Recently in protocols Category

The SIBYLS beamline has recently been awarded 50,000 hours on the NERSC (National Energy Research Scientific Computing Center) to perform solution structure modeling using experimental SAXS data. Besides the usual ab-initio reconstructions programs a new approach in rigid body modeling BILBOMD has been parallelized on the NERSC supercomputer. It is commonly acknowledged that flexibility between domains of proteins is often critical for function. These motions, and proteins with large scale flexibility in general, are often not readily amenable to conventional structural analysis such as X-ray crystallography, NMR, or electron microscopy. We have developed an analysis tool using experimental SAXS measurements to identify flexibility and validate a constructed minimal ensemble of models which represent highly populated conformations in solution. The resolution is sufficient to address questions about the extent of the domain conformational sampling in solution? In our rigid body modeling strategy BILBOMD, molecular dynamics (MD) simulations are used to explore conformational space. A typical experiment involves  MD simulation on the domain connections at very high temperature, where the additional kinetic energy prevents the molecule from becoming trapped in a local minimum. The MD simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. A genetic algorithm is then used to identify the minimal ensemble (Minimal Ensemble Search, MES) required to best fit the experimental data. If you are interested in learning about and/or using this valuable SAXS analysis tool please contact Michal Hammel (MHammel at lbl dot gov).

Burgeoning crystallographers may find the high-throughput screening (HTS) laboratory, which is part of the Center for High-Throughput Structural Biology (CHTSB) at the Hauptman-Woodward Institute (HWI) to be a very logical starting point for determining the suitability of a particular sample for macromolecular crystallography studies. The HWI will prepare crystal-growth screening experiments in 1536-well microassay plates for about $300 per sample. More details are available on their website and in the FAQ.

Quen Cheng in the Cooper lab has done a nice set of experiments to address the usefulness of various readily available detergents for improving the behavior proteins in SAXS experiments.

A new review on macromolecular SAXS has been published in the Quarterly Reviews in Biophysics by Putnam, C.D., Hammel, M., Hura, G.L., and Tainer, J.A.

"This six part review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high-resolution structures."

I added an entry in the PX protocol section that should help more advanced general users to switch from SAXS to PX and then tune up the beam for PX use.