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An Open-Faced Chaperonin: Crystal Structures of a Group II Chaperonin Reveal Open and Cosed States Print
Thursday, 16 September 2010 14:37

Chaperonins are complexes that promote the proper folding of newly synthesized or denatured proteins by encapsulating them in a protective shell. Chaperonins come in two classes, group I and group II, which differ in their localization and closing requirements; group I members require a ring-shaped cofactor to fully close the folding chamber whereas group II members contain a built-in “lid.” Interestingly, as of yet, the structures of group II chaperonins have only been solved in the closed conformation, but in this Paper of the Week, Jose Pereira and colleagues present crystal structures of the group II chaperonin from the archaeal Methanococcus maripaludis in both closed and open states. This comparative information revealed that the closing mechanism for group II chaperonins is quite distinct from group I; during closing, all three domains—equatorial, apical, and intermediate—rotate as a single rigid body, whereas in group I chaperonins the equatorial domains remain relatively stationary. As a result, there is a significant reduction in the size and shape of the folding chamber during closing. However, substrate binding sites and sites for allosteric regulation are conserved between the two groups, suggesting they arose from a common ancestor. Together, the structures shed new light on this important class of proteins. Article Link (PDF)

The Nature of Nitrate at the Ice Surface Studied by XPS and NEXAFS Print
Friday, 20 August 2010 15:41

Trace contaminants such as strong acids have been suggested to affect the thickness of the quasi-liquid layer at the ice/air interface, which is at the heart of heterogeneous chemical reactions between snowpacks or cirrus clouds and the surrounding air. We used X-ray photoelectron spectroscopy (XPS) and electron yield near edge X-ray absorption fine structure (NEXAFS) spectroscopy at the Advanced Light Source (ALS) to probe the ice surface in the presence of HNO3 formed from the heterogeneous hydrolysis of NO2 at 230 K. We studied the nature of the adsorbed species at the ice/vapor interfaces as well as the effect of HNO3 on the hydrogen bonding environment at the ice surface. The NEXAFS spectrum of ice with adsorbed HNO3 can be represented as linear combination of the clean ice and nitrate solution spectrum, thus indicating that in the presence of HNO3 the ice surface consists of a mixture of clean ice and nitrate ions that are coordinated as in a concentrated solution at the same temperature but higher HNO3 pressures. ... Article Link (PDF)

Imaging Cell Wall Architecture in Single Zinnia elegans Tracheary Elements Print
Wednesday, 30 June 2010 00:00

The chemical and structural organization of the plant cell wall was examined in Zinnia elegans tracheary elements (TEs), which specialize by developing prominent secondary wall thickenings underlying the primary wall during xylogenesis in vitro. Three imaging platforms were used in conjunction with chemical extraction of wall components to investigate the composition and structure of single Zinnia TEs. Using fluorescence microscopy with a green fluorescent protein-tagged Clostridium thermocellum family 3 carbohydrate-binding module specific for crystalline cellulose, researchers working at ALS Beamline 1.4 found that cellulose accessibility and binding in TEs increased significantly following an acidified chlorite treatment. ...

Therapeutic Antibody Targeting of Individual Notch Receptors Print
Thursday, 15 April 2010 00:00

Notch receptors are widely expressed transmembrane proteins through which mammalian cells communicate to regulate cell fate and growth, and defects in Notch signalling are linked to many cancers. Using phage display technology, a multi-department team at Genentech has produced synthetic antibodies that act as potent and specific antagonists of Notch1 and Notch2. The cover, by Gregóire Vion of Salamander Design Studios (, depicts communication between a ligand-expressing cell (right) stimulating Notch signalling in an adjacent cell. The receptor-cell membrane expresses Notches 1 and 2 (red and blue); action of a specific antagonist means that only the blue signal is transduced to the nucleus. Article Link (PDF)

Doping Graphene into Superconductivity (Extended van Hove Singularity and Superconducting Instability in Doped Graphene) Print
Friday, 02 April 2010 00:00

Graphene’s singular transport characteristics derive from its band structure, whose features include saddle points at the edges of the Brillouin zone that affect the topology of the Fermi surface.

In their article in Physical Review Letters, Jessica McChesney and her collaborators from the US, Germany, and Spain check for superconductivity in graphene because of a similarity—also caused by a saddle point in the band structure (a van Hove singularity)—with the density of states of high-temperature superconductors.

They chemically dope graphene to significantly higher levels than previously achieved and then probe its band structure with angle-resolved photoemission spectroscopy. The saddle point becomes more extended than localized as the Fermi surface moves across it. The authors calculate that, under these conditions of doping and Fermi surface topology, graphene can achieve superconductivity, in principle due to electron-electron interactions alone. – Sami Mitra, (Physics Synopsis)

The Effect of π-Stacking, H-Bonding, and Eectrostatic Interactions on the Ionization Energies of Nucleic Acid Bases Print
Sunday, 14 March 2010 00:00

A combined theoretical and experimental study of the ionized dimers of thymine and adenine, TT, AA, and AT, is presented. Experimentally observed and computed adiabatic and vertical ionization energies (IEs) for monomers and dimers as well as thresholds for the appearance of the protonated species are reported and analyzed. Non-covalent interactions strongly affect the observed IEs. The magnitude and the nature of the effect is different for different isomers of the dimers. The computations reveal that for TT, the largest changes in vertical IEs (0.4 eV) relative to the monomer occur in asymmetric H-bonded and symmetric -stacked isomers, whereas in the lowest-energy symmetric H-bonded dimer the shift in IEs is much smaller (0.2 eV). The origin of the shift and the character of the ionized states is different in asymmetric H-bonded and symmetric stacked isomers. ... Article Link (PDF)

Probing the Hydrogen-Bond Network of Water via Time-Resolved Soft X-Ray Spectroscopy Print
Thursday, 28 May 2009 00:00

We report time-resolved studies of hydrogen bonding in liquid H2O, in response to direct excitation of the O–H stretch mode at 3 m, probed via soft X-ray absorption spectroscopy at the oxygen K-edge. This approach employs a newly developed nanofluidic cell for transient soft X-ray spectroscopy in the liquid phase. Distinct changes in the near-edge spectral region (XANES) are observed, and are indicative of a transient temperature rise of 10 K following transient laser excitation and rapid thermalization of vibrational energy. The rapid heating occurs at constant volume and the associated increase in internal pressure, estimated to be 8 MPa, is manifested by distinct spectral changes that differ from those induced by temperature alone. We conclude that the near-edge spectral shape of the oxygen K-edge is a sensitive probe of internal pressure, opening new possibilities for testing the validity of water models and providing new insight into the nature of hydrogen bonding in water. Article Link (PDF)

Nickel alpha-Keto-beta-Diimine Initiators for Olefin Polymerization Print
Wednesday, 28 January 2009 00:00

In order to design and improve a catalyst, it is important to understand the structure of the present one. Whether they work in the solid state or in solution, if the catalysts can be crystallized, then their structure can be determined by single crystal x-ray diffraction on
station 11.3.1. Some chemical reactions can occur in such a way that two different handedness, i.e., mirror images of the same molecule, are produced. For applications in the pharmaceutical industry, only one of these handedness may have the desired biologically activity, the other
may have negligible or adverse affects. Separation of these mirror image molecules is very difficult and costly, therefore a catalyst which makes only the desired handedness both reduces the energy required for separation and waste at the same time. Article Link (PDF)

Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis Print
Friday, 01 December 2006 00:00

Cell CoverNew structures of RNA polymerase II (pol II) transcribing complexes reveal a likely key to transcription. The trigger loop swings beneath a correct nucleoside triphosphate (NTP) in the nucleotide addition site, closing off the active center and forming an extensive network of interactions with the NTP base, sugar, phosphates, and additional pol II residues. A histidine side chain in the trigger loop, precisely positioned by these interactions, may literally "trigger" phosphodiester bond formation. Recognition and catalysis are thus coupled, ensuring the fidelity of transcription. Article Link (PDF)

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