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Chwastyk M, Panek EA, Malinowski J, et al. Properties of Cavities in Biological Structures-A Survey of the Protein Data Bank. Front Mol Biosci. 2020;7:591381doi: 10.3389/fmolb.2020.591381.
Chwastyk, M., Panek, E. A., Malinowski, J., Jaskólski, M., & Cieplak, M. (2020). Properties of Cavities in Biological Structures-A Survey of the Protein Data Bank. Frontiers in molecular biosciences, 7591381. https://doi.org/10.3389/fmolb.2020.591381
Chwastyk, Mateusz, et al. "Properties of Cavities in Biological Structures-A Survey of the Protein Data Bank." Frontiers in molecular biosciences vol. 7 (2020): 591381. doi: https://doi.org/10.3389/fmolb.2020.591381
Chwastyk M, Panek EA, Malinowski J, Jaskólski M, Cieplak M. Properties of Cavities in Biological Structures-A Survey of the Protein Data Bank. Front Mol Biosci. 2020 Nov 06;7:591381. doi: 10.3389/fmolb.2020.591381. eCollection 2020. PMID: 33240933; PMCID: PMC7677499.
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Front Mol Biosci. 2020 Nov 06;7:591381. doi: 10.3389/fmolb.2020.591381. eCollection 2020.

Properties of Cavities in Biological Structures-A Survey of the Protein Data Bank.

Frontiers in molecular biosciences

Mateusz Chwastyk, Ewa A Panek, Jan Malinowski, Mariusz Jaskólski, Marek Cieplak

Affiliations

  1. Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
  2. Department of Biometry, Warsaw University of Life Sciences, Warsaw, Poland.
  3. Faculty of Physics, University of Warsaw, Warsaw, Poland.
  4. Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Pozna?, Poland.
  5. Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Pozna?, Poland.

PMID: 33240933 PMCID: PMC7677499 DOI: 10.3389/fmolb.2020.591381

Abstract

We performed a PDB-wide survey of proteins to assess their cavity content, using the SPACEBALL algorithm to calculate the cavity volumes. In addition, we determined the hydropathy character of the cavities. We demonstrate that the cavities of most proteins are hydrophilic, but smaller proteins tend to have cavities with hydrophobic walls. We propose criteria for distinguishing between cavities and pockets, and single out proteins with the largest cavities.

Copyright © 2020 Chwastyk, Panek, Malinowski, Jaskólski and Cieplak.

Keywords: cavity volume calculation; hydrophobicity; plant pathogenesis-related proteins; proteins; signaling proteins; transport proteins

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