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Related Experiment Videos

Target selection and deselection at the Berkeley Structural Genomics Center.

John-Marc Chandonia1, Sung-Hou Kim, Steven E Brenner

  • 1Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

Proteins
|November 9, 2005
PubMed
Summary
This summary is machine-generated.

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The Berkeley Structural Genomics Center strategically selected protein targets for Mycoplasma pathogens, significantly advancing structural biology coverage with a focused approach. Their efforts demonstrate the impact of efficient target selection in structural genomics.

Area of Science:

  • Structural Biology
  • Genomics
  • Proteomics
  • Mycoplasma Pathogens

Background:

  • The Berkeley Structural Genomics Center (BSGC) aims to structurally characterize proteins from Mycoplasma genitalium and M. pneumoniae, two related pathogens.
  • Protein structure determination is crucial for understanding pathogen biology and developing therapeutics.

Purpose of the Study:

  • To report on the target selection and deselection process at BSGC.
  • To assess the impact of BSGC's solved structures on proteome-wide structure prediction coverage.
  • To project the potential increase in structural annotation and modeling accuracy for Mycoplasma proteomes.

Main Methods:

  • Multi-stage target selection prioritizing tractable proteins and novel structural information.

Related Experiment Videos

  • Target deselection to avoid redundancy with existing structural data.
  • Analysis of BSGC's contribution to Mycoplasma protein fold assignment and proteome modeling.
  • Utilizing public databases like TargetDB and PEPCdb for data dissemination.

    • Main Results:

    • BSGC solved 69 structures by July 2004, contributing significantly to Mycoplasma structural genomics.
    • BSGC's structures enabled the first reliable fold assignment for 24 M. pneumoniae and 21 M. genitalium proteins.
    • Despite contributing <1% of worldwide structures, BSGC's focused strategy yielded substantial coverage increases.

    Conclusions:

    • A focused target selection strategy in structural genomics is highly effective.
    • Completion of BSGC's targets could increase M. pneumoniae fold assignment to 80% and modeling to 64%.
    • Further structural annotation and modeling of M. genitalium proteome is expected with remaining targets.