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 (~ 0.5 μs). A biased simulation had to be used to facilitate the opening, which revealed a possible way for the two catalytic domains to separate. The α-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.

CEITEC Central European Institute of Technology Masaryk University Kamenice 5 625 00 Brno Czech Republic

National Centre for Biomolecular Research Faculty of Science Masaryk University Kamenice 5 625 00 Brno Czech Republic

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J Mol Biol. 2004 Jan 2;335(1):307-19 PubMed

Nucleic Acids Res. 2000 Jan 1;28(1):235-42 PubMed

J Biol Chem. 1989 Jan 15;264(2):675-8 PubMed

Cell Mol Life Sci. 2005 Mar;62(6):685-707 PubMed

Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10037-41 PubMed

Proteins. 2006 Nov 15;65(3):712-25 PubMed

J Chem Theory Comput. 2013 Sep 10;9(9):3878-88 PubMed

Nucleic Acids Res. 2008 Nov;36(19):6109-17 PubMed

J Chem Theory Comput. 2011 Feb 8;7(2):525-37 PubMed

Nat Struct Biol. 1998 Oct;5(10):910-6 PubMed

Proteins. 1993 Dec;17(4):412-25 PubMed

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W665-7 PubMed

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W522-5 PubMed

J Biol Chem. 2005 Feb 18;280(7):5605-10 PubMed

Structure. 2001 Feb 7;9(2):133-44 PubMed

J Chem Theory Comput. 2013 Jul 9;9(7):3084-95 PubMed

Gene. 1997 Mar 25;188(1):35-9 PubMed

Annu Rev Biophys Biomol Struct. 2000;29:291-325 PubMed

Phys Biol. 2011 Oct;8(5):056001 PubMed

Biomed Res Int. 2014;2014:304563 PubMed

EMBO J. 2006 May 17;25(10):2219-29 PubMed

J Mol Graph. 1996 Feb;14(1):33-8, 27-8 PubMed

Biophys J. 2009 Apr 8;96(7):2808-22 PubMed

Sci Rep. 2015 Feb 12;5:8425 PubMed

J Phys Chem A. 2006 Jan 19;110(2):548-63 PubMed

Biopolymers. 1996 Mar;38(3):305-20 PubMed

Biophys J. 2007 Jun 1;92(11):3817-29 PubMed

Mol Cell. 2005 Oct 7;20(1):155-66 PubMed

J Biol Chem. 1985 May 25;260(10):6160-6 PubMed

Nucleic Acids Res. 2003 Sep 1;31(17):5108-21 PubMed

Biophys J. 1998 Jul;75(1):422-7 PubMed

Nucleic Acids Res. 1998 Jan 1;26(1):338-50 PubMed

Curr Protoc Protein Sci. 2007 Nov;Chapter 2:Unit 2.9 PubMed