Volume 2

  • No. 12 December 2006

    The development of new therapeutic agents has required the close collaboration of chemists and biologists in identifying drug targets or lead compounds and developing them toward the clinic. This month we include a series of articles that focus on how chemical biologists in academic and industrial settings enhance our understanding of biological systems and advance the next generation of therapeutic agents. Cover art by Erin Boyle.

  • No. 11 November 2006

    The budding yeast Saccharomyces cerevisiae has historically been important in elucidating the various membrane trafficking events in eukaryotic cells. One of the defining moments in this field was the identification of conditional mutants in the secretory pathway, called sec mutants. This image of a sec1 mutant shows the typical accumulation of membranous vesicles in these strains. In this particular case, the accumulation of vesicles is due to a defect in docking and fusion of exocytic vesicles to the membrane. In an Elements piece in this issue (p 568), Randy Schekman shares his views of the membrane field 26 years later. Cover art by Erin Boyle based on imagery provided by Susan Hamamoto, Bob Lesch and Randy Schekman.

  • No. 10 October 2006

    Small-molecule activation switches on apoptosis. Putt et al. (p 543) identify the first small molecule (PAC-1) that directly causes cleavage of procaspase-3 to generate the active executioner enzyme caspase-3. Thus, PAC-1 bypasses the normal apoptosis circuitry in causing cell death - an effect that may be especially important in cancer cells, in which these signal cascades are often interrupted by faulty wiring (see also News & Views by Porter, p 509). Cover art by Erin Boyle, based on a transmission electron microscope image of lymphocytes provided by Paul Hergenrother, courtesy of Carolyn Bertozzi.

  • No. 9 September 2006

    Chondroitin sulfate small molecules contain diverse patterns of sulfation that are critical for biological activity. Gama et al. (p 467) synthesized chondroitin sulfate tetrasaccharides of defined sulfation sequence and found that the CS-E motif (but not other sulfation motifs) functions as a molecular recognition element to engage growth factors and their receptors and to enhance neuronal growth (see also News & Views by Turnbull and Linhardt, p 449). Cover art by Erin Boyle based on imagery of compounds and neurons provided by Heather E. Murrey and Cristal I. Gama.

  • No. 8 August 2006

    Coupling ligand structure to specific conformational switches in the β2 adrenoceptor. Yao et al. (p 417) showed that activation of the G protein-coupled receptor β2-AR is accompanied by at least two distinct molecular switches. The 'ionic lock' that holds together two of the transmembrane domains (red and blue) is broken upon receptor activation. Both the ionic lock switch and a 'rotamer toggle switch', which modulates helix conformation around a conserved proline kink, are required for full receptor activation (see also News & Views by Vilardaga, p 395). The authors examined the effect of agonist structure on activation of these molecular switches. Cover art by Erin Boyle based on imagery of β2-AR and small-molecule agonists provided by Charles Parnot and Xavier Deupi.

  • No. 7 July 2006

    Paradoxical hot spots for guanine oxidation by a chemical mediator of inflammation. Margolin et al. (p 365) describe the unusual sequence selectivity for DNA oxidation by an important chemical mediator of inflammation, nitrosoperoxycarbonate. Contrary to classical one-electron oxidants, which selectively produce damage at guanine bases having the lowest sequence-dependent ionization potential, this macrophage-derived oxidant produces the most damage at guanines in sequence contexts that confer the highest ionization potentials (see also News & Views by Cadet, Douki & Ravant, p 348). This observation complicates models that attempt to predict the location of oxidative DNA damage in cells. Cover art by Jeff Dixon (http://www.jeffdixon.ca) depicts an activated macrophage generating nitric oxide and superoxide that, along with carbon dioxide, react to form nitrosoperoxycarbonate. Homolytic bond cleavage produces nitrogen dioxide and carbonate radical anion, and the latter oxidizes a solvent-accessible guanine in DNA.

  • No. 6 June 2006

    Identifying off-target effects and hidden phenotypes of drugs in human cells. MacDonald et al. (p 329) develop a strategy to directly probe biochemical pathways that underlie therapeutic or toxic mechanisms in intact, living cells. The authors used high-content protein-fragment complementation assays (PCAs) based on fluorescent proteins to measure spatial and temporal changes in protein complexes in response to drugs that perturb specific pathways. They observed known structure-function relationships and deduced 'hidden', antiproliferative activities for four drugs. This study suggests a strategy for discovering unpredicted mechanisms of drug action (see also News and Views by Abraham, p 295). Cover art by Erin Boyle, based on an image of human HEK 293 cells and fluorescence arising from complexes of regulators of G protein signaling (RGS2) and the Frizzled 4 receptor, provided by Jane Lamerdin.

  • No. 5 May 2006

    Chemical regulation of angiogenesis in adult zebrafish. Bayliss (p 265) developed a regenerative angiogenesis assay in the tail fin of adult zebrafish (Danio rerio). In the assay, a kinase inhibitor (PTK787) blocked angiogenesis in adult caudal fins. Vascular endothelial growth factor receptor (VEGFR) signaling was required for blood vessel regeneration, but bone and tissue growth were unaffected by this chemical inhibitor. The study offers a way to discover genes and biochemical mechanisms involved in angiogenesis and a method for the identification and evaluation of anti-angiogenic compounds (see also News and Views by De Smet, Carmeliet and Autiero, p 228). Cover art by Erin Boyle, based on an image of a zebrafish tail fin that has undergone regeneration, provided by Heather Robbins.

  • No. 4 April 2006

    The common gorgonian Isis hippuris grows in coral reefs of the western Pacific Ocean. Bordeleau et al. (p 213) determined that its cytotoxic principle, hippuristanol (structure shown), is a selective inhibitor of the DEAD-box helicase eIF4A. Because hippuristanol can act as an inhibitor of translation initiation, it was used to inhibit poliovirus replication. Cover art by Erin Boyle, based on a photograph of Isis hippuris taken off the coast of Okinawa by Junichi Tanaka (see also News and Views by Pestova and Hellen, p 176).

  • No. 3 March 2006

    Understanding the preference for glycine in the C-terminal cap of an α-helix. Bang et al. (p 139) used chemical protein synthesis to generate ubiquitin variants in which different D-amino acids were inserted at the glycine cap position. Because D-amino acids can favorably adopt a left-handed conformation, comparison of the D-amino acid variant with the corresponding L-amino acid-containing protein provided a method for separating the energetic effects of conformation from those of changes in backbone solvation. This analysis demonstrates that glycine is preferred because it can favorably adopt a left-handed conformation (see also News & Views by Rose, p 123). Cover art by Erin Boyle, based on images provided by Duhee Bang, Valentina Tereshko and Stephen Kent.

  • No. 2 February 2006

    Real-time observation of enzymatic turnovers at the single-molecule level. English et al. (p 87) continuously moni-tored fluorescent spikes of individual products from enzymatic reactions of a single immobilized -galactosidase molecule. They observed large fluctua-tions of the enzymatic activity across a range of timescales that they attributed to a rugged energy landscape, in which a single enzyme molecule interconverts among conformers with different enzy-matic activities. This result was recon-ciled with, and provided new insights into, the classic Michaelis-Menten equation of enzyme kinetics (see also News Views by Walter, p 66). Cover art by Erin Boyle, based on images of Badlands National Park, South Dakota (USA) provided by Brian English.

  • No. 1 January 2006

    Optical control of glutamate receptors. Volgraf et al. (p 47) have created a glutamate receptor that can be turned on and off by light. This light-sensitive receptor was engineered by tethering an agonist to the receptor using a chemical linker that undergoes a conformation change in response to a specific wavelength of light (see also News & Views by Bayley, p 11). The image shows models for the open and closed forms of the engineered receptor and the chemical structure of the covalently attached small molecule in the cis and trans conformations. Cover art by Erin Boyle, based on images provided by Dirk Trauner.