Crystal structure of a monomeric retroviral protease solved by protein folding game players

Journal name:
Nature Structural & Molecular Biology
Volume:
18,
Pages:
1175–1177
Year published:
DOI:
doi:10.1038/nsmb.2119
Received
Accepted
Published online
Corrected online

Following the failure of a wide range of attempts to solve the crystal structure of M-PMV retroviral protease by molecular replacement, we challenged players of the protein folding game Foldit to produce accurate models of the protein. Remarkably, Foldit players were able to generate models of sufficient quality for successful molecular replacement and subsequent structure determination. The refined structure provides new insights for the design of antiretroviral drugs.

At a glance

Figures

  1. Successful CASP9 predictions by the Foldit Void Crushers Group.
    Figure 1: Successful CASP9 predictions by the Foldit Void Crushers Group.

    (a) Starting from the fourth-ranked Rosetta Server model (red) for CASP9 target T0581, the Foldit Void Crushers Group (yellow) generated a model that was closer to the crystal structure later determined (blue). (b) Starting from a modified Rosetta model built using the Alignment Tool (red), the Foldit Void Crushers Group generated a model (yellow) considerably closer to the later determined crystal structure (blue). Images were produced using PyMOL software (http://www.pymol.org).

  2. M-PMV retroviral protease structure improvement by the Foldit Contenders Group.
    Figure 2: M-PMV retroviral protease structure improvement by the Foldit Contenders Group.

    (a) Progress of structure refinement over the first 16 d of game play. The x axis shows progression in time, and the y axis shows the Phaser log-likelihood (LLG) of each model in a near-native orientation. To identify a solution as correct by molecular replacement using Phaser, the model must have an LLG better than the best random models. The distribution of these best random predictions is indicated by the intensity of the pale blue band. (Because almost all the models are too poor to allow correct placement in the unit cell, Phaser LLGs are calculated after optimal superposition of each model onto the solved crystal structure and rigid-body optimization.) (b) Starting from a quite inaccurate NMR model (red), Foldit player spvincent generated a model (yellow) considerably more similar to the later determined crystal structure (blue) in the β-strand region. (c) Starting from spvincent's model, Foldit player grabhorn generated a model (magenta) considerably closer to the crystal structure with notable improvement of side-chain conformations in the hydrophobic core. (d) Foldit player mimi made additional improvements (in the loop region at the top left) and generated a model (green) of sufficient accuracy to provide an unambiguous molecular replacement solution which allowed rapid determination of the ultimate crystal structure (blue).

  3. CPK representation of retropepsin surface.
    Figure 3: CPK representation of retropepsin surface.

    (a) The surface of HIV-1 PR protomer extracted from the dimeric molecule (PDB 3hvp), as seen from the direction of the removed dimerization partner. (b) M-PMV PR monomer shown in the same orientation and scale. In this view, the N and C termini (missing in M-PMV PR) are at the bottom, and the flap loop is at the top. The active-site cavity (ASC) is clearly seen between the flap and the body of the HIV-1 PR molecule. In M-PMV PR, the cavity is completely covered by the curled flap.

Accession codes

Primary accessions

Protein Data Bank

Referenced accessions

Protein Data Bank

Change history

Corrected online 20 December 2011
In the version of this article initially published, the location for the Academy of Sciences of the Czech Republic was given as Poznan. The Academy is in Prague. The error has been corrected in the HTML and PDF versions of the article.

Author information

Affiliations

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

    • Firas Khatib,
    • Frank DiMaio,
    • James Thompson &
    • David Baker
  2. Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA.

    • Seth Cooper &
    • Zoran Popović
  3. Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.

    • Maciej Kazmierczyk,
    • Miroslaw Gilski,
    • Szymon Krzywda &
    • Mariusz Jaskolski
  4. Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.

    • Miroslaw Gilski &
    • Mariusz Jaskolski
  5. Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.

    • Helena Zabranska &
    • Iva Pichova
  6. Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.

    • David Baker

Consortia

  1. Foldit Contenders Group

  2. Foldit Void Crushers Group

Contributions

F.K., F.D., S.C., J.T., Z.P. and D.B. contributed to the development and analysis of Foldit and to the writing of the manuscript; the F.C.G. and F.V.C.G. contributed through their gameplay, which generated the results for this manuscript; M.K. grew the crystals and collected X-ray diffraction data; M.G. processed X-ray data and analyzed the structure; S.K. refined the structure; H.Z. cloned, expressed and purified the protein; I.P. designed and coordinated the biochemical experiments, and contributed to writing the manuscript; M.J. coordinated the crystallographic study, analyzed the results and contributed to writing the manuscript.

Competing financial interests

The authors declare no competing financial interests.

Corresponding author

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Supplementary information

PDF files

  1. Supplementary Text and Figures (1M)

    Supplementary Figures 1–3, Supplementary Table 1 and Supplementary Discussion

Additional data