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 and Petr KULHÁNEK

Basic information

Original name

Behavior of BsoBI endonuclease in the presence and absence of DNA

Authors

ŠTĚPÁN, Jakub (203 Czech Republic, belonging to the institution), Ivo KABELKA (203 Czech Republic, belonging to the institution), Jaroslav KOČA (203 Czech Republic, belonging to the institution) and Petr KULHÁNEK (203 Czech Republic, guarantor, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 1.335

RIV identification code

RIV/00216224:14310/18:00102342

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1007/s00894-017-3557-8

UT WoS

000422667900034

Keywords in English

Conformational change; Enzyme opening; Molecular dynamics; Metadynamics

Abstract

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.

Links

LM2015085, research and development project

Name: CERIT Scientific Cloud (Acronym: CERIT-SC)

Investor: Ministry of Education, Youth and Sports of the CR, CERIT Scientific Cloud

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

ŠTĚPÁN, Jakub, Ivo KABELKA, Jaroslav KOČA and Petr KULHÁNEK. Behavior of BsoBI endonuclease in the presence and absence of DNA. Journal of Molecular Modeling. New York: Springer, 2018, vol. 24, No 1, p. 22-31. ISSN 1610-2940. Available from: https://dx.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 = {http://dx.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 and Petr KULHÁNEK. Behavior of BsoBI endonuclease in the presence and absence of DNA. \textit{Journal of Molecular Modeling}. New York: Springer, 2018, vol.~24, No~1, p.~22-31. ISSN~1610-2940. Available from: https://dx.doi.org/10.1007/s00894-017-3557-8.

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