research advances
April 2009 news
PSI in the Spotlight
PSI-SGKB [doi:10.1038/nw_psisgkb.2009.22]
This column presents announcements and other notable news related to the Protein Structure Initiative.
John Norvell, director of the PSI, retires; Peter Preusch to take the lead
John Norvell, who directed the Protein Structure Initiative and oversaw structural biology grants at NIH’s National Institute of General Medical Sciences (NIGMS) for more than 30 years, retired on 2 March. For the past decade, he coordinated the research of 23 collaborative PSI teams that created structure-determination pipelines and new technologies to solve and study more than 3,500 protein shapes.
“John has worked extremely hard to turn NIGMS’s largest project into an incredible resource for the biomedical research community, and he has helped transition it to what it will be in the future,” said Catherine Lewis, director of the NIGMS Division of Cell Biology and Biophysics, which houses the PSI. “It’s hard to imagine anyone filling his shoes in quite the same way.”
Peter Preusch will serve as acting director of the PSI, including its next PSI:Biology phase. At NIH, Preusch has overseen grants in chemistry, biochemistry, pharmacology and biophysics, and he leads the NIH Roadmap structural biology working group initiative.
To read more, see an article from the NIH record.
Structural genomics largest contributor of novel structural leverage
With more than 56,000 protein structures available in the Protein Data Bank (PDB), this number still represents less than 1% of the total number of protein sequences (over 7 million) cataloged in the current release of the UniProt protein knowledgebase. If we are to have a better understanding of protein function and protein evolution, strategies are needed to ensure that the range of protein structures in the protein universe is more adequately covered. Structural genomics is a hypothesis-generating field that aims to increase our knowledge of protein space by studying families of similar protein sequences and making sure that each has at least one experimentally determined structural ‘representative’. This representative can then be leveraged for computational comparative modeling studies, which can more quickly give clues to the structures and functions of the rest of the sequences within the family.
Recently, the PSI assessed how well it was doing in generating modeling leverage, and found that its target-selection strategies have indeed made a measurable impact in novel structure coverage, thus increasing leverage. Nair et al. explain that although only a small number of targeted protein families (of unknown function) have yielded experimental structures, that small number still assisted in the calculation of more than 300,000 new reliable protein-structure models. World-wide structural genomics efforts have contributed 18% of the total number of protein structures in the PDB, with the PSI centers contributing half of these. At the rates at which the structural genomics centers are solving ‘representatives’, it was estimated that nearly all of the protein space could be covered (experimentally or theoretically) within the next two decades.
To read more,
Structural genomics is the largest contributor of novel structural leverage
R. Nair, et al.
J Struct Funct Genomics (2009) 10:181-191.
[doi:10.1007/s10969-008-9055-6]
To read more articles about the PSI, visit the About PSI section of the SGKB Research Library.
Upcoming meetings
Want to learn more about the PSI SGKB? Representatives will be available at these upcoming meetings.
ASBMB/Experimental Biology 2009
18 April, 2009–22 April, 2009
New Orleans (Louisiana), USA
39th Mid-Atlantic Macromolecular Crystallography Meeting
28 May, 2009–30 May, 2009
College Park (Maryland), USA
17th Annual International Conference on Intelligent Systems for Molecular Biology (ICMB) and 8th European Conference on Computational Biology (ECCB)
27 June, 2009–2 July, 2009
Stockholm, Sweden
