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Thursday, July 24, 2014
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Advances in Crystallographic Hardware for Structural Biology
Matthew Benning and Michael Ruf, Bruker AXS Inc., East Cheryl Parkway

The number of life science investigators utilizing crystallography in their research increases every year. Synchrotrons are an invaluable resource for structural work but not everyone has unlimited access to a beamline. In-house diffraction systems complement synchrotron access and can provide increased productivity in the home lab. In recent years, the performance and versatility of in-house systems has greatly improved. The enhanced performance allows data collection on demanding projects such

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MED-SuMo and MED-Hybridise: exploit all PDB macromolecule structures to design/optimize innovative leads
Moriaud F., Oguievetskaia K., Adcock S.A., Vorotynsev A.M., Martin L., Doppelt-Azeroual O. and Delfaud F.

Obtaining structural information on fragment-protein target is a key factor and also a major limitation. We’ve used MED-SuMo and MED-Hybridise to query and mine the PDB seeking for similar interaction surfaces. MED-portions were used to design novel scaffolds (GPCR) and decorate a given scaffold (kinase). We have analysed the scaffolds in regard to their diversity, their presence in PubChem, PDB and other libraries.

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Phase Diagram Visualization via Continuously-Fed Crystallization: Experiments and Model
Masano Sugiyama and Victor Barocas

A continuously-fed crystallization chamber is manufactured to allow phase diagram visualization. This microfluidic system allows the experimenter to screen a large range of salt and protein concentrations in one experiment. This allows the experimenter to predict the protein phase diagram in a single experiment. A continuous-feed crystallization chamber has been successfully fabricated and characterized in terms of its flow profile, and has successfully predicted the phase diagram for lysozyme.

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Low Volume Liquid Handling of Organic Solvents for Compound Storage and Dissolution using mosquito
Gillian Lewis, Tristan Cope, Joby Jenkins, David Gledhill & Rob Lewis

mosquito® is a positive displacement liquid handling system capable of pipetting solutions with a high degree of accuracy (to within 5%) and precision (CVs of <10%) in the nanolitre range. Here, we demonstrate mosquito’s ability to dispense accurately low volumes of organic solvents of low surface tension and to re-dissolve compounds which have been previously dried in storage wells.

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Inferring synaptotagmin function from C2 domain stability: Analysis of structurally defined mutations in synaptotagmin 1 C2A
K.L Fuson, Kristofer Knutson, Anil Bhatta, Greg Gillispie, Candace Lange, Anne Hinderliter, R. Bryan Sutton

Synaptotagmin 1 (Syt1) triggers the release of neurotransmitter from docked synaptic vesicles through its interactions with Ca+2, phospholipid and the SNARE complex. We tested whether the disruption of this single H-bond can affect the shape of the Ca+2 binding pocket of C2A by causing loop 3 to collapse.

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Lead Optimization Computational Protocol at PDB Scale to Rationally Optimize Attachments to a Given Kinase Inhibitor Scaffold
Moriaud F., Henry T., Adcock S.A., Vorotynsev A.M., Martin L., Doppelt O.

We’ve used MED-SuMo to query and mine the Protein’s Surface Chemical Functions surrounding fragments of PDB ligands, seeking similarities with the kinase of interest (Vegfr DFGout, pdb code 2oh4, ligand code GIG) and collecting a library of 1129 unique fragments positioned in the vegfr’s active site and annotated with the counts of contacts and h-bonds. With them we optimize a substructure of the GIG ligand to find others DFGout ligands.

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New Developments for a Full Automation of the FIP Beamline at the ESRF
Jacquamet L., Bertoni A., Borel F., Charrault P., Israel-Gouy P., Iwema T., Kahn R., Joly J., Ohana J., Pirocchi M., Robin A., Serre L., Vernede X. and Ferrer J. L.

FIP (French beamline for the Investigation of Proteins) at the ESRF (European Synchrotron Radiation Facility) pushed developments in automation to reach a fully automated beamline. - The energy adjustment and beam optimization are completely automated. - The screening of the different protein crystals is ensured by a robotic system.In addition, this robot offers the possibility to analyze crystals directly as they grow in drops inside crystallization plates.

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Insights into the Mechanism of Partial Agonism: Crystal Structures of the Peroxisome Proliferator-activated Receptor-gamma Ligand-Binding Domain in the Complex with Two Enantiomeric Ligands
Giorgio Pochetti, Cristina Godio, Nico Mitro, Donatella Caruso, Samuele Scurati, Andrea Galmozzi, Fulvio Loiodice, Giuseppe Fracchiolla, Paolo Tortorella, Antonio Laghezza, Antonio Lavecchia, Ettore Novellino, Fernando Mazza, Maurizio Crestani

The peroxisome proliferator-activated receptors (PPARs) are transcriptional regulators of glucose and lipid metabolism. They are activated by natural ligands, such as fatty acids, and are also target of synthetic antidiabetic and hypolipidemic drugs. By using cell-based reporter assays, we studied the transactivation activity of two enantiomeric ureidofibrate derivatives.

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Methods For Automated Structure Determination for Ligands Within a Protein-Ligand Complex
Gregory L. Warren and Matthew T. Stahl

Afitt is a software package for automated ligand conformation generation and placement within algorithmically identified unfilled electron density. Following real space refinement, the ligand solution is sent for subsequent refinement by Refmac or CNX, via coordinate and dictionary files. We have validated Afitt on forty publicly available data sets, chosen because it contains examples of highly strained ligand conformations.

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Showing Results 11 - 20 of 26
Scientific News
Innovative Technology Enables First Crystal Structure of mGlu5 Transmembrane Domain to be Determined
Several novel drug candidates have been identified to help treat specific neuropsychiatric disorders.
Penn Researchers: Consider the ‘Anticrystal’
The study published in Nature Physics was conducted by Andrea Liu, Carl Goodrich and Sidney Nagel.
How Developing Neurons Sense a Chemical Cue
An embryo organizes itself into left and right halves as it grows. But a certain set of nerve cells do something unusual: they cross from one side to the other.
High-speed Snapshots of Biomolecules
PETRA III pioneers protein serial crystallography at synchrotrons.
Stanford Researchers Discover Immune System’s Rules of Engagement
Study finds surprising similarities in the way immune system defenders bind to disease-causing invaders.
Discovery of New Structure of Cell’s Communication Channel Could Aid Drug Development
Researchers hope discovery will lead to improvements in drugs that act on the sodium channel to treat a range of cardiac and pain conditions.
Til’ Death Do Us Part - in the Plant World
Study describes the ultimate act of sacrifice and survival in the plant world.
Unlocking a Mystery of Human Disease . . . in Space
Researchers analyze crystals of full-length protein with X-ray crystallography to determine huntingtin's structure.
Scripps Researchers Find New Point of Attack on HIV for Vaccine Development
The newly identified site can be attacked by human antibodies in a way that neutralizes the infectivity of a wide variety of HIV strains.
Lab Scale Manufacturing Using Continuous Crystallization
A new METTLER TOLEDO On-demand webinar explores recent research that could revolutionize pharmaceutical production.
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