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 b-sheet and a variable a-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.

The volume of cavities in proteins and virus capsids

“…The gray‐walled squares marked with a cross indicate the sites (i.e., grid points) that can house a probing particle (e.g., a molecule of water, shown in blue) without touching the protein. The crossed squares within the protein cavity contributed to the cavity volume in the previous algorithm . In the present algorithm, we also count the thick squares without crosses.…”

“…This characteristic fold is termed PR‐10 fold or Betv1 fold. In a previous study, we used molecular dynamics simulations and a coarse‐grained model to demonstrate that their physical properties and the outside surface, S out , are very similar despite significant variations in the volume, V c , of the cavities . The physical properties that were investigated included thermodynamic and mechanical stabilities, as well as the kinetics of folding.…”

“…We have recently proposed a novel algorithm, called SPACEBALL, in which an effective cavity‐closure procedure was implemented automatically and which allowed the determination of V c with high accuracy, by finding the location of the cavity in an unbiased way. The idea is that one surrounds the protein under study by a rectangular parallelepiped (box) at various orientations with respect to the protein.…”

Criteria for folding in structure-based models of proteins

“…[22][23][24]. Furthermore, there are many Go-model-based proteins for which the supposedly well folding chains are technically bad folders as they have a T f that is smaller or nearly equal to the corresponding value of T g .…”

Overexpression of RSOsPR10, a root-specific rice PR10 gene, confers tolerance against drought stress in rice and drought and salt stresses in bentgrass

“…Furthermore, a Bet v1-superfamily has been defined based on protein structural similarities (Radauer et al 2008), and includes the PR10 family and the PYR1/PYL1/RCAR family of abscisic acid receptors (Ma et al 2009). This superfamily can be divided into numerous subfamilies with low sequence similarities, but a fold that acts as a versatile scaffold for the binding of bulky hydrophobic ligands is a common structural feature that results in a variety of functions (Fernandes et al 2013;Chwastyk et al 2014). Therefore, PR10 family proteins may have developed diverse tissue-and stage-specific functions in response to multiple environmental challenges.…”