Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Poster Session I

7 – POS Board 7 PR10 - Proteins with Cavities Mateusz Chwastyk 1 , Mariusz Jaskólski 2,3 , Marek Cieplak 1 . 1 Institute of Physics PAS, Warsaw, Poland, 2 Center for Biocrystallographic Research, Poznań, Poland, 3 Faculty of Chemistry, A. Mickiewicz University, Poznań, Poland. 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 ß-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.

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