Structure-based analysis of thermodynamic and mechanical properties of cavity-containing proteins - case study of plant pathogenesis-related proteins of class 10

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 -sheet and a variable -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.