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5 Publications

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    09/28/05 | Mechanism of positive allosteric modulators acting on AMPA receptors.
    Jin R, Clark S, Weeks AM, Dudman JT, Gouaux E, Partin KM
    The Journal of Neuroscience: The Official Journal of the Society for Neuroscience. 2005 Sep 28;25(39):9027-36. doi: 10.3389/fnana.2010.00147

    Ligand-gated ion channels involved in the modulation of synaptic strength are the AMPA, kainate, and NMDA glutamate receptors. Small molecules that potentiate AMPA receptor currents relieve cognitive deficits caused by neurodegenerative diseases such as Alzheimer’s disease and show promise in the treatment of depression. Previously, there has been limited understanding of the molecular mechanism of action for AMPA receptor potentiators. Here we present cocrystal structures of the glutamate receptor GluR2 S1S2 ligand-binding domain in complex with aniracetam [1-(4-methoxybenzoyl)-2-pyrrolidinone] or CX614 (pyrrolidino-1,3-oxazino benzo-1,4-dioxan-10-one), two AMPA receptor potentiators that preferentially slow AMPA receptor deactivation. Both potentiators bind within the dimer interface of the nondesensitized receptor at a common site located on the twofold axis of molecular symmetry. Importantly, the potentiator binding site is adjacent to the "hinge" in the ligand-binding core "clamshell" that undergoes conformational rearrangement after glutamate binding. Using rapid solution exchange, patch-clamp electrophysiology experiments, we show that point mutations of residues that interact with potentiators in the cocrystal disrupt potentiator function. We suggest that the potentiators slow deactivation by stabilizing the clamshell in its closed-cleft, glutamate-bound conformation.

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    09/21/05 | A dynamic coupling model for sum frequency chiral response from liquids composed of molecules with a chiral side chain and an achiral chromophore.
    Ji N, Shen Y
    Journal of the American Chemical Society. 2005 Sep 21;127(37):12933-42. doi: 10.1021/ja052715d

    A theoretical formulation for optically active sum frequency generation (OA-SFG) from isotropic chiral solutions was proposed for molecules with a chiral side chain and an intrinsically achiral chromophore. Adapting an electron correlation model first proposed by Höhn and Weigang for linear optical activity, we presented a dynamic coupling model for OA-SFG near the electronic resonance of the achiral chromophore. As a demonstration, we used this model to explain the observed OA-SFG spectra of a series of amino acids near the electronic resonance of the intrinsically achiral carboxyl group. Our model shows that the nonlinear chiroptical response comes about by the through-space correlative electronic interactions between the chiral side chain and the achiral chromophore, and its magnitude is determined by the position and orientation of the bonds that make up the chiral side chain. Using the bond polarizability values in the literature and the conformations of amino acids obtained from calculation, we were able to reproduce the relative OA-SFG strength from a series of amino acids.

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    Cardona Lab
    09/01/05 | An in situ hybridization protocol for planarian embryos: monitoring myosin heavy chain gene expression.
    Cardona A, Fernández J, Solana J, Romero R
    Development Genes & Evolution. 2005 Sep;215(9):482-88. doi: 10.1007/s00427-005-0003-1

    The monitoring of gene expression is fundamental for understanding developmental biology. Here we report a successful experimental protocol for in situ hybridization in both whole-mount and sectioned planarian embryos. Conventional in situ hybridization techniques in developmental biology are used on whole-mount preparations. However, given that the inherent lack of external morphological markers in planarian embryos hinders the proper interpretation of gene expression data in whole-mount preparations, here we used sectioned material. We discuss the advantages of sectioned versus whole-mount preparations, namely, better probe penetration, improved tissue preservation, and the possibility to interpret gene expression in relation to internal morphological markers such as the epidermis, the embryonic and definitive pharynges, and the gastrodermis. Optimal fixatives and embedding methods for sectioning are also discussed.

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    09/01/05 | Molecular genetic analysis of the yeast repressor Rfx1/Crt1 reveals a novel two-step regulatory mechanism.
    Zhang Z, Reese JC
    Molecular and Cellular Biology. 2005 Sep;25(17):7399-411. doi: 10.1128/MCB.25.17.7399-7411.2005

    In Saccharomyces cerevisiae, the repressor Crt1 and the global corepressor Ssn6-Tup1 repress the DNA damage-inducible ribonucleotide reductase (RNR) genes. Initiation of DNA damage signals causes the release of Crt1 and Ssn6-Tup1 from the promoter, coactivator recruitment, and derepression of transcription, indicating that Crt1 plays a crucial role in the switch between gene repression and activation. Here we have mapped the functional domains of Crt1 and identified two independent repression domains and a region required for gene activation. The N terminus of Crt1 is the major repression domain, it directly binds to the Ssn6-Tup1 complex, and its repression activities are dependent upon Ssn6-Tup1 and histone deacetylases (HDACs). In addition, we identified a C-terminal repression domain, which is independent of Ssn6-Tup1 and HDACs and functions at native genes in vivo. Furthermore, we show that TFIID and SWI/SNF bind to a region within the N terminus of Crt1, overlapping with but distinct from the Ssn6-Tup1 binding and repression domain, suggesting that Crt1 may have activator functions. Crt1 mutants were constructed to dissect its activator and repressor functions. All of the mutants were competent for repression of the DNA damage-inducible genes, but a majority were "derepression-defective" mutants. Further characterization of these mutants indicated that they are capable of receiving DNA damage signals and releasing the Ssn6-Tup1 complex from the promoter but are selectively impaired for TFIID and SWI/SNF recruitment. These results imply a two-step activation model of the DNA damage-inducible genes and that Crt1 functions as a signal-dependent dual-transcription activator and repressor that acts in a transient manner.

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    09/01/05 | The temporal requirements for insulin signaling during development in Drosophila.
    Shingleton AW, Das J, Vinicius L, Stern DL
    PLoS Biol. 2005 Sep;3(9):e289. doi: 10.1371/journal.pbio.0030289

    Recent studies have indicated that the insulin-signaling pathway controls body and organ size in Drosophila, and most metazoans, by signaling nutritional conditions to the growing organs. The temporal requirements for insulin signaling during development are, however, unknown. Using a temperature-sensitive insulin receptor (Inr) mutation in Drosophila, we show that the developmental requirements for Inr activity are organ specific and vary in time. Early in development, before larvae reach the "critical size" (the size at which they commit to metamorphosis and can complete development without further feeding), Inr activity influences total development time but not final body and organ size. After critical size, Inr activity no longer affects total development time but does influence final body and organ size. Final body size is affected by Inr activity from critical size until pupariation, whereas final organ size is sensitive to Inr activity from critical size until early pupal development. In addition, different organs show different sensitivities to changes in Inr activity for different periods of development, implicating the insulin pathway in the control of organ allometry. The reduction in Inr activity is accompanied by a two-fold increase in free-sugar levels, similar to the effect of reduced insulin signaling in mammals. Finally, we find that varying the magnitude of Inr activity has different effects on cell size and cell number in the fly wing, providing a potential linkage between the mode of action of insulin signaling and the distinct downstream controls of cell size and number. We present a model that incorporates the effects of the insulin-signaling pathway into the Drosophila life cycle. We hypothesize that the insulin-signaling pathway controls such diverse effects as total developmental time, total body size and organ size through its effects on the rate of cell growth, and proliferation in different organs.

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