Newsletter

Dear Consortium Members and Affiliates,

It should be the dog-days of August here in Boston, with daily complaints about the heat and humidity. Instead we've had cool nights and comfortable days and the notion that summer can't possibly be nearing its end. But the days march along and we're gearing up for the start of the academic season. For those of you that aren't lounging at the seaside, we have a short newsletter update including a new webinar schedule, a story on John Williams, one new member to welcome, and a software update.

Our webinar series will restart in September, with a plan to broadcast on Tuesdays at noon EDT/EST once or twice each month. We'll send around announcements closer to the date, but you can mark your calendars for the following webinars now:

• Sept 9th: Geneious R7: Sequence Analysis Tool for Biologists -- presented by Christian Olsen of Biomatters
• Sept 23rd: Geneious R7: Molecular Cloning Tools for Biologists -- presented by Christian Olsen of Biomatters
• October: more info coming soon
• Nov 18th: Advanced Applications of Biological Small Angle Scattering -- presented by Thomas Grant of the Hauptman-Woodward Medical Research Institute

John Williams, Associate Professor at City of Hope, is the subject of our August Tale. For Williams, it seems, getting scooped was a hidden blessing; it prompted him to change directions and start down a path that would reshape his career. Read more of his story here

Anirban Banerjee became our newest member in August. He joins us from the NIH/NICHD. Welcome to Dr. Banerjee!

Th August software updates included new versions of frealign, pdb_redo, Phenix, IMOD, PyMOL, knuspr/knuspr-gui, and HKL2000 along with one new software title: PDBstat. See below for more details.

Software Changes

Frealign version 9.08 was pushed out earlier this month with new capabilities for parallelization of 3D.

HKL2000 version 706 brings with it 64-bit versions for Linux and Mac along with updates to the data auto index procedure.

IMOD release 4.7 was added to the software tree. This release includes a variety of bug fixes along with major functionality improvements to Tomogram Processing, Etomo, and 3dmod.

knuspr and the knuspr-gui were updated to version 20180812.

PDB_REDO was updated to version 5.34. This version includes modifications to allow RCAL and RFCAL to update after the resolution cutoff is changed along with several fixes to extractor.

PDBstat was added to the collection per a user request. PDBstat provides a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats.

Phenix nightly build 1.9-1760 was added to the tree.

PyMOL release 1.7.2 gives users an option for real-time antialiasing and sets the default for volume objects to pre-integrated volume rendering.

Publications

The following publications have appeared from Consortium member laboratories over the past 30 days:

• Gaya Amarasinghe, Washington U School of Medicine: Ebola Virus VP24 Targets a Unique NLS Binding Site on Karyopherin Alpha 5 to Selectively Compete with Nuclear Import of Phosphorylated STAT1.
• James Berger's Lab, Johns Hopkins U School of Medicine: DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome.
• Titus Boggon's Group, Yale, U School of Medicine:
  • Structural determinants for binding of Sorting Nexin 17 (SNX17) to the cytoplasmic adaptor protein Krev Interaction Trapped 1 (KRIT1)*
  • Boggon: Global Analysis of Human Nonreceptor Tyrosine Kinase Specificity Using High-Density Peptide Microarrays.
  • Tyr-301 phosphorylation inhibits pyruvate dehydrogenase by blocking substrate binding, and promotes the Warburg effect.
  • Differential binding to the ILK complex determines kindlin isoform adhesion localization and integrin activation.
• James Bradner's Group, Dana-Farber Cancer Institute: PRC2 loss amplifies Ras-driven transcription and confers sensitivity to BRD4-based therapies.
• Axel Brunger's Group, Stanford U: Complexin inhibits spontaneous release and synchronizes Ca2+-triggered synaptic vesicle fusion by distinct mechanisms.
• Pamela Bjorkman's Group at California Institute of Technology: Passive transfer of modest titers of potent and broadly neutralizing anti-HIV monoclonal antibodies block SHIV infection in macaques.
• Amedeo Caflisch's Group, U Zurich:
  • Fragment-based docking: Development of the CHARMMing Web user interface as a platform for Computer-Aided Drug Design.
  • Pyrrolo[3,2-b]quinoxaline Derivatives as Types I_1/2 and II Eph Tyrosine Kinase Inhibitors: Structure-Based Design, Synthesis, and in Vivo Validation.
  • Molecular dynamics in drug design.
• Jamie Cate's Group, UC Berkeley: Selection of chromosomal DNA libraries using a multiplex CRISPR system.
• Walter Chazin's Group, Vanderbilt U: Redefining the DNA-Binding Domain of Human XPA.
• Jonathan Cohen's Group, Harvard Medical School: Multiple Propofol Binding Sites in a γ-Aminobutyric Acid Type A Receptor (GABAAR) Identified Using a Photoreactive Propofol Analog.
• Kevin Corbett's Group, UC San Diego: A new piece in the kinetochore jigsaw puzzle.
• Peter Davies's Group, Queen's University: A prospective study of the introduction of complementary foods in contemporary Australian infants: What, when and why?
• Seth Darst's Group, Rockefeller U: RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement.
• Gang Dong's Group, Max F. Perutz Laboratories: Structure of the C. elegans ZYG-1 Cryptic Polo Box Suggests a Conserved Mechanism for Centriolar Docking of Plk4 Kinases.
• Jennifer Doudna's Group, UC Berkeley:
  • Evolutionarily Conserved Roles of the Dicer Helicase Domain in Regulating RNAi Processing.
  • RNA-guided assembly of Rev-RRE nuclear export complexes.
• Catherine Drennan's Group at MIT: The class III ribonucleotide reductase from Neisseria bacilliformis can utilize thioredoxin as a reductant.
• Brian Fox's Group, U Wisconsin-Madison: Spectroscopic and Computational Investigation of Fe(III) Cysteine Dioxygenase: Implications for the Nature of the Putative Superoxo-Fe(III) Intermediate.
• Daved Fremont's Group, Washington U School of Medicine: Manipulation of receptor oligomerization as a strategy to inhibit signaling by TNF superfamily members.
• Tamir Gonen's Group, HHMI Janelia Farms:
  • Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE.
  • A Type VI Secretion-Related Pathway in Bacteroidetes Mediates Interbacterial Antagonism.
  • High-resolution structure determination by continuous-rotation data collection in MicroED.
• Patrick Hogan's Group at La Jolla Institute for Allergy and Immunology: InsStructure-Based Optimization of a Peptidyl Inhibitor against Cal-cineurin-Nuclear Factor of Activated T Cell (NFAT) Interaction.
• James Hurley's Group, UC Berkeley: Assembly and dynamics of the autophagy-initiating Atg1 complex.
• Tina Iverson's Group, Vanderbilt U: Activation of the C-N bond of N-heterocyclic carbenes by inorganic elements.
• Theodore Jardetzky's Group, Standford U:
  • Probing the functions of the paramyxovirus glycoproteins F and HN with a panel of synthetic antibodies (sABs).
  • The Epstein-Barr virus (EBV) glycoprotein B (gB) cytoplasmic C-terminal tail domain (CTD) regulates the energy requirement for EBV-induced membrane fusion.
• Daniel Kahne's Group, Harvard University: Reconstitution of Peptidoglycan Cross-Linking Leads to Improved Fluorescent Probes of Cell Wall Synthesis.
• Peter Kwong's Group, NIH: Enhanced potency of a broadly neutralizing HIV-1 antibody in vitro improves protection against lentiviral infection in vivo.
• Galina Lepsheva's Group, Vanderbilt U: Structural Basis for Rational Design of Inhibitors Targeting Trypanosoma cruzi Sterol 14α-Demethylase: Two Regions of the Enzyme Molecule Potentiate Its Inhibition.
• Lima, Memorial Sloan-Kettering Cancer Center: Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA.
• Craig Lindsley's Group, Vanderbilt U: A new impact factor: the upward momentum continues.
  • Chemical modulation of mutant mGlu1 receptors derived from deleterious GRM1 mutations found in schizophrenics.
  • Selective Activation of M₄ Muscarinic Acetylcholine Receptors Reverses MK-801-Induced Behavioral Impairments and Enhances Associative Learning in Rodents.
• Karolin Luger's Group, Colorado State U: Automodification switches PARP-1 function from chromatin architectural protein to histone chaperone.
• John Markley's Group, U Wisconsin-Madison:
  • Nucleotide-Dependent Interactions within a Specialized Hsp70/Hsp40 Complex Involved in Fe-S Cluster Biogenesis.
  • pH-Induced Conformational Change of IscU at Low pH Correlates with Protonation/Deprotonation of Two Conserved Histidine Residues.
• Lawrence Marnett's Group, Vanderbilt U:
  • Mechanism of Repair of Acrolein- and Malondialdehyde-Derived Exocyclic Guanine Adducts by the α-Ketoglutarate/Fe(II) Dioxygenase AlkB.
  • ω-Alkynyl Lipid Surrogates for Polyunsaturated Fatty Acids: Free Radical and Enzymatic Oxidations.
  • Stable Histone Adduction by 4-Oxo-2-nonenal: A Potential Link between Oxidative Stress and Epigenetics.
• Dirk Niessing's Group, Institute of Structural Biology: mRNA transport meets membrane traffic.
• Zbyszek Otwinowski's Group, U Texas Southwestern Medical Center: A tethered delivery mechanism explains the catalytic action of a microtubule polymerase.
• Dinshaw Patel's Group, Memorial Sloan-Kettering Cancer Center:
  • A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36.
  • Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE.
  • c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets.
• Ivan Rayment's Group, U Wisconsin-Madison: Kinesin-2 KIF3AB Exhibits Novel ATPase Characteristics.
• Douglas Rees's Group, California Institute of Technology: Structure and mechanism of Zn²⁺-transporting P-type ATPases.
• Bernd Reif's Group, Institute of Structural Biology: A Residue-specific Shift in Stability and Amyloidogenicity of Antibody Variable Domains.
• Karin Reinisch's Group, Yale U School of Medicine: Sac1-Vps74 structure reveals a mechanism to terminate phosphoinositide signaling in the Golgi apparatus.
• Michael Sattler's Group at Institute of Structural Biology, Germany: A Novel Protein-Protein Interaction in the RES (REtention and Splicing) Complex.
• Celia Schiffer, University of Massachusetts Medical School: Drug Resistance Conferred by Mutations Outside the Active Site Through Alterations in the Dynamic and Structural Ensemble of HIV-1 Protease.
• Frank Sicheri's Group at U Toronto: Structure and mechanism of action of the hydroxy-aryl-aldehyde class of IRE1 endoribonuclease inhibitors.
• Georgios Skiniotis's Group, U Michigan: Visualization of arrestin recruitment by a G-protein-coupled receptor.
• Piotr Sliz's Group, Harvard Medical School: Chemical Interrogation of the Malaria Kinome.
• Brian Smith's Group, La Trobe U:
  • Protective hinge in insulin opens to enable its receptor engagement.
  • Transition state mimetics of the Plasmodium export element are potent inhibitors of plasmepsin V from P. falciparum and P. vivax.
• Oleg Tsodikov's Group, U Kentucky: U 2',6'-dihalostyrylanilines, pyridines, and pyrimidines for the inhibition of the catalytic subunit of methionine s-adenosyltransferase-2.
• Gerhard Wagner's Lab, Harvard Medical School:
  • Selective methyl labeling of eukaryotic membrane proteins using cell-free expression.:
  • Solid-State NMR Structure Determination from Diagonal-Compensated, Sparsely Nonuniform-Sampled 4D Proton-Proton Restraints.
  • Structure of the eukaryotic translation initiation factor eIF4E in complex with 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G.
• Suzanne Walker's Group, Harvard Medical School: Compound-gene interaction mapping reveals distinct roles for Staphylococcus aureus teichoic acids.
• Loren Walensky's Group, Dana-Farber Cancer Institute: Hydrocarbon-stapled peptides: principles, practice, and progress.
• Tom Walz's Group, Harvard Medical School: Structure and Dynamics of AMPA Receptor GluA2 in Resting, Pre-Open, and Desensitized States.
• Andrew H-J Wang's Group, Academia Sinica: The T4 Phage DNA Mimic Protein Arn Inhibits the DNA-binding Activity of the Bacterial Histone-like Protein H-NS.
• Dong Wan'g Group at U California San Diego: Pyrene-Based Quantitative Detection of the 5-Formylcytosine Loci Symmetry in the CpG Duplex Content during TET-Dependent Demethylation.
• Jia-huai Wang's Group, Dana-Farber Cancer Institute: The immunology connection-my first T cell receptor structure projects.
• David Wilson's Group, La Trobe U: Facile formation of a homoleptic Au(III) trications via simultaneous oxidation and ligand delivery from [PhI(pyridine)2]2+
• Cynthia Wolberger's Group, Johns Hopkins U School of Medicine: The bromodomain of Gcn5 regulates site-specificity of lysine acetylation on histone H3.
• Hongtao Yu's Group at U Texas Southwestern Medical School: Synergistic blockade of mitotic exit by two chemical inhibitors of the APC/C.
• Kai Wucherpfennig's Group at Dana-Farber Cancer Institute: B cell homeostasis and follicle confines are governed by fibroblastic reticular cells.
• Andrei Yudin, University of Toronto:
  • α-Borylcarbonyl compounds: from transient intermediates to robust building blocks.
  • Solid-Phase Synthesis of Piperazinones via Disrupted Ugi Condensation.
  • Small Heterocycles in Multicomponent Reactions.
• Ning Zheng's Group, U Washington: Molecular assembly of the period-cryptochrome circadian transcriptional repressor complex.

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.