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At least 1,315 records · Page 73

A molecular mechanism for the generation of ligand-dependent differential outputs by the epidermal growth factor receptor

The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that couples the binding of extracellular ligands, such as EGF and transforming growth factor-α (TGF-α), to the initiation of intracellular signaling pathways. EGFR binds to EGF and TGF-α with similar affinity, but generates different signals from these ligands. To address the mechanistic basis of this phenomenon, we have carried out cryo-EM analyses of human EGFR bound to EGF and TGF-α. We show that the extracellular module adopts an ensemble of dimeric conformations when bound to either EGF or TGF-α. The two extreme states of this ensemble represent distinct ligand-bound quaternary structures in which the membrane-proximal tips of the extracellular module are either juxtaposed or separated. EGF and TGF-α differ in their ability to maintain the conformation with the membrane-proximal tips of the extracellular module separated, and this conformation is stabilized preferentially by an oncogenic EGFR mutation. Close proximity of the transmembrane helices at the junction with the extracellular module has been associated previously with increased EGFR activity. Our results show how EGFR can couple the binding of different ligands to differential modulation of this proximity, thereby suggesting a molecular mechanism for the generation of ligand-sensitive differential outputs in this receptor family.

59 BASIC BIOLOGICAL SCIENCES↗

An auto-inhibited state of protein kinase G and implications for selective activation

Cyclic GMP-dependent protein kinases (PKGs) are key mediators of the nitric oxide/cyclic guanosine monophosphate (cGMP) signaling pathway that regulates biological functions as diverse as smooth muscle contraction, cardiac function, and axon guidance. Understanding how cGMP differentially triggers mammalian PKG isoforms could lead to new therapeutics that inhibit or activate PKGs, complementing drugs that target nitric oxide synthases and cyclic nucleotide phosphodiesterases in this signaling axis. Alternate splicing of PRKG1 transcripts confers distinct leucine zippers, linkers, and auto-inhibitory (AI) pseudo-substrate sequences to PKG Iα and Iβ that result in isoform-specific activation properties, but the mechanism of enzyme auto-inhibition and its alleviation by cGMP is not well understood. Here, we present a crystal structure of PKG Iβ in which the AI sequence and the cyclic nucleotide-binding (CNB) domains are bound to the catalytic domain, providing a snapshot of the auto-inhibited state. Specific contacts between the PKG Iβ AI sequence and the enzyme active site help explain isoform-specific activation constants and the effects of phosphorylation in the linker. We also present a crystal structure of a PKG I CNB domain with an activating mutation linked to Thoracic Aortic Aneurysms and Dissections. Similarity of this structure to wildtype cGMP-bound domains and differences with the auto-inhibited enzyme provide a mechanistic basis for constitutive activation. We show that PKG Iβ auto-inhibition is mediated by contacts within each monomer of the native full-length dimeric protein, and using the available structural and biochemical data we develop a model for the regulation and cooperative activation of PKGs.

59 BASIC BIOLOGICAL SCIENCES↗

Staphylococcus aureus FtsZ and PBP4 bind to the conformationally dynamic N-terminal domain of GpsB

In the Firmicutes phylum, GpsB is a membrane associated protein that coordinates peptidoglycan synthesis with cell growth and division. Although GpsB has been studied in several bacteria, the structure, function, and interactome of Staphylococcus aureus GpsB is largely uncharacterized. To address this knowledge gap, we solved the crystal structure of the N-terminal domain of S. aureus GpsB, which adopts an atypical, asymmetric dimer, and demonstrates major conformational flexibility that can be mapped to a hinge region formed by a three-residue insertion exclusive to Staphylococci. When this three-residue insertion is excised, its thermal stability increases, and the mutant no longer produces a previously reported lethal phenotype when overexpressed in Bacillus subtilis. In S. aureus, we show that these hinge mutants are less functional and speculate that the conformational flexibility imparted by the hinge region may serve as a dynamic switch to fine-tune the function of the GpsB complex and/or to promote interaction with its various partners. Furthermore, we provide the first biochemical, biophysical, and crystallographic evidence that the N-terminal domain of GpsB binds not only PBP4, but also FtsZ, through a conserved recognition motif located on their C-termini, thus coupling peptidoglycan synthesis to cell division. Taken together, the unique structure of S. aureus GpsB and its direct interaction with FtsZ/PBP4 provide deeper insight into the central role of GpsB in S. aureus cell division.

59 BASIC BIOLOGICAL SCIENCES↗

Energy coupling and stoichiometry of Zn 2+ /H + antiport by the prokaryotic cation diffusion facilitator YiiP

YiiP from Shewanella oneidensis is a prokaryotic Zn 2+ /H + antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for homeostasis of transition metal ions. Previous studies of YiiP as well as related CDF transporters have established a homodimeric architecture and the presence of three distinct Zn 2+ binding sites named A, B, and C. In this study, we use cryo-EM, microscale thermophoresis and molecular dynamics simulations to address the structural and functional roles of individual sites as well as the interplay between Zn 2+ binding and protonation. Structural studies indicate that site C in the cytoplasmic domain is primarily responsible for stabilizing the dimer and that site B at the cytoplasmic membrane surface controls the structural transition from an inward facing conformation to an occluded conformation. Binding data show that intramembrane site A, which is directly responsible for transport, has a dramatic pH dependence consistent with coupling to the proton motive force. A comprehensive thermodynamic model encompassing Zn 2+ binding and protonation states of individual residues indicates a transport stoichiometry of 1 Zn 2+ to 2–3 H + depending on the external pH. This stoichiometry would be favorable in a physiological context, allowing the cell to use the proton gradient as well as the membrane potential to drive the export of Zn 2+ .

59 BASIC BIOLOGICAL SCIENCES↗

Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter

Tripartite ATP-independent periplasmic (TRAP) transporters are secondary-active transporters that receive their substrates via a soluble-binding protein to move bioorganic acids across bacterial or archaeal cell membranes. Recent cryo-electron microscopy (cryo-EM) structures of TRAP transporters provide a broad framework to understand how they work, but the mechanistic details of transport are not yet defined. Here we report the cryo-EM structure of the Haemophilus influenzae N-acetylneuraminate TRAP transporter (HiSiaQM) at 2.99 Å resolution (extending to 2.2 Å at the core), revealing new features. The improved resolution (the previous HiSiaQM structure is 4.7 Å resolution) permits accurate assignment of two Na + sites and the architecture of the substrate-binding site, consistent with mutagenic and functional data. Moreover, rather than a monomer, the HiSiaQM structure is a homodimer. We observe lipids at the dimer interface, as well as a lipid trapped within the fusion that links the SiaQ and SiaM subunits. We show that the affinity (K D ) for the complex between the soluble HiSiaP protein and HiSiaQM is in the micromolar range and that a related SiaP can bind HiSiaQM. This work provides key data that enhances our understanding of the ‘elevator-with-an-operator’ mechanism of TRAP transporters.

59 BASIC BIOLOGICAL SCIENCES↗

Novel Charge-Ordered States in 1 T -IrTe 2

1T-IrTe 2 exhibits an intriguing series of charge-ordered states in both bulk and atomically thin layers. The charge orders in IrTe 2 emerge with consecutive first-order structural transitions involving in-plane Ir–Ir dimerization and interlayer Te–Te depolymerization, resulting in stripe patterns with various periods. Upon chemical doping, 1T-IrTe 2 can also be driven into a superconductor. Despite the intense research effort, a comprehensive understanding of the nature of the charge ordering and its relation to the superconductivity is yet to be reached. This review provides an overview of the novel charge orders and the emergence of superconductivity in IrTe 2 . Finally, we further introduce the recent studies on IrTe 2 nanoflake, in which novel charge orders attainable only in two-dimensional limits lay the grounds for an exotic phase diagram.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Tnseq to identify catabolism of b-5 linked aromatics by Novosphingobium aromaticivorans

This study investigates the catabolism of the b-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans. We used genome wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidates elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans.

Noguera, Daniel R.↗

Tnseq to identify catabolism of b-5 linked aromatics by Novosphingobium aromaticivorans

This study investigates the catabolism of the b-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans. We used genome wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidates elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans.

aromatic compounds↗

Polyimidazopyrrolone model compounds.

Study of model reactions between phthalic anhydride and o-phenylenediamine under conditions analogous to the polymerization and post cyclization of dianhydrides with bis(o-diamines) to form polyimidazopyrrolones (Pyrrones). Solid-state thermal conversion of the amide-acid-amine affords a unique dimeric species containing amide, imide, and benzimidazole functions. It was confirmed that melt techniques lead to disproportionation products. The application of these findings to related polymer syntheses is discussed.

Young, P. R.↗

Polyimidazopyrrolone model compounds.

The model reactions between phthalic anhydride and o-phenylenediamine were studied under conditions analogous to the polymerization and post-cyclization of dianhydrides with bis(o-diamines) to form polyimidazopyrrolones (Pyrrones). The route from the initial amide-acid-amine to the tetracyclic Pyrrone model when the reactions are conducted in aprotic solvents is highly competitive between isolatable benzimidazole-acid and imide-amine intermediates. Solid-state thermal conversion of the amide-acid-amine affords a unique dimeric species containing amide, imide, and benzimidazole functions. It was confirmed that melt techniques lead to disproportionation products. The application of these findings to related polymer synthesis is discussed.

Young, P. R.↗

Condensation in CO2 free jet expansions. II - Growth of small clusters.

An investigation into the kinetics of molecular clustering processes which occur in the highly supersaturated vapor of a CO2 free jet is described. Terminal cluster concentrations in expansions from room temperature and reservoir pressures in the range from 400 to 900 torr were determined for trimeric CO2 for nozzle diameters of .0076 cm, .015 cm, and .023 cm and in the case of CO2 tetramer and pentamer for .015 cm nozzle diameter. The measurements were made mass spectrometrically in a supersonic molecular beam apparatus. A kinetic analysis was developed from an extension of the critical nucleus concept of nucleation theory and rate equations based on intermolecular collisions. The observed cluster populations could be accounted for by the theory by adopting sticking probabilities of approximately .03 for monomer impinging on dimer, trimer, and tetramer.

Dorfeld, W. G.↗

Photochromism of heterocyclic systems

The preparations of photochromic dimers of a 2-aryl-4,5-di-phenylimidazyl radical and of a 2,5-diphenyl-3,4-isobenzopyrrole with different substituents in the homocyclic ring are reported. Of the dienes investigated, only 1-4-diphenyl-1,3-butadiene and 2,3-dimethyl-1,3-butadiene gave isolable amounts of the Diels-Adler adducts.

Silversmith, E. F.↗