Bioisis

General Information

SCATTER 3.0     (posted: 09 June 2016)

Scatter has been updated to release 3.0. The program was completely re-written and utilizes several new structures for handling datasets. PDB files can be dropped in like *.dat files which will then create corresponding P®-distribution function and Intensity files. This is useful for comparing models in real-space against experimental data. There is also a new archiving feature for taking selected data and writing them to a separate directory with associated image files. The release has been tested for the past 4 months and should be stable (requires Jave 1.7 or greater).


TUESDAY MORNING AT ACA 2013     (posted: 24 July 2013)

There were some exciting and diverse membrane protein SAS talks this morning. Two different talks focused on modeling lipid interactions around an oligomeric membrane protein: Javier Perez described his useful SEC-SAXS setup at the SWING beamline, which measures RI and UV alongside the SAXS to obtain stoichiometry information about detergent-protein complexes. He took several useful strategies to model the Aquaporin-0-lipid structure, and validate his models. In the same session, Shuo Qian also wanted to understand how detergents wrap around the protein photosystem 1, and is making great progress using SANS methods. Cecile Fradin spoke about her fluorescence imaging, SANS and AFM studies to characterize the pore forming mechanism involving Bax and Bak proteins’ interactions with mitochondrial membrane, leading to apoptosis. She used a series of contrast matching experiments and vesicle of a variety of lipids to visualize protein vs lipid contributions to the pore forming process and test her “mushroom vs. umbrella” model. Wei Liu of the Cherezov group described how SAXS on lipid matrices is aiding their abilities to define and characterize new lipid mesophases for membrane protein crystallization. Their LCPs form in 5 minutes, and a goal is to characterize structural parameters such as size of the water channel for different matrices in high throughput. Andrew Whitten described his SAXS, SANS and cross linking studies to characterize interactions of Munc18-1:Syntaxins, which can form open and closed states relevant to a synaptic vesicle fusion mechanism. Shuo Qian also gave an overview of the Bio-SANS/CSMB user facility at Oak Ridge National Lab. There are 2 SANS stations from the reactor, with large q-range and are are also setting up an onsite SAXS station for testing SANS samples. The facility also has ongoing GI-SANS efforts to characterize membrane structure around proteins. They also have a biodeuteration Lab (user facility) for preparing contrast matching samples and deuterated lipids for extraction from E. coli.


ANOTHER POINT FROM ACA 2013     (posted: 23 July 2013)

Dr. Trewhella also re-introduced the ongoing efforts toward developing SAXS guidelines for evaluation and publication, and encouraged the SAXS community to get involved with the discussion at: http://sas.wwpdb.org


MORE FROM ACA 2013     (posted: 23 July 2013)

Jill Trewhella spoke about her ongoing work on understanding molecular events in muscle relaxation/contraction via cardiac myosin binding protein c and its assembly with actin. Due to the large size of these filaments, her team had to start from a 2D model to look at the cross sectional information (she developed a “2D bead modeling variant of DAMMIN”), and then optimize rotation/translation of components in the 3D model. In the cell, only one cMyBP-C tends to bind per 30 actin units, but in her case, they are looking at saturated actin, which has provided beneficial symmetry information. EM studies showed agreement with the SAS model interaction of the actin central core to the C0 subunit of within ~17 Å, which for a model of this complexity, seemed great. She also addressed species differences in the proteins, as the “PA” linker length between domains of cMyBP-c apparently correlates with heart rate. By forming these filaments in the NMR tube, she also confirmed the C0 residue-level positioning. So she has now used MX, SAXS, SANS, EM and NMR information to validate her model, since, as she put it, actin is very sticky, so why should such an intricate model be believed?


MX AT ACA 2013     (posted: 23 July 2013)

Jane Richardson gave a nice update on structure improvement criteria in Molprobity v4, with goal to continue incorporating this within existing software. There was focus on proper positioning of H atoms in density (nuclear vs. center of e- cloud), all-atom contacts, side chain rotamers, improving clash scores (some old values too strict), and RNA structures. She presented a convincing plot of reported clash scores in deposited PDBs that has been steadily falling since Molprobility was implemented in 2002. She described unreliability of Ramachandran plots for low resolution data (and danger of forcing atoms into density at low resolution), and also mentioned benefits of modeling partial water occupancy in high resolution structures, which maybe doesn’t happen enough. For RNA, she says, bases and phosphates are generally modeled acceptably, with the problem lying in backbone. Of the 6-9 variables to optimize from sugar to sugar, 7 are now addressed by Molprobity. She mentioned the ERRASER tool (Enumerative Refinement of RNA ASsisted by Electron density in Rosetta) for exhaustive local searching. Using these improvements, she is working with collaborators to re-analyze ligands and conformers in RNA structures of ribozymes and the ribosome to provide new biological insights (though she admits the ribosome will be a big undertaking). She concludes: “The zen of model anamolies: Correct most of them; Treasure the meaningful valid few; live serenely with the rest”