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PRISM: topologically constrained phased refinement for macromolecular crystallography.

D Baker1, C Bystroff, R J Fletterick

  • 1Howard Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, USA.

Acta Crystallographica. Section D, Biological Crystallography
|September 1, 1993
PubMed
Summary

Phase refinement by iterative skeletonization (PRISM) improves protein structure determination by creating a connected atomic skeleton from electron-density maps. This method effectively restores missing phase and amplitude information, even with noisy or incomplete data.

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Area of Science:

  • Structural Biology
  • Crystallography
  • Computational Biology

Background:

  • Accurate phase information is crucial for solving protein structures from electron-density maps.
  • Existing phase refinement methods may struggle with incomplete or inaccurate initial data.
  • Proteins possess inherent structural properties, such as connected linear atomic chains, that can be leveraged.

Purpose of the Study:

  • To describe further developments of the Phase Refinement by Iterative Skeletonization (PRISM) method.
  • To demonstrate PRISM's effectiveness in improving electron-density maps and restoring phase information.
  • To evaluate PRISM's performance against other methods like solvent flattening, especially in challenging scenarios.

Main Methods:

  • Development of an iterative skeletonization strategy (PRISM) utilizing protein chain linearity.

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  • Construction of a connected atomic skeleton from an initial electron-density map using a modified Greer's algorithm.
  • Iterative refinement involving Fourier transformation of skeletonized maps to generate new phases.

    • Main Results:

    • PRISM successfully generated interpretable electron-density maps from limited initial structural information.
    • The method demonstrated robustness against random noise and missing data, outperforming solvent flattening.
    • PRISM could restore both missing phase and amplitude information, enabling a 'free R factor'-like optimization test.

    Conclusions:

    • PRISM is a powerful phase refinement strategy that effectively utilizes the linear and connected nature of protein structures.
    • The method shows significant advantages over solvent flattening for improving electron-density maps, particularly with sparse data.
    • PRISM's ability to restore missing data and its optimization potential make it valuable for complex crystallographic problems.