title: Structure-based analysis of thermodynamic and mechanical properties of cavity-containing proteins--case study of plant pathogenesis-related proteins of class 10.
abstract: We provide theoretical comparisons of the physical properties of eighteen proteins with the pathogenesis-related proteins of class 10 (PR-10) fold, which is characterized by a large hydrophobic cavity enclosed between a curved β-sheet and a variable α-helix. Our novel algorithm to calculate the volume of internal cavities within protein structures is used to demonstrate that, although the sizes of the cavities of the investigated PR-10 proteins vary significantly, their other physical properties, such as thermodynamic and mechanical parameters or parameters related to folding, are very close. The largest variations (in the order of 20%) are predicted for the optimal folding times. We show that, on squeezing, the PR-10 proteins behave differently from typical virus capsids.
authors.affiliation: Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
authors.forename: Mateusz
authors.initials: M
authors.lastname: Chwastyk
authors.forename: Mariusz
authors.initials: M
authors.lastname: Jaskolski
authors.forename: Marek
authors.initials: M
authors.lastname: Cieplak
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D020134:Catalytic Domain; D057927:Hydrophobic and Hydrophilic Interactions; D008962:Models, Theoretical; D010940:Plant Proteins / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D010940:Plant Proteins; D011506:Proteins; C053376:pathogenesis-related proteins, plant
keywords: cavity volume calculation; ligand-binding cavity; plant pathogenesis-related proteins; protein squeezing; protein stretching