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Contact order and ab initio protein structure prediction.

Richard Bonneau1, Ingo Ruczinski, Jerry Tsai

  • 1Department of Biochemistry, University of Washington, Seattle 98195, USA.

Protein Science : a Publication of the Protein Society
|July 27, 2002
PubMed
Summary

Protein folding rates correlate with contact order (CO), impacting ab initio structure prediction. Simulations show a bias against high CO proteins, suggesting improved sampling with more computing power is needed for accurate predictions.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein science

Background:

  • Experimental protein folding studies aim to improve computational structure prediction.
  • Recent years have seen limited connection between experimental folding studies and computational prediction.
  • The relationship between protein folding rates and native structure contact order (CO) is explored.

Purpose of the Study:

  • To investigate the implications of protein folding rates and contact order on ab initio protein structure prediction.
  • To analyze biases in Rosetta ab initio folding simulations regarding protein contact order.
  • To identify strategies for improving protein structure prediction accuracy, particularly for complex proteins.

Main Methods:

  • Utilized Rosetta ab initio folding simulations.

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  • Analyzed simulation output for biases in structures based on contact order.
  • Examined failure cases from the CASP4 (Critical Assessment of Structure Prediction) experiment.
  • Proposed strategies involving increased simulation numbers and selective filtering.

    • Main Results:

    • Rosetta simulations showed a lack of high CO structures and an excess of low CO structures.
    • Ab initio prediction failures in CASP4 predominantly involved high CO structures.
    • Increased simulations and filtering offered modest improvements in prediction quality.
    • High CO proteins require significantly more computational resources for thorough conformational sampling.

    Conclusions:

    • The contact order of native structures significantly impacts ab initio protein structure prediction.
    • Current simulation methods exhibit a bias against predicting high CO proteins.
    • Enhanced high-performance computing is crucial for accurately predicting complex protein structures.
    • Simulation convergence can serve as an indicator for the need for improved sampling of high CO conformations.
    • Observed low CO structures in simulations may resemble precursors to amyloid formation.