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Welcome to BIOISIS ... the resource for macromolecular SAXS.
Experimental Highlight
Splicing factor complex of phosphorylated (P)SF1 residues 1-255 and U2AF65 residues 148-375
Low_res_thumbnail Human SF1 ULM-KH-QUA2, which is phosphorylated on Ser80Ser82, bound to U2AF65 RRM1-RRM2-UHM in a splicing factor complex.
    

Recent Posts

DENFERT: BEAD MODELING WITH HYDRATION  

New dummy atom modeling algorithm that uses the Debye equation instead of spherical harmonic expansions. The algorithm attempts to model the hydration layer assuming a biphasic composition of the scattering volume.


SCATTER 2.2B RELEASED  

Scatter 2.2b has been released and features several updates. Loading files is much faster due to truncation of the data for autoRg calculations. Scatter can now calculate P®-distributions from PDB files for easy direct comparison in P® plots. The Subtraction Tab has been improved, and has been adapted for SEC SAXS data. Please see the tutorial for more information.


TUESDAY MORNING AT ACA 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.


ACA 2013 MONDAY SESSION  

Greg Hura from SIBYLS beamline at ALS/LBNL talked about learning new biology with high-throughput SAXS by getting back to hypothesis testing and the scientific method. How? He described several applications of his new Volatility-of-ratio metric applied to comparison heatmaps, which SAXS users can access at http://bl1231.als.lbl.gov/saxs_similarity/. Michal Hammel from SIBYLS beamline presented a talk, “Prediction of Protein Crystallizibility from SAXS” aka “You Never Know.” Kratky plots and Porod exponents did not help him in these efforts. His main summary: the worst looking SAXS profiles may indicate crystallizable constructs. Bragg peaks (even at low concentrations) can indicate nucleation and be informative as to positioning within complexes. SAXS is a tool of comparison, but there is a high level of false positive/false negative. Philip Anfinrud brought up the notion of undoing the orientational averaging in SAXS by polarizing the system via illuminating a chromatically active protein coupled to 100 ps timeresolved SAXS.