Behavior of BsoBI endonuclease in the presence and absence of DNA

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F18%3A00102342" target="_blank" >RIV/00216224:14310/18:00102342 - isvavai.cz</a>

Výsledek na webu

<a href="https://link.springer.com/article/10.1007%2Fs00894-017-3557-8" target="_blank" >https://link.springer.com/article/10.1007%2Fs00894-017-3557-8</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/s00894-017-3557-8" target="_blank" >10.1007/s00894-017-3557-8</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Behavior of BsoBI endonuclease in the presence and absence of DNA

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Behavior of BsoBI endonuclease in the presence and absence of DNA

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10600 - Biological sciences

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2018

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Molecular Modeling

ISSN

1610-2940

e-ISSN

—

Svazek periodika

24

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

CZ - Česká republika

Počet stran výsledku

10

Strana od-do

22

Kód UT WoS článku

000422667900034

EID výsledku v databázi Scopus

2-s2.0-85039046647