09 June 2016  SCATTER 3.0

• 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).

• Excellent review on SAXS, this should be required reading material for anyone wanting to learn SAXS.
• Comput Struct Biotechnol J. 2013; 8: e201308006

• 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.

• 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.