Origin of mechanical strength of bovine carbonic anhydrase studied by molecular dynamics simulation.
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.
Ohta
Satoko
S
Laboratory of Biodynamics, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan.
Alam
Mohammad Taufiq
MT
Arakawa
Hideo
H
Ikai
Atsushi
A
D000818:Animals; D002256:Carbonic Anhydrases / Q000737:chemistry* / Q000648:ultrastructure*; D002417:Cattle; D003198:Computer Simulation; D004548:Elasticity; D008846:Micromanipulation / Q000379:methods*; D018625:Microscopy, Atomic Force / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D011489:Protein Denaturation; D013314:Stress, Mechanical; D013329:Structure-Activity Relationship; D013718:Tensile Strength
D002256:Carbonic Anhydrases