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Improved molecular replacement by density- and energy-guided protein structure optimization

Author

Listed:
  • Frank DiMaio

    (University of Washington)

  • Thomas C. Terwilliger

    (Los Alamos National Laboratory)

  • Randy J. Read

    (University of Cambridge, Cambridge Institute for Medical Research)

  • Alexander Wlodawer

    (Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick)

  • Gustav Oberdorfer

    (Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3)

  • Ulrike Wagner

    (Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3)

  • Eugene Valkov

    (University of Cambridge)

  • Assaf Alon

    (Weizmann Institute of Science)

  • Deborah Fass

    (Weizmann Institute of Science)

  • Herbert L. Axelrod

    (Joint Center for Structural Genomics and SSRL, SLAC National Accelerator Laboratory)

  • Debanu Das

    (Joint Center for Structural Genomics and SSRL, SLAC National Accelerator Laboratory)

  • Sergey M. Vorobiev

    (Northeast Structural Genomics Consortium, Columbia University)

  • Hideo Iwaï

    (University of Helsinki, Institute of Biotechnology)

  • P. Raj Pokkuluri

    (Argonne National Laboratory)

  • David Baker

    (University of Washington)

Abstract

Protein structures you can bank on With more than 60,000 structures now available in the Protein Data Bank, it is frequently possible to create homology-based models to help solve the X-ray crystal structure of a protein with an unknown three-dimensional structure. But current techniques usually fail when the protein of interest has less than 30% sequence identity to known structures. A new method able to overcome this limitation has been developed and used successfully in 8 of 13 X-ray diffraction datasets that could not be solved by conventional means. The new method should allow rapid structure determination without experimental phase information for more than half the cases in which current methods fail, as long as resolution is 3.2 Å or better, with four or fewer copies in the asymmetric unit and the availability of structures of homologous proteins with more than 20% sequence identity.

Suggested Citation

  • Frank DiMaio & Thomas C. Terwilliger & Randy J. Read & Alexander Wlodawer & Gustav Oberdorfer & Ulrike Wagner & Eugene Valkov & Assaf Alon & Deborah Fass & Herbert L. Axelrod & Debanu Das & Sergey M. , 2011. "Improved molecular replacement by density- and energy-guided protein structure optimization," Nature, Nature, vol. 473(7348), pages 540-543, May.
    • Handle: RePEc:nat:nature:v:473:y:2011:i:7348:d:10.1038_nature09964
    DOI: 10.1038/nature09964
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