title: The volume of cavities in proteins and virus capsids.
abstract: An improved algorithm for the calculation of the volume of internal cavities within protein structures and virus capsids as well as the volumes occupied by single amino acid residues were presented. The geometrical approach was based on atomic van der Waals radii. The results obtained with two sets of the radii, those proposed by Pauling and those determined by Tsai et al were compared. The main improvement compared with our previous approach is a more elaborate treatment of the regions at the very boundary of the cavities, which yields a more accurate volume estimate. The cavity volume of a number of Plant Pathogenesis-Related proteins of class 10 (PR-10) were reevaluated and the volumes and other geometrical parameters for about 400 capsids of icosahedral viruses were reported. Using the same approach the volumes of amino acid residues in polypeptides as mean values averaged over multiple conformations of the side chain were also estimated. Proteins 2016; 84:1275-1286. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Institute of Physics, Polish Academy of Sciences, 02-668, Warsaw, Poland.
authors.forename: Mateusz
authors.initials: M
authors.lastname: Chwastyk
authors.affiliation: Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.|Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, 61-614, Poznan, Poland.
authors.forename: Mariusz
authors.initials: M
authors.lastname: Jaskolski
authors.affiliation: Institute of Physics, Polish Academy of Sciences, 02-668, Warsaw, Poland.
authors.forename: Marek
authors.initials: M
authors.lastname: Cieplak
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D002213:Capsid / Q000737:chemistry* / Q000648:ultrastructure; D036022:Capsid Proteins / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D013816:Thermodynamics; D014780:Viruses / Q000737:chemistry* / Q000145:classification / Q000648:ultrastructure
chemical_list: D000596:Amino Acids; D036022:Capsid Proteins
keywords: cavity volume calculation; plant pathogenesis-related proteins; van der Waals volume; virus capsids; volumes of amino acids