Structures containing novel folds from the JCSG structure
... the beam line. The automated mounting system has been integrated with software for loop alignment and diffraction image collection to provide a complete crystal detection solution within the BLU-ICE graphical interface. With this tool it is possible to filter a crystal every 3.5 minutes, including two 30 s exposures per crystal (at 0 and 90 degrees phi). The results of the selection process are organized in a directory structure that reflects the purpose and identification of the crystal for future review by the user. In this way, the system can be used to screen a single 96-crystal cassette in less than 6 h. The robot is highly accurate and therefore samples can survive multiple mount / dismount cycles without undesirable ice buildup or glass damage. The system was initially installed at BL11-1 at SSRL, where it was used by the SDC to filter ϳ 3000 crystals.
The same system is now being installed on all other protein crystallography beamlines, where it will be a standard piece of beamline equipment in the near future. All data resulting from the crystal selection process is kept in the JCSG tracking database. Communication with the monitoring database is facilitated through an Excel spreadsheet that includes detailed detection results for each crystal. This Excel spreadsheet is currently completed by the user on the fly while mounting the crystals and collecting the images. The user assesses both the visual appearance of the crystal / loop as well as the quality of the diffraction images.
The presence of ice rings, spot quality, diffraction force, and resolution are noted. A computer program has been developed to automate the analysis of diffraction images and thus allow the entire screening process to run without supervision. Work is underway to automate the configuration and collection of complete data sets. For example, many of the steps required to perform a fluorescence scan and select wavelengths for a MAD experiment have already been automated . Moving forward, a smart experimental strategy will be used to fully automate the data collection step.
Determination of the structure is carried out using a variety of standard crystallographic applications. These programs run within a management environment that organizes the required input files and the resulting output files. Many programs can be run in parallel, therefore it is possible to try to solve the structure in multiple groups of space at the same time without any additional effort and all the results are kept in a standard directory tree. All aspects of the framework determination process are coupled to the JCSG tracking database so that any JCSG staff can download the latest files related to any given goal. The vast amount of genomic data available for many organisms has set the stage for the next phase of structure-function analysis.
High-throughput structural genomics is currently the method of choice for the rapid analysis of relationships between structure and function of proteins throughout the proteome. The Joint Center for Structural Genomics (JCSG), established in 2000 under the NIH / NIGMS Protein Structure Initiative, has developed and implemented a high-throughput integrated framework framework and applied it in a 2-tier approach to extract the proteome from thermophilic bacteria.
Thermotoga maritima. At the first level, successful application of this integrated pipeline has resulted in the cloning and expression of 73% of the T. maritima proteome (1,376 out of 1,877 predicted genes) and has identified 465 proteins that produced crystal impacts. These 465 proteins were compared to existing structural information and a subset of 269 targets were selected for processing toward structure determination in a second-level effort.
To date, the JCSG tubing applied to the Thermotoga maritima proteome has resulted in 55 new structures and has identified 6 novel folds and continues to identify structures with novel characteristics.