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Protein surface analysis for function annotation in high-throughput structural genomics pipeline.

T Andrew Binkowski1, Andrzej Joachimiak, Jie Liang

  • 1Department of Bioengineering, The University of Illinois, 851 South Morgan St., Room 218, Chicago, IL 60607, USA. jliang@uic.edu.

Protein Science : a Publication of the Protein Society
|December 3, 2005
PubMed
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Structural genomics efforts yield many novel protein structures. A new method, pvSOAR, analyzes protein surfaces to uncover hidden functional relationships for uncharacterized proteins.

Area of Science:

  • Structural biology
  • Bioinformatics
  • Protein science

Background:

  • Structural genomics (SG) initiatives rapidly determine novel protein structures.
  • Many SG proteins lack known biochemical or cellular functions.
  • Traditional methods struggle to assign functions to uncharacterized proteins.

Purpose of the Study:

  • To introduce and apply a novel computational method, pvSOAR (pocket and void Surface of Amino Acid Residues).
  • To infer biochemical functions for uncharacterized proteins from structural genomics.
  • To identify novel functional relationships using protein surface comparisons.

Main Methods:

  • Development of pvSOAR for comparing geometrically defined pockets and voids on protein surfaces.
  • Application of pvSOAR to several structural genomics proteins, including YecM, BioH, RpiB, and various CBS domain proteins.

Related Experiment Videos

  • Analysis of protein surface features to infer functional information.

    • Main Results:

    • pvSOAR successfully detected previously unrecognized functional relationships.
    • The method provided insights into the potential functions of studied structural genomics proteins.
    • Novel functional connections were identified between protein surface features.

    Conclusions:

    • pvSOAR is a valuable tool for functional inference in structural genomics.
    • The method overcomes limitations of traditional sequence and structure-based analyses.
    • pvSOAR aids in assigning function to uncharacterized proteins, expanding biological understanding.