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Automatic protein structure solution from weak X-ray data

Author

Listed:
  • Pavol Skubák

    (Leiden University)

  • Navraj S. Pannu

    (Leiden University)

Abstract

Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 Å RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing.

Suggested Citation

  • Pavol Skubák & Navraj S. Pannu, 2013. "Automatic protein structure solution from weak X-ray data," Nature Communications, Nature, vol. 4(1), pages 1-6, December.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3777
    DOI: 10.1038/ncomms3777
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    Cited by:

    1. Guillaume Tetreau & Michael R. Sawaya & Elke Zitter & Elena A. Andreeva & Anne-Sophie Banneville & Natalie A. Schibrowsky & Nicolas Coquelle & Aaron S. Brewster & Marie Luise Grünbein & Gabriela Nass , 2022. "De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    2. Gergely N. Nagy & Xiao-Feng Zhao & Richard Karlsson & Karen Wang & Ramona Duman & Karl Harlos & Kamel El Omari & Armin Wagner & Henrik Clausen & Rebecca L. Miller & Roman J. Giger & E. Yvonne Jones, 2024. "Structure and function of Semaphorin-5A glycosaminoglycan interactions," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Martin Hagan & Genady Pankov & Ramses Gallegos-Monterrosa & David J. Williams & Christopher Earl & Grant Buchanan & William N. Hunter & Sarah J. Coulthurst, 2023. "Rhs NADase effectors and their immunity proteins are exchangeable mediators of inter-bacterial competition in Serratia," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
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    5. Jinzhu Zhang & Minghai Tang & Yujie Chen & Dan Ke & Jie Zhou & Xinyu Xu & Wenxian Yang & Jianxiong He & Haohao Dong & Yuquan Wei & James H. Naismith & Yi Lin & Xiaofeng Zhu & Wei Cheng, 2021. "Catalytic flexibility of rice glycosyltransferase OsUGT91C1 for the production of palatable steviol glycosides," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    6. Emma J. Banks & Mauricio Valdivia-Delgado & Jacob Biboy & Amber Wilson & Ian T. Cadby & Waldemar Vollmer & Carey Lambert & Andrew L. Lovering & R. Elizabeth Sockett, 2022. "Asymmetric peptidoglycan editing generates cell curvature in Bdellovibrio predatory bacteria," Nature Communications, Nature, vol. 13(1), pages 1-15, December.

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