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

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...

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Autores principales: Chwastyk, Mateusz, Panek, Ewa A., Malinowski, Jan, Jaskólski, Mariusz, Cieplak, Marek
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Molecular Biosciences
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7677499/
https://www.ncbi.nlm.nih.gov/pubmed/33240933
http://dx.doi.org/10.3389/fmolb.2020.591381
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author Chwastyk, Mateusz
Panek, Ewa A.
Malinowski, Jan
Jaskólski, Mariusz
Cieplak, Marek
author_facet Chwastyk, Mateusz
Panek, Ewa A.
Malinowski, Jan
Jaskólski, Mariusz
Cieplak, Marek
author_sort Chwastyk, Mateusz
collection PubMed
description 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.
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spelling pubmed-76774992020-11-24 Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank Chwastyk, Mateusz Panek, Ewa A. Malinowski, Jan Jaskólski, Mariusz Cieplak, Marek Front Mol Biosci Molecular Biosciences 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. Frontiers Media S.A. 2020-11-06 /pmc/articles/PMC7677499/ /pubmed/33240933 http://dx.doi.org/10.3389/fmolb.2020.591381 Text en Copyright © 2020 Chwastyk, Panek, Malinowski, Jaskólski and Cieplak. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Chwastyk, Mateusz
Panek, Ewa A.
Malinowski, Jan
Jaskólski, Mariusz
Cieplak, Marek
Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank
title Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank
title_full Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank
title_fullStr Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank
title_full_unstemmed Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank
title_short Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank
title_sort properties of cavities in biological structures—a survey of the protein data bank
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7677499/
https://www.ncbi.nlm.nih.gov/pubmed/33240933
http://dx.doi.org/10.3389/fmolb.2020.591381
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