Publication details

Behavior of BsoBI endonuclease in the presence and absence of DNA

Authors

ŠTĚPÁN Jakub KABELKA Ivo KOČA Jaroslav KULHÁNEK Petr

Type Article in Periodical
Magazine / Source Journal of Molecular Modeling
MU Faculty or unit

Faculty of Science

Citation
Web https://link.springer.com/article/10.1007%2Fs00894-017-3557-8
Doi http://dx.doi.org/10.1007/s00894-017-3557-8
Keywords Conformational change; Enzyme opening; Molecular dynamics; Metadynamics
Description BsoBI is a type II restriction endonuclease belonging to the EcoRI family. There is only one previously published X-ray structure for this endonuclease: it shows a homodimer of BsoBI completely encircling DNA in a tunnel. In this work, molecular dynamics simulations were employed to elucidate possible ways in which DNA is loaded into this complex prior to its cleavage. We found that the dimer does not open spontaneously when DNA is removed from the complex on the timescale of our simulations (similar to 0.5 mu s). A biased simulation had to be used to facilitate the opening, which revealed a possible way for the two catalytic domains to separate. The alpha-helices connecting the catalytic and helical domains were found to act as a hinge during the separation. In addition, we found that the opening of the BsoBI dimer was influenced by the type of counterions present in the environment. A reference simulation of the BsoBI/DNA complex further showed spontaneous reorganization of the active sites due to the binding of solvent ions, which led to an active-site structure consistent with other experimental structures of type II restriction endonucleases determined in the presence of metal ions.
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