Dear Consortium Members and Affiliates,
For this Halloween edition of the SBGrid newsletter we have a story about UCSF Chimera, tricks to help you navigate SBGrid in a new webinar along with a listing of future webinars you can join, new and updated software information, news on some creepy bugs to avoid in the latest OS releases, and five new members to welcome.
Our October Tale gives us a glimpse into the history of molecular graphics with a look at UCSF Chimera, where it came from and where it's going. Bob Langridge and Tom Ferrin took some time to describe how Chimera's precursors replaced the room-sized wire models built by hand in the 1950s and how it is now producing some of the first 3D images of cells in motion.
On Wednesday we recorded a webinar to help members Getting Started with SBGrid, which has been posted to YouTube. If you're new to SBGrid or just want to learn some tricks for navigating the environment, be sure to take a look. Up next is a Nov 18th presentation from Thomas Grant, who will talk about advanced applications for SAXS, a follow up to his very popular Intro to SAXS webinar given earlier this year.
Our webinar schedule for the next 6 months is coming together nicely and we have a number of great topics in the lineup, but still a few empty spots. Please let us know if you would like to hear more about a particular application.
- Nov 18th: Thomas Grant will do a follow up to his popular SAXS webinar
- Dec 2014: open - please send your ideas
- Jan 20th: SPARX with Pawel Penczek
- Feb 2015: open - please send your ideas
- March 2015: RELION with Sjors Scheres
- April 2015: EMAN2 with Steven Ludtke
In software news, we pushed out updates to CrystFEL, Phenix, PyMOL, Schrodinger, Theseus, and XMIPP, along with one new application: ProDy. More details are included in the software changes section below. We also have some information for you on new operating system gotchas and requirements:
- Linux 32-bit tree: We will continue supporting and maintaining the existing 32-bit linux tree, but as of January 1, 2015 we will no longer install new software applications. If you are still running a 32-bit version of linux, we urge you to upgrade to take advantage of performance benefits and ensure you have access to the most recent software updates. You can use the "lscpu" command to find out if you are running a 32-bit OS and if your computer supports the x86_64 64-bit architecture.
- OS Upgrades -- we've noticed a couple of bugs as members have upgraded to the newest Mac and CentOS versions:
- MAC 10.10 Yosemite: for applications that require X11, the 10.10 upgrade process appears to remove a symlink that is critical for xquartz on Mac and results in a missing library error: dyld: Library not loaded: /usr/X11/lib/libXt.6.dylib. The easiest way to fix this problem is to install the latest version of Xquartz from xquartz.macosforge.org.
- CentOS 7: There is a problem with Mesa software rendering, which PyMOL relies upon, that results in segfault due to a bug in a graphic library. Since most users utilize hardware graphics acceleration, this problem isn't significant, but please be aware.
For the month of October we are welcoming five new members: Klaus Schulten from the University of Illinois at Urbana-Champaign, John Buolamwini from Rosalind Franklin University, Cameron Mura from the University of Virginia, and two new PIs from Harvard Medical School: Maofu Liao and Andrew Kruse.
CrystFEL was updated a couple of steps to version 0.5.4a. You'll see a fix for the longstanding bug in pattern_sim's handling of symmetry, new version options for everything, and a number of other improvements that are detailed here.
ProDy has been added to the software tree. ProDy is a protein dynamics and sequence analysis application from the Bahar Lab at the University of Pittsburgh.
The PyMOL update to version 220.127.116.11 fixes the "dots" ray tracing bug.
The Schrodinger suite was updated by two versions to 2014-3. New features are detailed on their website.
For Theseus 3.0 the developers note an improved algorithm and a change in the target criterion that should improve stability in certain rare pathological cases, along with lots of code restructuring and streamlining.
XMIPP was updated to version 3.1, which adds a number of useful protocols, including those for import or export using EMX formats, using Relion, and studying continuous heterogeneity through Normal Mode Analysis.
Included below is a selection of publications that have appeared from Consortium member laboratories over the past 30 days. For the full list of publications please visit the Member Publications page on the SBGrid website.
- Erin Adams's Group, U Chicago:
- γδ T cell surveillance via CD1 molecules.
- Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by αβ T cells.
- Karen Anderson's Group, Yale U School of Medicine: Current Perspectives on HIV-1 Antiretroviral Drug Resistance.
- Nenad Ban's Group, ETH Zurich: The complete structure of the large subunit of the mammalian mitochondrial ribosome.
- Pamela Bjorkman's Group, California Institute of Technology: Design and characterization of structured protein linkers with differing flexibilities.
- Gunter Blobel's Group, Rockefeller U: Structure of an integral membrane sterol reductase from Methylomicrobium alcaliphilum.
- Titus Boggon's Group, Yale U School of Medicine:
- Differences in binding to the ILK complex determines kindlin isoform adhesion localization and integrin activation.
- Global analysis of human nonreceptor tyrosine kinase specificity using high-density Peptide microarrays.
- Alexandre Bonvin's Group, Utrecht U: Mass spec studio for integrative structural biology.
- James Bradner's Group, Dana-Farber Cancer Institute: Therapeutic Strategies to Inhibit MYC.
- Jamie Cate's Group, U CA, Berkeley: Construction of a quadruple auxotrophic mutant of an industrial polyploidy Saccharomyces cerevisiae using RNA-guided Cas9 nuclease.
- Rick Cerione's Group, Cornell U: Microfluidic isolation of cancer-cell-derived microvesicles from hetergeneous extracellular shed vesicle populations.
- Brian Crane's Group, Cornell U:
- Copper-Based Pulsed Dipolar ESR Spectroscopy as a Probe of Protein Conformation Linked to Disease States.
- Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes.
- Walter Chazin's Group, Vanderbilt U: The Host Protein Calprotectin Modulates the Helicobacter pylori cag Type IV Secretion System via Zinc Sequestration.
- 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.
- Michael Cosgrove's Group, SUNY Upstate Medical U: Characterization of the Grp94/OS-9 Chaperone-Lectin Complex.
- Enrico Di Cera's Group, St. Louis U: Prothrombin structure: unanticipated features and opportunities.
- Gang Dong's Group, Max F. Perutz Laboratories: Expression, purification and preliminary crystallographic analysis of the cryptic polo-box domain of Caenorhabditis elegans ZYG-1.
- Jennifer Doudna's Group, U California, Berkeley: Evolutionarily conserved roles of the dicer helicase domain in regulating RNA interference processing.
- Raimund Dutzler's Group, U Zurich: Crystal structure of a SLC11 (NRAMP) transporter reveals the basis for transition-metal ion transport.
- Juan Fontecilla-Camps's Group, IBS Grenoble:
- Crystal Structure of Tryptophan Lyase (NosL): Evidence for Radical Formation at the Amino Group of Tryptophan.
- Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states.
- James Fraser's Group, U CA San Francisco: Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine.
- Tamir Gonen, HHMI Janelia Farms:
- High thermodynamic stability of parametrically designed helical bundles.
- Structure of catalase determined by MicroED.
- Patrick Hogan's Group, La Jolla Institute for Allergy and Immunology: STIM1 triggers a gating rearrangement at the extracellular mouth of the ORAI1 channel.
- James Hogle's Group, Harvard Medical School: lHuman Cytomegalovirus UL97 Phosphorylates the Viral Nuclear Egress Complex.
- Mitsuhiko Ikura's Group, U Toronto: A coiled-coil clamp controls both conformation and clustering of stromal interaction molecule 1 (STIM1).
- Theodore Jardetzky's Group, Stanford The Epstein-Barr Virus (EBV) Glycoprotein B Cytoplasmic C-Terminal Tail Domain Regulates the Energy Requirement for EBV-Induced Membrane Fusion.
- Daniel Kahne's Group, Harvard U: Detection of lipid-linked peptidoglycan precursors by exploiting an unexpected transpeptidase reaction.
- Shohei Koide's Group U Chicago:
- Synthetic Antibody Fragment Targeting Nicastrin Affects Assembly and Trafficking of γ-Secretase.
- Proof of dual-topology architecture of Fluc F(-) channels with monobody blockers.
- John Kuriyan's Group, U California Berkeley: Structural insights into the role of iron-histidine bond cleavage in nitric oxide-induced activation of H-NOX gas sensor proteins.
- Peter Kwong's Group, NIH:
- Structure and immune recognition of trimeric pre-fusion HIV-1 Env.
- Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions.
- Craig Lindsley's Group, Vanderbilt U:
- Pharmacoeconomics and the medicinal chemist.
- Substituted indoles as selective protease activated receptor 4 (PAR-4) antagonists: Discovery and SAR of ML354.
- Elias Lolis's Group, Yale U School of Medicine: Crystallographic and Receptor Binding Characterization of Plasmodium falciparum Macrophage Migration Inhibitory Factor Complexed to Two Potent Inhibitors.
- Steve Long's Group, Memorial Sloan Kettering Cancer Institute: Structure and insights into the function of a Ca(2+)-activated Cl(-) channel.
- Zhe Lu's Group, U Pennsylvania: Counteracting suppression of CFTR and voltage-gated K(+) channels by a bacterial pathogenic factor with the natural product tannic acid.
- Roderick MacKinnon's Group, Rockefeller U: Phosphatidic acid modulation of Kv channel voltage sensor function.
- John Markley's Group, U Wisconsin-Madison: Response to On prompt update of literature references in the Protein Data Bank.
- Filippo Mancia's Group, Columbia U: Multi-crystal native SAD analysis at 6 keV.
- Lawrence Marnett's Group, Vanderbilt U:
- Protein modification by adenine propenal.
- Identification of the Major Prostaglandin Glycerol Ester Hydrolase in Human Cancer Cells.
- Jens Meiler's Group, Vanderbilt U: Discoidin domain receptor 1 (DDR1) kinase as target for structure-based drug discovery.
- Keith Miller's Group, Mass General Hospital: Anesthetics target interfacial transmembrane sites in nicotinic acetylcholine receptors.
- Par Nordlund's Group, Nanyang Technological U: Proteomics. Tracking cancer drugs in living cells by thermal profiling of the proteome.
- Emil Pai's Group, U Toronto: Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2.
- Olve Peersen's Group, Colorado State U: Structure-Function Relationships Underlying the Replication Fidelity of Viral RNA-dependent RNA Polymerases.
- Gil Privé's Group, U Toronto: Prostate cancer. Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer.
- Anna Pyle's Group, Yale U: Looking at LncRNAs with the Ribozyme Toolkit.
- Ivan Rayment's Group, U of Wisconsin-Madison: Kinesin-2 KIF3AB Exhibits Novel ATPase Characteristics.
- Douglas Rees's Group, California Institute of Technology: The Structure of a Conserved Piezo Channel Domain Reveals a Topologically Distinct β Sandwich Fold.
- Antonia Roll-Mecak's Group, NIH: Intrinsically disordered tubulin tails: complex tuners of microtubule functions?
- Michael Rosen's Group, U Texas Southwestern: Phase transitions of multivalent proteins can promote clustering of membrane receptors.
- Gabrielle Rudenko's Group, UTexas Medical Branch: Calsyntenin3: Molecular Architecture and Interaction with Neurexin 1alpha.
- Chuck Sanders's Group, Vanderbilt U: The Homology Model of PMP22 Suggests Mutations Resulting in Peripheral Neuropathy Disrupt Transmembrane Helix Packing.
- Klaus Schulten's Group, U Illinois at Urbana-Champaign:
- GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting.
- Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores.
- Michael Sattler's Group: Institute of Structural BiologyA Novel Protein-Protein Interaction in the RES (REtention and Splicing) Complex.
- Phillipp Selenko's Group, Leibniz Institute of Molecular Pharmacology: Efficient Modification of Alpha-Synuclein Serine 129 by Protein Kinase CK1 Requires Phosphorylation of Tyrosine 125 as a Priming Event.
- Tobin Sosnick's Group, U Chicago: Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations. Benchmarking all-atom simulations using hydrogen exchange.
- Daniel Southworth's Group, UMichigan: The Protein Targeting Factor Get3 Functions as ATP-Independent Chaperone under Oxidative Stress Conditions.
- Michael Stone's Group, Vanderbilt U: Major Groove Orientation of the (2S)-N(6)-(2-Hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA Adduct Induced by 1,2-Epoxy-3-butene.
- Gerhard Wagner's Group, Harvard Medical School: Human Translation Initiation Factor eIF4G1 Possesses a Low-Affinity ATP Binding Site Facing the ATP-Binding Cleft of eIF4A in the eIF4G/eIF4A Complex.
- Suzanne Walker's Group, Harvard Medical School:
- Detection of lipid-linked peptidoglycan precursors by exploiting an unexpected transpeptidase reaction.
- The Making of a Sweet Modification: Structure and Function of O-GlcNAc Transferase.
- Andrew H-J Wang's Group, Academia Sinica: Crowning Proteins: Modulating the Protein Surface Properties using Crown Ethers.
- Kenneth Westover's Group, U Texas Southwestern: Neutrophil-lymphocyte and platelet-lymphocyte ratios as prognostic factors following stereotactic radiation therapy for early-stage non-small cell lung cancer.
- David Wilson's Group, La Trobe U: A computational study on a strategy for isolating a stable cyclopentadienyl cation.
- Hongtao Yu's Group, U Texas Southwestern:
- Substrate-Specific Activation of the Mitotic Kinase Bub1 through Intramolecular Autophosphorylation and Kinetochore Targeting.
- Synergistic blockade of mitotic exit by two chemical inhibitors of the APC/C.
- Andrei Yudin's Group, U Toronto: Stereocontrolled Disruption of the Ugi Reaction toward the Production of Chiral Piperazinones: Substrate Scope and Process Development.
- Chloe Zubieta's Group, Institute of Life Sciences Research and Technologies: Biochemical and biophysical characterization of the Selenium binding and reducing site in Arabidopsis thaliana homologue to mammals Selenium Binding Protein 1.
Please cite eLife 2013;2:e01456 for all projects completed with SBGrid compiled software.
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.