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.
Highlights
Cavities appear in many biological structures (Andrews and Tata, 1971; Martin et al, 1991; Jin and Brennan, 2002; Hartl et al, 2011)
Properties of Cavities in Biological Structures (Dawson et al, 2017; Lewis et al, 2018) and (2) of all 160,233 structures released by the Protein Data Bank (PDB) (Berman et al, 2000) on February 9, 2020, with 148,516 of them corresponding to proteins without any admixture of nucleic acids. In the former case, we calculated the volume of the cavities within each single chain deposited in the CATH database, but if there were several chains of the same protein, we considered only the case with the largest cavity
For each of the analyzed proteins, we determined the position of the largest cavity, its volume VC, and we identified the residues that form the cavity shell
Summary
Cavities appear in many biological structures (Andrews and Tata, 1971; Martin et al, 1991; Jin and Brennan, 2002; Hartl et al, 2011). Cavities are observed in single-domain proteins (Marion et al, 2007), in multimeric protein aggregates, in virus capsids, (Zandi et al, 2004; Zlotnick, 2005; Michel et al, 2006; Cieplak and Robbins, 2010, 2013; Roos et al, 2010), and in still larger complexes, such as the ribosomes. Biological cavities may enclose space completely, as in the majority of icosahedral virus capsids. The closure is not complete since there are openings or connections to the outside solvent. This situation is encountered, e.g., in the Pathogenesis-Related class 10 proteins (PR-10) (Fernandes et al, 2013). The opening is a part of the peptide exit channel
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