Dear Consortium Members and Affiliates,
Summer has arrived and life around the campus has grown a little quieter, even if the pace has not slackened. In this month's newsletter we've got a few notes of interest to pass on from the Computing School, a story on Tamir Gonen of HHMI, a reminder about next week's webinar, a welcome to four new members, and a software release including several updates and one new application.
Thanks to everyone who participated at the SBGrid/NE-CAT 2014: Data Processing in Crystallography computing school. We had a great turnout and three days of talks that were stimulating and dynamic. We've posted PDF copies of many of the speaker's presentations in dropbox and are in the process of editing and posting recordings of each talk on our YouTube channel.
For our June Member Tale, we're looking in on Tamir Gonen at the HHMI Janelia Farm campus. Gonen describes the risky moves he's made throughout his career, from business to science, New Zealand to the US, X-ray crystallography to electron microscopy, and now from employing existing EM techniques to developing the new.
On the webinar front, last week we heard from Xiang-Jun Lu on DSSR/3DNA, which will soon be posted on YouTube. July will bring a presentation from Japan, featuring Kazutaka Katoh & Daron Standley discussing Web services for structure-informed multiple sequence alignment. We'll take a break in August, but will resume in September. If you would like us to feature a particular software application in an upcoming webinar, please contact Michelle.
We welcomed four new members in the month of June: Chloe Zubieta from the Institute of Life Sciences Research and Technologies in Grenoble, France, Nikolaus Grigorieff in his new lab at HHMI, Jonathan Cohen at Harvard Medical School, and Chris Hill from University of Utah. Welcome to our new members!
A couple of software updates went out during the past month, which included new releases from CCP4, EMAN2, PyMOL, XDSGUI as well as a one new software application: ResMap. More details below.
CCP4 6.4.0 is now at patch 16.
EMAN2 has been updated to the first beta version of 2.1, which includes many improvements to e2refine_easy and refinement reports and full support for EMAN2 -> Relion, Relion -> EMAN2 and EMAN2 -> Frealign. Also included are fixes to tiltboxer, RCT and tilt-validation and expansion of single particle tomography along with a number of other improvements.
PyMOL was updated to version 18.104.22.168 and includes a number of bug fixes.
ResMap 1.1.4 has been added to the collection. ResMap computes the local resolution of 3D density maps, primarily electron cryo-microscopy (cryo-EM), through a GUI or a command line interface.
XDSGUI version 2014-06-02 includes bug fixes.
The following publications have appeared from Consortium member laboratories over the past 30 days:
- Christopher Ackerson's Group: Structural Basis for Ligand Exchange on Au25(SR)18.
- Erin Adams's Group, U Chicago: The CD3 Conformational Change in the γδ T Cell Receptor Is Not Triggered by Antigens but Can Be Enforced to Enhance Tumor Killing.
- Titus Boggon's Group, Yale U School of Medicine: Chemosensory regulation of a HEAT-repeat protein couples aggregation and sporulation in Myxococcus xanthus.
- James Bradner's Group, Dana-Farber Cancer Institute:
- An epigenomic approach to therapy for tamoxifen-resistant breast cancer.
- Activation of SOX2 Expression by BRD4-NUT Oncogenic Fusion Drives Neoplastic Transformation in NUT Midline Carcinoma.
- Samuel Butcher's Group, U Wisconsin-Madison: Structure and dynamics of the HIV-1 frameshift element RNA.
- Amedeo Caflisch's Group, U Zurich: Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking.
- Chung-I Chang's Group, Academia Sinica: Endocytotic Routes of Cobra Cardiotoxins Depend on the Spatial Distribution of Positively Charged and Hydrophobic Domains to Target Distinct Types of Sulfated Glycoconjugates on Cell Surface.
- Martin Egli's Group, Vanderbilt U: Intricate Protein-Protein Interactions in the Cyanobacterial Circadian Clock.
- Ernesto Fuentes's Group, U Iowa: Chemosensory regulation of a HEAT-repeat protein couples aggregation and sporulation in Myxococcus xanthus.
- Tamir Gonen's Group, HHMI Janelia Farm: Accurate design of co-assembling multi-component protein nanomaterials.
- Marianne Grant, Beth Israel Deaconess Medical Center: FoxO1-Mediated Activation of Akt Plays a Critical Role in Vascular Homeostasis.
- Daniel Kahne's Group, Harvard U: LptE binds to and alters the physical state of LPS to catalyze its assembly at the cell surface.
- Tom Kirchhausen's Group, Children's Hospital Boston: Key Interactions for Clathrin Coat Stability.
- Craig Lindsley's Group, Vanderbilt U: Synthesis and SAR of substituted pyrazolo[1,5-a]quinazolines as dual mGlu2/mGlu3 NAMs.
- Filippo Mancia's Group, Columbia U: Structural basis for catalysis in a CDP-alcohol phosphotransferase.
- Wayne Marasco's Group, Dana-Farber Cancer Institute: Molecular Signatures of Hemagglutinin Stem-Directed Heterosubtypic Human Neutralizing Antibodies against Influenza A Viruses.
- John Markley's Group, U Wisconsin-Madison: Solution Structure of the 2A Protease from a Common Cold Agent, Human Rhinovirus C2, Strain W12.
- Lawrence Marnett's Group Vanderbilt U: PET radiotracer [(18)F]-P6 selectively targeting COX-1 as a novel biomarker in ovarian cancer: Preliminary investigation.
- Dimitar Nikolov's Group, Memorial Sloan Kettering Cancer Center: Structures of netrin-1 bound to two receptors provide insight into its axon guidance mechanism.
- Jay Nix's Group, Molecular Biology Consortium: The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA.
- Joseph Piccirilli's Group, U Chicago: A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
- Anna Pyle's Group, Yale U: The linker region of NS3 plays a critical role in the replication and infectivity of hepatitis C virus.
- Tom Rapoport's Group, Harvard Medical School: A "Push and Slide" Mechanism Allows Sequence-Insensitive Translocation of Secretory Proteins by the SecA ATPase.
- Phillip Selenko's Group, Leibniz Institute of Molecular Pharmacology: Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins (IDPs).
- Georgios Skiniotis's Group, U Michigan:
- Structural rearrangements of a polyketide synthase module during its catalytic cycle.
- Structure of a modular polyketide synthase.
- Tim Springer's Group, Children's Hospital Boston: von Willebrand factor, Jedi knight of the bloodstream.
- Eric Sundberg, U Maryland School of Medicine: Molecular Determinants of Agonist and Antagonist Signaling through the IL-36 Receptor.
- Andrew H-J Wang's Lab, Academia Sinica: Squalene Synthase As a Target for Chagas Disease Therapeutics.
- Gerhard Wagner's Group, Harvard Medical School:
- 1H, 13C, and 15N backbone and sidechain chemical shift assignments for the HEAT2 domain of human eIF4GI.
- Synthesis of Rigidified eIF4E/eIF4G Inhibitor-1 (4EGI-1) Mimetic and Their in Vitro Characterization as Inhibitors of Protein-Protein Interaction.
- Kai Wucherpfennig's Group, Dana-Farber Cancer Institute: Membrane Association of the CD3ε Signaling Domain Is Required for Optimal T Cell Development and Function.
- Hongtao Yu's Group, U Texas Southwestern Medical Center: The Transcription Factor TFII-I Promotes DNA Translesion Synthesis and Genomic Stability.
- Andre Yudin's Group, U Toronto: α-Borylcarbonyl compounds: from transient intermediates to robust building blocks.
Please cite eLife 2013;2:e01456 for all projects completed with SBGrid compiled software.
For the full list of publications please visit the publication section on the SBGrid website.
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.