Behavior of BsoBI endonuclease in the presence and absence of
DNA

J 2018

Behavior of BsoBI endonuclease in the presence and absence of DNA

ŠTĚPÁN, Jakub; Ivo KABELKA; Jaroslav KOČA a Petr KULHÁNEK

Základní údaje

Originální název

Behavior of BsoBI endonuclease in the presence and absence of DNA

Autoři

ŠTĚPÁN, Jakub; Ivo KABELKA ; Jaroslav KOČA a Petr KULHÁNEK

Vydání

Journal of Molecular Modeling, New York, Springer, 2018, 1610-2940

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 1.335

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/18:00102342

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

Conformational change; Enzyme opening; Molecular dynamics; Metadynamics

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 23. 4. 2024 11:02, Mgr. Michal Petr

Anotace

V originále

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.

Návaznosti

LM2015085, projekt VaV

Název: CERIT Scientific Cloud (Akronym: CERIT-SC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CERIT Scientific Cloud

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

ŠTĚPÁN, Jakub; Ivo KABELKA; Jaroslav KOČA a Petr KULHÁNEK. Behavior of BsoBI endonuclease in the presence and absence of DNA. Journal of Molecular Modeling. New York: Springer, 2018, roč. 24, č. 1, s. 22-31. ISSN 1610-2940. Dostupné z: https://doi.org/10.1007/s00894-017-3557-8.

@article{1409455,
   author = {Štěpán, Jakub and Kabelka, Ivo and Koča, Jaroslav and Kulhánek, Petr},
   article_location = {New York},
   article_number = {1},
   doi = {https://doi.org/10.1007/s00894-017-3557-8},
   keywords = {Conformational change; Enzyme opening; Molecular dynamics; Metadynamics},
   language = {eng},
   issn = {1610-2940},
   journal = {Journal of Molecular Modeling},
   title = {Behavior of BsoBI endonuclease in the presence and absence of DNA},
   url = {https://link.springer.com/article/10.1007%2Fs00894-017-3557-8},
   volume = {24},
   year = {2018}
}

TY  - JOUR
ID  - 1409455
AU  - Štěpán, Jakub - Kabelka, Ivo - Koča, Jaroslav - Kulhánek, Petr
PY  - 2018
TI  - Behavior of BsoBI endonuclease in the presence and absence of DNA
JF  - Journal of Molecular Modeling
VL  - 24
IS  - 1
SP  - 22
EP  - 22
PB  - Springer
SN  - 16102940
KW  - Conformational change
KW  - Enzyme opening
KW  - Molecular dynamics
KW  - Metadynamics
UR  - https://link.springer.com/article/10.1007%2Fs00894-017-3557-8
N2  - 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.
ER  -

ŠTĚPÁN, Jakub; Ivo KABELKA; Jaroslav KOČA a Petr KULHÁNEK. Behavior of BsoBI endonuclease in the presence and absence of DNA. \textit{Journal of Molecular Modeling}. New York: Springer, 2018, roč.~24, č.~1, s.~22-31. ISSN~1610-2940. Dostupné z: https://doi.org/10.1007/s00894-017-3557-8.

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