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Autophagy Ubiquitin-Like Protein Transfer In Trans Print
Friday, 04 November 2011 00:00

The cover depicts how the autophagy ubiquitin-like protein Atg8 is transferred from its E1, Atg7, to its E2, Atg3 (Taherbhoy et al., pp. 451–461). The two halves of the yin-yang represent the homodimeric Atg7. The circles within the yin-yang represent the Atg7 catalytic cysteines to which the ubiquitin-like protein Atg8 is transiently covalently linked. Each Atg7 monomer is capable of recruiting Atg3. Structural, biophysical, and biochemical data indicate that Atg3 binds to one Atg7 protomer and reaches across to accept Atg8 from the opposite protomer of Atg7 within the dimer. Article Link (PDF)

Read more about this publication in the ALS Science Brief Understanding the Autophagy Pathway.

XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair Print
Wednesday, 20 July 2011 00:00

The cover shows a protein plasticity and filament formation of XRCC4 (gold) in complex with ligase IV tandem BRCT domains (red) and with XLF (XRCC4-like factor, green). The article by Hammel et al., pages 32638–32650, describes the combination of crystallography, small angle x-ray scattering, and hydrogen-deuterium exchange mass spectrometry in the characterization of the XRCC4-XLF-DNA complex that permits multiple protein interactions leading to double strand break repair. Article Link (PDF)

Building of a Novel Mn12 Single Molecule Magnet by Assembly of Anisotropic Triangles Print
Wednesday, 06 July 2011 12:58

Assembly of triangular {MnIII3(O)(salox)3}+ fragments mediated by azido ligands, results in the dodecanuclear [Mn12O4(salox)12(N3)4(MeOH)4(H2O)2] complex with S = 8 ground state and SMM response. After the discovery of the Single-Molecule-Magnet (SMM) behaviour of [Mn6(O)2(salox)6(R-COO)2] (salox = salicylaldoxime, R = Me, Ph) complexes in 2004,1 the chemistry of this family of [Mn6] clusters has been studied in depth: the systematic change of the carboxylato ligands, the study of substitutedR-saloxH2 related ligands,2 the effect of variation of the oxidation state,3 the response under pressure4 or the one-dimensional assembly of [Mn6] units into chains of clusters5 with Single-Chain-Magnet behaviour in some cases,5c,d turn this system into one of the best known in the SMM field. One of the main goals of this work, developed by Brechin et al. has been to modulate the value of the ground spin level, reaching the maximum possible spin S = 12 by means of the adequate choice of methyl or ethyl substituted salicylaldoximes and the understanding of the structural features that control the coupling inside the triangles. Article Link (PDF)

Computing in Thermal Equilibrium With Dipole-Coupled Nanomagnets Print
Monday, 23 May 2011 00:00

In the 1970s, work at IBM by Charles Bennett suggested the possibility of a computer operating near thermal equilibrium and dissipating energy near the thermodynamic limits. Here, we demonstrate experimentally that a computing architecture based on dipole-coupled nanomagnets can operate near thermal equilibrium without the assistance of externally applied magnetic fields. The dynamics of digital signal propagation is demonstrated with micromagnetic simulation and then verified experimentally using time-lapse photoemission electron microscopy. A logic gate that computes using energy from the thermal bath without external fields is also demonstrated. Nanomagnetic logic circuits operating under these conditions are expected to dissipate energy near the fundamental thermodynamic limits of computation. Article Link (PDF)

Internal structure, hygroscopic and reactive properties of mixed sodium methanesulfonate-sodium chloride particles Print
Friday, 13 May 2011 00:00

Scientists recently combined experimental approaches and molecular dynamics modeling to gain new insights into the internal structure of sea salt particles and relate it to their fundamental chemical reactivity in the atmosphere. This research shows that surface enhancement or depletion of chemical components in marine particles can occur because of the difference in the chemical nature of the species. Because the atmospheric chemistry of the salt particles takes place at the gas-particle interface, understanding their complex surfaces provides new insights about their effect on the environment and climate change. Article Link.

Read more about this publication in the EMSL News article Inside Sea Salt: Chemical imaging of individual sea salt particles advances aerosol research.

Coupled Crystallographic Order–Disorder and Spin State in a Bistable Molecule: Multiple Transition Dynamics Print
Monday, 07 March 2011 00:00

Within spin-crossover solids, strong intermolecular interactions afford a means for the propagation of molecular-scale changes and coupling with crystallographic phase transitions, which leads to intricate cooperative phenomena. In their Full Paper on page 3120 ff., J. S. Costa, O. Roubeau, G. Arom et al. report on a novel spin-crossover FeII complex that features a dense network of intermolecular interactions. This results in a large unsymmetrical hysteresis of the spin state, which correlates with a crystallographic order–disorder transition. Article Link (PDF)

Observation of Insulating-Insulating Monoclinic Structural Transition in Macro-Sized VO2 Single Crystals Print
Friday, 04 March 2011 10:35

To clarify the origin of metal–insulator transition (MIT) in VO2, it is of crucial importance to understand the interplay among monoclinic M1, monoclinic M2, and rutile R phases. The Letter by Bongjin Simon Mun et al. (pp. 107–109), based on data taken on ALS Beamline 12.3.2, reports the unusual insulator–insulator structural phase transition (SPT) of VO2 single crystals, which involves monoclinic M1 and M2 phase. The VO2 crystals exhibit an extremely abrupt MIT at 67.8 °C and an insulator–insulator transition (IIT) at ∼49 °C. Using synchrotron-based X-ray microdiffraction, it is found that the IIT in this VO2 crystal is related to a SPT between the M2 and M1 phases while the MIT occurs with a SPT of M1 and R phase. Also, a stable M2 phase is found at room temperature without any presence of external stress, which has not been reported previously. The authors believe that further investigations on this intriguing system will not only enrich the fundamental understanding of the system, but also will be exploited in future technologies. Article Link (PDF)

Crystal Structure of the Dynein Motor Domain Print
Friday, 04 March 2011 00:00

Artistic rendering of dynein motor proteins moving along microtubules, based on a crystal structure reported by Carter et al. on p. 1159. This study reveals the architecture of the molecular machine that powers the beating of cilia and intracellular transport and provides insight into the mechanism by which energy from adenosine triphosphate hydrolysis is converted into motion. Image: Graham Johnson, The Scripps Research Institute and Article Link .

Vacuum-Ultraviolet Photoionization and Mass Spectrometric Characterization of Lignin Monomers Coniferyl and Sinapyl Alcohols Print
Saturday, 19 February 2011 00:00

The fragmentation mechanisms of monolignols under various energetic processes are studied with jet-cooled thermal desorption molecular beam (TDMB) mass spectrometry (MS), 25 keV Bi3+ secondary ion MS (SIMS), synchrotron vacuum-ultraviolet secondary neutral MS (VUV-SNMS) and theoretical methods. Experimental and calculated appearance energies of fragments observed in TDMB MS indicate that the coniferyl alcohol photoionization mass spectra contain the molecular parent and several dissociative photoionization products. Similar results obtained for sinapyl alcohol are also discussed briefly. Ionization energies of 7.60 eV ( 0.05 eV for coniferyl alcohol and <7.4 eV for both sinapyl and dihydrosinapyl alcohols are determined. The positive ion SIMS spectrum of coniferyl alcohol shares few characteristic peaks (m/z = 137 and 151) with the TDMB mass spectra, shows extensive fragmentation, and does not exhibit clear molecular parent signals. VUV-SNMS spectra, on the other hand, are dominated by the parent ion and main fragments also present in the TDMB spectra. Molecular fragmentation in VUV-SNMS spectra can be reduced by increasing the extraction delay time. Some features resembling the SIMS spectra are also observed in the desorbed neutral products. The monolignol VUVSNMS peaks shared with the TDMB mass spectra suggest that dissociative photoionization of ion-sputtered neutral molecules predominate in the VUV-SNMS mass spectra, despite the extra internal energy imparted in the initial ion impact. The potential applications of these results to imaging MS of biomolecules are discussed. Article Link (PDF)

Writing Nanostructures: Scanning Probe Direct-Write of Germanium Nanostructures Print
Tuesday, 02 November 2010 00:00

The cover image depicts the direct writing of a germanium nanostructure with the tip of an atomic force microscope (AFM). Germanium writing occurs when the AFM tip traces the desired shape along a biased silicon sample while immersed in an organometallic precursor (diphenylgermane). The high-electric field and the electrons emitted from the tip cause the precursor to locally react and yield germanium nanostructures. This innovative AFM strategy creates sub-30 nm carbon-free germanium nanostructures with desired geometries and placement, as reported on p. 4639 by Marco Rolandi and co-workers. Article Link (PDF)

Synchrotron IR Spectromicroscopy: Chemistry of Living Cells Print
Monday, 01 November 2010 00:00

Advanced analytical capabilities of synchrotron IR spectromicroscopy meet the demands of modern biological research for studying molecular reactions in individual living cells. Article Link (PDF)

[MnIII4LnIII4] Calix[4]arene Clusters as Enhanced Magnetic Coolers and Molecular Magnets Print
Wednesday, 22 September 2010 00:00

The [Mn4Gd4] cluster pictured is a promising candidate for refrigeration in the ultra-low-temperature region, providing for example a valid alternative to the use of 3He, which is becoming rare and expensive. Article Link (PDF)

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. ...

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