BIOISIS is an open access database dedicated to the study of biological macromolecules by small angle X-ray scattering (SAXS). The project is supported by the Department of Energy Office of Science Integrated Diffraction Analysis Technologies, the National Cancer Institute Structural Cell Biology of DNA Repair Machines and the National Institute of General Medical Sciences project MINOS (Macromolecular INsights Optimized by Scattering).

BIOISIS aims to become the complete source for the deposition, distribution and maintenance of small angle X-ray scattering data and technologies.

 BIOISIS was built with the the Ruby on Rails framework and the MySQL relational database. Its chief designer and architect is Robert P. Rambo, Ph. D., of the Lawrence Berkeley National Lab. The need for a SAXS database for biological sciences was pursued by John Tainer, Ph.D., of the Scripps Research Institute in La Jolla, CA., nd Greg Hura, Ph.D., of the Lawrence Berkeley National Lab in Berkeley, CA.
The database is designed around the concept of an “experiment” and relates a specific experiment to a set of genes, organisms, computational models and experimental data.
Table_organization
If we consider the fact that the structure of a macromolecule in solution is condition specific, then the data and models from a refined SAXS experiment

 will reflect a condition specific conformational state. Since SAXS experiments at synchrotron sources are highly efficient, a typical data collection at a synchrotron may sample several different experimental conditions, thus yielding measurements of different conformational states. This was an important realization incorporated into the design of BIOISIS.
In contrast, those structures obtained from X-ray crystallography often measure a single conformational state due to both the nature of crystallography and the use of cryogenic temperatures during the experiment.

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Recent Posts
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).
RECONSTRUCTION OF SAXS PROFILES FROM PROTEIN STRUCTURES  
Excellent review on SAXS, this should be required reading material for anyone wanting to learn SAXS.
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. 

 

News and Updates

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).

27 February 2015  RECONSTRUCTION OF SAXS PROFILES FROM PROTEIN STRUCTURES

Excellent review on SAXS, this should be required reading material for anyone wanting to learn SAXS.

Comput Struct Biotechnol J. 2013; 8: e201308006

04 September 2014  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.

J. Appl. Cryst. (2013). 46, 1884-1888

Incorporation of a hydration layer in the `dummy atom’ ab initio structural modelling of biological macromolecule

04 September 2014  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.

24 July 2013  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.

 Latest Journal Articles


04 September 2014  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.

J. Appl. Cryst. (2013). 46, 1884-1888

Incorporation of a hydration layer in the `dummy atom’ ab initio structural modelling of biological macromolecules

Link to Article

26 March 2013  IMPACT OF MACROMOLECULAR CROWDING ON DNA REPLICATION

Novel application of SAXS using changes in the radius-of-gyration as a function of crowding agent to follow the compaction of an enzyme (in this case the large DNA replication machinery). These types of SAXS studies can be applied to other systems and highlight the effects of modulating water activity on macromolecular structure.

Nat Commun. 2013 Mar 19;4:1615. Akabayov B, Akabayov SR, Lee SJ, Wagner G, Richardson CC.

15 January 2011  NOVEL 2-BODY COMPUTATIONAL APPROXIMATION FOR SAXS CALCULATIONS

Excellent computational approach for calculating SAXS profiles from proteins using a 2-body model per amino acid. The authors show, to high scattering angles, the new method is accurate and similar to CRYSOL.

Calculation of Accurate Small Angle X-ray Scattering Curves from Coarse-Grained Protein Models. BMC Bioinformatics. 2010; 11: 429. Stovgaard K, Andreetta C, Hamelryck T.

Link to Article

13 January 2011  A NEW APPROACH TO ENSEMBLE REFINEMENT OF SAXS DATA

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions. Structure. 2011 12;19(1):109-16. Rozycki B, Kim YC, and Hummer G.

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