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Related Experiment Videos

TASSER-based refinement of NMR structures.

Seung Yup Lee1, Yang Zhang, Jeffrey Skolnick

  • 1Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York, USA.

Proteins
|February 4, 2006
PubMed
Summary

The TASSER algorithm refines Nuclear Magnetic Resonance (NMR) protein structures, often improving their accuracy toward X-ray crystallography counterparts. This computational method aids in enhancing structural biology data quality.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Nuclear Magnetic Resonance (NMR) and X-ray crystallography are key experimental methods for determining protein structures.
  • Discrepancies often exist between structures determined by NMR and X-ray crystallography.
  • Automatic refinement procedures are sought to bridge these structural differences.

Purpose of the Study:

  • To evaluate the effectiveness of the TASSER structure prediction algorithm in refining NMR-derived protein structures.
  • To assess whether TASSER refinement can move NMR structures closer to their corresponding X-ray structures.
  • To compare TASSER's refinement performance against other methods like RECOORD.

Main Methods:

  • Utilized the TASSER structure prediction algorithm for refinement.

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  • Employed a benchmark dataset of 61 nonhomologous proteins with both NMR and X-ray structures.
  • Compared root-mean-square deviation (RMSD) values between NMR, TASSER-refined, and X-ray structures.

    • Main Results:

    • TASSER refinement shifted the majority (79%) of NMR structures towards their X-ray counterparts.
    • Average RMSD to X-ray structures decreased from 2.080 Å (NMR) to 1.785 Å (TASSER refined).
    • TASSER showed consistent improvement for proteins with initial NMR-X-ray RMSD >2 Å, and comparable results to RECOORD for high-quality NMR structures.

    Conclusions:

    • TASSER serves as a valuable computational tool for improving the quality and accuracy of NMR-derived protein structures.
    • The algorithm demonstrates potential in reconciling structural data obtained from different experimental techniques.
    • Further investigation may be needed for cases with very high initial NMR structure quality.