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Reply to ‘Defining distance restraints in HADDOCK’

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Fig. 1: Crystal structure of the HOP2–MND1 heterodimer and selected best protein complex models obtained after the final HADDOCK docking step.

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Acknowledgements

Research was funded by the Austrian Science Fund (SFB F34: Z.O.-N., E.R., T.S.). We thank IMP and IMBA for general funding. Molecular graphics and analyses were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311). Images in Chimera were created using Persistence of Vision Raytracer (version 3.6), Persistence of Vision, Pty. Ltd. (2004), retrieved from http://www.povray.org/download/.

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Authors and Affiliations

  1. Mass Spectrometry and Protein Chemistry, Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria

    Zsuzsanna Orbán-Németh, Rebecca Beveridge, Evelyn Rampler, Thomas Stranzl, Otto Hudecz, Johannes Doblmann & Karl Mechtler

  2. Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria

    Zsuzsanna Orbán-Németh, Rebecca Beveridge, Evelyn Rampler, Thomas Stranzl, Otto Hudecz, Johannes Doblmann & Karl Mechtler

  3. Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria

    David M. Hollenstein

  4. Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria

    Evelyn Rampler

  5. Department of Chromosome Biology, Max F. Perutz Laboratories, University of Viehnna, Vienna, Austria

    Peter Schlögelhofer

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  1. Zsuzsanna Orbán-Németh
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  2. Rebecca Beveridge
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  9. Karl Mechtler
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Correspondence to Karl Mechtler.

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Supplementary Figure 1 Crystal structure of the PPP2R1A–PPP2CA complex and selected best protein complex models obtained after the final HADDOCK docking step.

(a) Selected model after re-calculation using the correct distance restraints between residues. This model displayed the best HADDOCK score among the models satisfying all three cross-links and a high XL score. (b) Selected model after re-calculation using the correct distance restraints between specific atoms. This model displayed the best HADDOCK score and XL score. (c) Selected model as presented in our protocol, calculated using the erroneously short distance restraints. (d) Crystal structure of the PPP2R1A–PPP2CA complex: PDB entry 2IAE. (a-d) Cross-links are shown in green. PPP2R1A and PPP2CA are colored light and dark, respectively

Supplementary Figure 2 Crystal structure of the plectin-calmodulin complex and selected best protein complex models obtained after the final HADDOCK docking step.

(a) Selected model after re-calculation using the correct distance restraints between residues. This model displayed the best HADDOCK score and XL score. (b) Selected model after re-calculation using the correct distance restraints between specific atoms. This model displayed the best combination of HADDOCK score and XL score. (c) Selected model as presented in our protocol, calculated using the erroneously short distance restraints. (d) Crystal structure of the plectin-calmodulin complex: PDB ID 4Q57. (a-d) The calmodulin chain is colored red

Supplementary Figure 3 Inter-protein cross-links mapped onto the predicted best model of the plectin-calmodulin complex derived from re-calculation using the corrected distance restraints between residues for HADDOCK.

(a) Compatible and (b) incompatible cross-links are mapped onto the selected model and are colored green and orange, respectively. (a and b) The calmodulin chain is colored red, the plectin chain blue, calcium is shown as green spheres. E14 of calmodulin and R40 of plectin, the residues involved in formation of a salt bridge, are shown as sticks and are colored green and yellow, respectively

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Orbán-Németh, Z., Beveridge, R., Hollenstein, D.M. et al. Reply to ‘Defining distance restraints in HADDOCK’. Nat Protoc 13, 1503–1505 (2018). https://doi.org/10.1038/s41596-018-0018-5

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