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Related Experiment Videos

Finding functional sites in structural genomics proteins.

Alexander Stark1, Alexander Shkumatov, Robert B Russell

  • 1EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Structure (London, England : 1993)
|August 7, 2004
PubMed
Summary
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Comparing protein structures and their functional sites helps assign functions to uncharacterized proteins, even those with novel folds. This method aids structural genomics by identifying potential protein functions and binding sites.

Area of Science:

  • Structural biology
  • Proteomics
  • Bioinformatics

Background:

  • Structural genomics projects often yield structures of uncharacterized proteins.
  • Determining protein function is crucial for understanding biological processes.
  • Traditional function assignment relies on sequence similarity, which can be limited.

Purpose of the Study:

  • To assess the applicability of functional site comparison for assigning function to proteins.
  • To identify novel protein functions using structural information.
  • To provide a resource for structure-based function inference.

Main Methods:

  • Analysis of 157 proteins from structural genomics initiatives.
  • Structure alignment to identify similarities.

Related Experiment Videos

  • Comparison of local functional sites involving key residues.
  • Investigating proteins with novel folds.

    • Main Results:

    • Functional site comparison bolstered confidence in function predictions for 17 proteins.
    • For 12 proteins with novel folds, this method suggested functions, including a phosphotyrosine binding site and a ribose isomerase active site.
    • The approach is applied weekly to new structures.

    Conclusions:

    • Functional site comparison is a valuable method for inferring protein function, especially for proteins lacking sequence similarity or possessing novel folds.
    • This strategy complements traditional structure-based function assignment methods.
    • The developed approach provides a valuable resource for the scientific community.