding a value of −0.77 between the calculated highest energy barriers and experimental maximum current amplitudes. These findings contribute to our understanding of GlyR activation, identify the key residues of GlyRs, and provide guidance for mechanistic studies on other pLGICs. 

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2. Infrared multiple photon dissociation spectra of cesiated complexes of the aliphatic amino acids: Challenges for conformational-space calculations by density functional theory

   https://doi.org/10.1016/j.ijms.2024.117201  

   Armentrout, P.B.; Steele, Ryan P.; Stevenson, Brandon C.; Jones, Roland M.; Martens, Jonathan; Berden, Giel; Oomens, Jos (April 2024, International Journal of Mass Spectrometry)

   Cesiated complexes of the aliphatic amino acids (Gly, Ala, hAla, Val, Leu, and Ile) were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light from a free-electron laser (FEL). To identify structures, the experimental spectra were compared to linear spectra calculated at the B3LYP-GD3BJ/def2-TZVP level of theory. Relative energies at 0 and 298 K for various possible conformers of all complexes were calculated at B3LYP, B3LYP-GD3BJ, and MP2(full) levels using the def2-TZVP basis set. Spectral comparison for all complexes indicates that the dominant conformation has the cesium cation binding to the carbonyl and hydroxyl oxygens, [CO,OH]. This conclusion contrasts with previous work for Cs+(Gly), which suggested that the [CO] binding motif was prevalent. This dichotomy is explored theoretically in detail using coupled-cluster calculations with single, double, and perturbative triple excitations, CCSD(T), as well as advanced density functional theory (DFT) approaches. The comparisons show that the [CO,OH] – [CO] double-well potential found for most DFT approaches disappears at the higher level of theory with only the [CO,OH] well remaining. An exploration of this effect indicates that electron correlation is critically important and that DFT approaches incorrectly handle the internal hydrogen bonding in these molecules, thereby over-delocalizing the charges on the amino acid ligands. 

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3. Non-covalent complexes of the peptide fragment Gly-Asn-Asn-Gln-Gln-Asn-Tyr in the gas-phase. Photodissociative cross-linking, Born–Oppenheimer molecular dynamics, and ab initio computational binding study

   https://doi.org/10.1039/c8cp06893c  

   Huang, Shu R.; Liu, Yang; Tureček, František (January 2019, Physical Chemistry Chemical Physics)

   Non-covalent complexes of the short amyloid peptide motif Gly-Asn-Asn-Gln-Gln-Asn-Tyr (GNNQQNY) with peptide counterparts that were tagged with a diazirine ring at the N-termini (*GNNQQNY) were generated as singly charged ions in the gas phase. Specific laser photodissociation (UVPD) of the diazirine tag in the gas-phase complexes at 355 nm generated transient carbene intermediates that underwent covalent cross-linking with the target GNNQQNY peptide. The crosslinking yields ranged between 0.8 and 4.5%, depending on the combinations of peptide C-terminal amides and carboxylates. The covalent complexes were analyzed by collision-induced dissociation tandem mass spectrometry (CID-MS 3 ), providing distributions of cross-links at the target peptide amino acid residues. A general preference for cross-linking at the target peptide Gln-4-Gln-5-Asn-6-Tyr-7 segment was observed. Born–Oppenheimer molecular dynamics calculations were used to obtain 100 ps trajectories for nine lowest free-energy conformers identified by ωB97X-D/6-31+G(d,p) gradient geometry optimizations. The trajectories were analyzed for close contacts between the incipient carbene atom and the X–H bonds in the target peptide. The close-contact analysis pointed to the Gln-5 and Tyr-7 residues as the most likely sites of cross-linking, consistent with the experimental CID-MS 3 results. Non-covalent binding in the amide complexes was evaluated by DFT calculations of structures and energies. Although antiparallel arrangements of the GNNQQNY and *GNNQQNY peptides were favored in low-energy gas-phase and solvated complexes, the conformations and peptide–peptide interface surfaces were found to differ from the secondary structure of the dry interface in GNNQQNY motifs of amyloid aggregates. 

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4. In Situ Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States

   https://doi.org/10.1128/mBio.00973-19  

   Yang, Wen; Cassidy, C. Keith; Ames, Peter; Diebolder, Christoph A.; Schulten, Klaus; Luthey-Schulten, Zaida; Parkinson, John S.; Briegel, Ariane; Harwood, Caroline S. (August 2019, mBio)

   ABSTRACT Tsr, the serine chemoreceptor in Escherichia coli , transduces signals from a periplasmic ligand-binding site to its cytoplasmic tip, where it controls the activity of the CheA kinase. To function, Tsr forms trimers of homodimers (TODs), which associate in vivo with the CheA kinase and CheW coupling protein. Together, these proteins assemble into extended hexagonal arrays. Here, we use cryo-electron tomography and molecular dynamics simulation to study Tsr in the context of a near-native array, characterizing its signaling-related conformational changes at both the individual dimer and the trimer level. In particular, we show that individual Tsr dimers within a trimer exhibit asymmetric flexibilities that are a function of the signaling state, highlighting the effect of their different protein interactions at the receptor tips. We further reveal that the dimer compactness of the Tsr trimer changes between signaling states, transitioning at the glycine hinge from a compact conformation in the kinase-OFF state to an expanded conformation in the kinase-ON state. Hence, our results support a crucial role for the glycine hinge: to allow the receptor flexibility necessary to achieve different signaling states while also maintaining structural constraints imposed by the membrane and extended array architecture. IMPORTANCE In Escherichia coli , membrane-bound chemoreceptors, the histidine kinase CheA, and coupling protein CheW form highly ordered chemosensory arrays. In core signaling complexes, chemoreceptor trimers of dimers undergo conformational changes, induced by ligand binding and sensory adaptation, which regulate kinase activation. Here, we characterize by cryo-electron tomography the kinase-ON and kinase-OFF conformations of the E. coli serine receptor in its native array context. We found distinctive structural differences between the members of a receptor trimer, which contact different partners in the signaling unit, and structural differences between the ON and OFF signaling complexes. Our results provide new insights into the signaling mechanism of chemoreceptor arrays and suggest an important functional role for a previously postulated flexible region and glycine hinge in the receptor molecule. 

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5. Pincer-Ligated Iridium Complexes with Low-Field Ancillary Ligands: Complexes of ( ^iPr PCP)IrCl ₂ and Comparison with ( ^iPr PCP)IrHCl

   https://doi.org/10.1021/acs.organomet.4c00162  

   Parihar, Ashish; Emge, Thomas J; Chakravartula, Srinivas_V S; Goldman, Alan S (June 2024, Organometallics)

   Pincer-ligated iridium complexes have been widely developed, and (pincer)Ir(III) complexes, particularly five-coordinate, are central to their chemistry. Such complexes typically bear two formally anionic ligands in addition to the pincer ligand itself. Yet despite the prevalence of halides as anionic ligands in transition metal chemistry there are relatively few examples in which both of these ancillary anionic ligands are halides or even other monodentate low-field anions. We report a study of the fragment (iPrPCP)IrCl2 (iPrPCP = 3 2,6 C6H3(CH2PiPr2)), and adducts thereof. These species are found to be thermodynamically disfavored relative to the corresponding hydridohalides. For example, DFT calculations and experiment indicate that one Ir-Cl bond of (iPrPCP)IrCl2 complexes will undergo reaction with H2 to give (iPrPCP)IrHCl or an adduct thereof. In the presence of aqueous HCl, (iPrPCP)IrCl2 adds a chloride ion to give an unusual example of an anionic transition metal complex ((iPrPCP)IrCl3–) with a Zundel cation (H5O2+). (iPrPCP)IrCl2 is not stable as a monomer at room temperature but exists in solution as a mixture of clusters which can add various small molecules. DFT calculations indicate that dimerization and trimerization of (iPrPCP)IrCl2 is more favorable than the analogous reactions of (iPrPCP)IrHCl, in accord with cluster formation being observed only for the dichloride complex. 

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