research advances

PSI in the Spotlight – April 2009

PSI-SGKB [doi:10.1038/nw_psisgkb.2009.14]

This column presents announcements and other notable news related to the Protein Structure Initiative.

2009 NIGMS Workshop enables scientists with new methods and technologies

A practical during this year's 2009 NIGMS Workshop demonstrates the PSI CESG's wheat germ cell-free translation system. After only 2 hours of incubation with green gluorescent protein (GFP) messenger RNA, fully functional GFP was visible in the right sample vial as compared to the control on the left, which lacked mRNA.

Organized by the PSI and NIGMS, the 2009 NIGMS Workshop: Enabling Technologies for Structural Biology was held March 4–6, 2009 at the NIH-Natcher Conference Center in Bethesda, MD. This two and a half day workshop presented the latest technical solutions for today's research obstacles, and these topics and solutions could apply to any level of research, from the bench scientist to the high-throughput centers.

Michael Rossmann (Purdue University) began the conference by talking about how “the limits of structural biology mark the beginnings of biology”, citing examples from structural studies to understand invasion mechanisms used by viral pathogens. In a session on protein–protein interactions and complexes, Donald Petrey (Columbia University) described a new comparative modeling method that predicts protein–protein interactions for proteins with unknown functions, whereas in the “traditional bottlenecks” session, Robert Thorne (Cornell University) talked about a way to “slow cool” a protein crystal, producing ice-free diffraction without increasing the crystal's mosaicity. During day two of the workshop, Frank Raushel delivered a keynote lecture about deciphering substrate specificity of enzymes of unknown function to begin the “Protein Function” session, and Antonio Rosato (University of Florence) described the eNMR platform for structural biology and their motivation to create a unified portal for NMR data analysis in the session about New and Improved Technologies.

Tutorials on enabling technologies and resources were also very popular during the workshop. These tutorials focused on protein expression and purification techniques as well as structural methods and analysis. Shin-Ichi Makino (Ehime University) gave a demonstration of the Wheat Germ Cell-Free Translation system using GFP mRNA as an example (see picture), whereas Youngchang Kim (Argonne National Laboratory) showed users how reductive methylation of surface residues, a method highlighted previously, can improve protein crystallization. Talks on Structural Methods and Analysis included those from Cory Gerdts (Emerald Biosciences), who invited participants to bring their protein samples to try the Microcapillary Protein Crystallization System, and Adam Godzik (The Burnham Institute) described how to determine the most information from your protein structure (including if it has a novel fold). The PSI SGKB provided a walkthrough of the site to show how it can be used for research. This year's Enabling Technologies workshop assembled innovative techniques, explored interesting results obtained by such practices, and provided an ideal forum for sharing ways to push through today's research bottlenecks.

Materials such as the presentations and posters from this year's workshop are available on the 2009 NIGMS Workshop News page on the PSI SGKB.

“Blind” test data for structural bioinformatics

PSI policy requires that all structures must be deposited, for immediate release, upon completion. However, it is also recognized that certain technology development projects could benefit from “blind test” data for assessing the accuracy of new methods before the corresponding structures are released to the public. These include methods for protein structure prediction, as well as hybrid methods that use sparse experimental data in combination with computational methods.

To facilitate the development of such methods, the PSI will allow a limited number of structures (10–12 per center, per year) to be deposited into the PDB with 8-week hold times. In addition, certain data (e.g. NMR chemical shift data or limited numbers of experimental constraints) for these structures will be made available on the public web sites of the corresponding PSI centers. Information about currently available data, along with links to the corresponding center, will be centrally located on the PSI SGKB's See Latest Structures, which is updated weekly.

You can read the full PSI Policy on Structures for Methods Development for more details.

Upcoming meetings

Want to learn more about the PSI SGKB? Representatives will be available at these upcoming meetings.

ASBMB/Experimental Biology 2009
April 18, 2009 – April 22, 2009
New Orleans (Louisiana), USA

39th Mid-Atlantic Macromolecular Crystallography Meeting
May 28. 2009 – May 30, 2009
College Park (Maryland), USA

17th Annual International Conference on Intelligent Systems for Molecular Biology (ICMB) and 8th European Conference on Computational Biology (ECCB)
June 27, 2009 - July 2, 2009
Stockholm, Sweden

Margaret Gabanyi

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