Origin of mechanical strength of bovine carbonic anhydrase studied by molecular dynamics simulation

Biophysical Journal
Satoko OhtaAtsushi Ikai

Abstract

The forced unfolding process of bovine carbonic anhydrase II (BCA II) was examined at the atomic level by the molecular dynamics (MD) simulation. By force spectroscopy, experimentally obtained force-extension curves (F-E curves) showed a prominent force peak after 50 nm extension. F-E curves obtained from our simulation had three force peaks appearing after extensions of 10-17 nm, 40 nm, and 53 nm, each signifying a brittle fracture of a specific local structure. Upon undergoing the final fracture at 53 nm of extension, the entire molecule became a single flexible chain and was further extended to its full theoretical length, almost as a random coil. This feature of the 53-nm peak strongly suggested its close correspondence to the experimentally observed force peak at approximately 60-nm extension. The 53-nm peak in the molecular dynamics simulation corresponded to the unfolding process of the beta-sheeted core that includes zinc-coordinating histidine residues. These results suggest that the structural change occurring at 50-60 nm in atomic force microscopy experiments corresponded to the destruction of the zinc coordination site.

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Citations

Mar 18, 2006·Naunyn-Schmiedeberg's Archives of Pharmacology·Alexej Kedrov, Daniel J Müller
Jun 26, 2007·The Protein Journal·Shahrokh SafarianNader Sheibani
Jun 12, 2012·Proceedings of the National Academy of Sciences of the United States of America·Joanna I SułkowskaAndrzej Stasiak
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Jun 22, 2006·Journal of Biochemistry·Shahrokh SafarianAli Akbar Moosavi-Movahedi
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Sep 23, 2010·Journal of the American Chemical Society·Joanna I SułkowskaMarek Cieplak

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