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Related Experiment Videos

Protein structural alignments and functional genomics.

J A Irving1, J C Whisstock, A M Lesk

  • 1Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia.

Proteins
|January 11, 2001
PubMed
Summary
This summary is machine-generated.

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Predicting protein function from structure is challenging. This study shows that analyzing aligned substructures can identify protein active sites, even for proteins with unknown functions.

Area of Science:

  • Computational molecular biology
  • Structural biology
  • Bioinformatics

Background:

  • Structural genomics generates many protein structures with unknown functions.
  • Predicting protein function from 3D structure is a significant computational challenge.
  • Homologous proteins often share conserved active site conformations.

Purpose of the Study:

  • To develop a method for predicting protein function from structure.
  • To identify conserved active sites in homologous proteins.
  • To correlate structural alignment parameters with protein function prediction.

Main Methods:

  • Analyzing the relationship between size and goodness-of-fit of aligned substructures in homologous proteins.
  • Calculating root-mean-square deviation (RMSD) as a function of aligned residues.

Related Experiment Videos

  • Examining the exponential and linear variation of RMSD for different substructure sizes.

    • Main Results:

    • The exponent of RMSD dependence for large common substructures correlates with core RMSD, reconciling alignment methods.
    • Small common substructures, when reduced, define active sites.
    • This method can suggest active site locations in homologous proteins.

    Conclusions:

    • Structural alignment analysis provides a robust method for identifying protein active sites.
    • This approach aids in predicting protein function, especially for novel structures.
    • The findings bridge structural alignment procedures and functional site identification.