Skip to main content
SpringerLink
Log in

Behavior of BsoBI endonuclease in the presence and absence of DNA

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2a–f
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  1. Roberts RJ, Macelis D (1998) REBASE—restriction enzymes and methylases. Nucleic Acids Res. 26:338–350. https://doi.org/10.1093/nar/26.1.338

  2. Pingoud A, Fuxreiter M, Pingoud V, Wende W (2005) Type II restriction endonucleases: structure and mechanism. Cell Mol Life Sci CMLS 62:685–707. https://doi.org/10.1007/s00018-004-4513-1

    Article  CAS  Google Scholar 

  3. Ruan H, Lunnen K, Pelletier J, Xu S (1997) Overexpression of BsoBI restriction endonuclease in E-coli, purification of the recombinant BsoBI, and identification of catalytic residues of BsoBI by random mutagenesis. Gene 188:35–39. https://doi.org/10.1016/S0378-1119(96)00773-1

  4. van der Woerd M, Pelletier J, Xu S, Friedman A (2001) Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis. Structure 9:133–144. https://doi.org/10.1016/S0969-2126(01)00564-0

    Article  Google Scholar 

  5. Zhou XE, Wang Y, Reuter M et al (2004) Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. J Mol Biol 335:307–319. https://doi.org/10.1016/j.jmb.2003.10.030

    Article  CAS  Google Scholar 

  6. Golovenko D, Manakova E, Tamulaitiene G et al (2009) Structural mechanisms for the 5′-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. Nucleic Acids Res 37:6613–6624. https://doi.org/10.1093/nar/gkp699

  7. Hashimoto H, Shimizu T, Imasaki T et al (2005) Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA. J Biol Chem 280:5605–5610. https://doi.org/10.1074/jbc.M411684200

    Article  CAS  Google Scholar 

  8. Oroguchi T, Hashimoto H, Shimizu T et al (2009) Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics simulations and X-ray scattering data analysis. Biophys J 96:2808–2822. https://doi.org/10.1016/j.bpj.2008.12.3914

    Article  CAS  Google Scholar 

  9. Szczepanowski RH, Carpenter MA, Czapinska H et al (2008) Central base pair flipping and discrimination by PspGI. Nucleic Acids Res 36:6109–6117. https://doi.org/10.1093/nar/gkn622

    Article  CAS  Google Scholar 

  10. Bochtler M, Szczepanowski RH, Tamulaitis G et al (2006) Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease. EMBO J 25:2219–2229. https://doi.org/10.1038/sj.emboj.7601096

    Article  CAS  Google Scholar 

  11. Viadiu H, Aggarwal AK (1998) The role of metals in catalysis by the restriction endonuclease Bam HI. Nat Struct Mol Biol 5:910–916. https://doi.org/10.1038/2352

    Article  CAS  Google Scholar 

  12. Uyar A, Kurkcuoglu O, Nilsson L, Doruker P (2011) The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases. Phys Biol 8:056001. https://doi.org/10.1088/1478-3975/8/5/056001

    Article  CAS  Google Scholar 

  13. Ehbrecht HJ, Pingoud A, Urbanke C et al (1985) Linear diffusion of restriction endonucleases on DNA. J Biol Chem 260:6160–6166

    CAS  Google Scholar 

  14. von Hippel PH, Berg OG (1989) Facilitated target location in biological systems. J Biol Chem 264:675–678

    Google Scholar 

  15. Berman HM, Westbrook J, Feng Z et al (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242. https://doi.org/10.1093/nar/28.1.235

  16. Marti-Renom MA, Stuart AC, Fiser A et al (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291–325. https://doi.org/10.1146/annurev.biophys.29.1.291

    Article  CAS  Google Scholar 

  17. Eswar N, Webb B, Marti-Renom MA et al (2007) Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci Chap 2:Unit 2.9. https://doi.org/10.1002/0471140864.ps0209s50

  18. Grubmuller H (1996) Solvate 1.0. Ludwig-Maximilians-Universität, München

  19. Case D, Darden T, Cheatham T et al (2012) AMBER 12. University of California, San Francisco

    Google Scholar 

  20. Hornak V, Abel R, Okur A et al (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins Struct Funct Bioinf 65:712–725. https://doi.org/10.1002/prot.21123

    Article  CAS  Google Scholar 

  21. Pérez A, Marchán I, Svozil D et al (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys J 92:3817–3829. https://doi.org/10.1529/biophysj.106.097782

    Article  Google Scholar 

  22. Jorgensen W, Chandrasekhar J, Madura J et al (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(935):926

    Article  CAS  Google Scholar 

  23. Aqvist J (1990) Ion water interaction potentials derived from free-energy perturbation simulations. J Phys Chem 94:8021–8024

    Article  Google Scholar 

  24. Smith DE, Dang LX (1994) Computer simulations of NaCl association in polarizable water. J Chem Phys 100:3757–3766. https://doi.org/10.1063/1.466363

    Article  CAS  Google Scholar 

  25. Darden T, York D, Pedersen L (1993) Particle mesh Ewald—an N.log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092. https://doi.org/10.1063/1.464397

  26. Salomon-Ferrer R, Götz AW, Poole D et al (2013) Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald. J Chem Theory Comput 9:3878–3888. https://doi.org/10.1021/ct400314y

    Article  CAS  Google Scholar 

  27. Roe DR, Cheatham TE (2013) PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput 9:3084–3095. https://doi.org/10.1021/ct400341p

    Article  CAS  Google Scholar 

  28. Kulhánek P, Štěpán J, Oľha J et al (2016) Conversion and analysis tools. https://lcc.ncbr.muni.cz/whitezone/development/cats/index.html

  29. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(33–38):27–28

    Google Scholar 

  30. Stone J (1998) An efficient library for parallel ray tracing and animation. Master’s thesis. Computer Science Department, University of Missouri–Rolla, Rolla

  31. Lu X-J, Olson WK (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31:5108–5121. https://doi.org/10.1093/nar/gkg680

    Article  CAS  Google Scholar 

  32. Sanner MF, Olson AJ, Spehner JC (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38:305–320. https://doi.org/10.1002/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y

    Article  CAS  Google Scholar 

  33. Amadei A, Linssen A, Berendsen H (1993) Essential dynamics of proteins. Proteins Struct Funct Genet 17:412–425. https://doi.org/10.1002/prot.340170408

    Article  CAS  Google Scholar 

  34. VanAalten DMF, DeGroot BL, Findlay JBC et al (1997) A comparison of techniques for calculating protein essential dynamics. J Comput Chem 18:169–181

    Article  CAS  Google Scholar 

  35. Baker NA, Sept D, Joseph S et al (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci 98:10037–10041. https://doi.org/10.1073/pnas.181342398

    Article  CAS  Google Scholar 

  36. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA (2004) PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations. Nucleic Acids Res 32:W665–W667. https://doi.org/10.1093/nar/gkh381

    Article  CAS  Google Scholar 

  37. Dolinsky TJ, Czodrowski P, Li H et al (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35:W522–W525. https://doi.org/10.1093/nar/gkm276

    Article  Google Scholar 

  38. Konig PH, Ghosh N, Hoffmann M et al (2006) Toward theoretical analyis of long-range proton transfer kinetics in biomolecular pumps. J Phys Chem A 110:548–563. https://doi.org/10.1021/jp052328q

    Article  CAS  Google Scholar 

  39. Olsson MHM, Sondergaard CR, Rostkowski M, Jensen JH (2011) PROPKA3: consistent treatment of internal and surface residues in empirical pK(a) predictions. J Chem Theory Comput 7:525–537. https://doi.org/10.1021/ct100578z

    Article  CAS  Google Scholar 

  40. Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl Acad Sci USA 99:12562–12566. https://doi.org/10.1073/pnas.202427399

    Article  CAS  Google Scholar 

  41. Kulhánek P, Štěpán J, Fuxreiter M et al (2013) PMFLib—a toolkit for free energy calculations. https://lcc.ncbr.muni.cz/whitezone/development/pmflib/index.html

  42. Lee J, Chang J, Joseph N et al (2005) MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage. Mol Cell 20:155–166. https://doi.org/10.1016/j.molcel.2005.08.019

    Article  CAS  Google Scholar 

  43. Jin L, Ye F, Zhao D et al (2014) Metadynamics simulation study on the conformational transformation of hhai methyltransferase: an induced-fit base-flipping hypothesis. Biomed Res Int 2014:304563. https://doi.org/10.1155/2014/304563

    Google Scholar 

  44. Formoso E, Limongelli V, Parrinello M (2015) Energetics and structural characterization of the large-scale functional motion of adenylate kinase. Sci Rep 5:srep08425. https://doi.org/10.1038/srep08425

    Article  Google Scholar 

  45. Pace CN, Scholtz JM (1998) A helix propensity scale based on experimental studies of peptides and proteins. Biophys J 75:422–427

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II. Computational resources were provided by CESNET LM2015042, CERIT Scientific Cloud LM2015085, and the IT4Innovations National Supercomputing Center LM2015070, as provided under the program “Large Infrastructures for Research, Experimental Development and Innovations” by the Ministry of Education, Youth and Sports.

Author information

Author notes

  1. Jakub Štěpán and Ivo Kabelka contributed equally to this work.

Authors and Affiliations

  1. CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic

    Jakub Štěpán, Ivo Kabelka, Jaroslav Koča & Petr Kulhánek

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

    Jakub Štěpán, Ivo Kabelka, Jaroslav Koča & Petr Kulhánek

Authors
  1. Jakub Štěpán
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ivo Kabelka
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jaroslav Koča
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Petr Kulhánek
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Petr Kulhánek.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Dedicated to Dr. Peter Politzer on the occasion of his 80th birthday.

This paper belongs to Topical Collection P. Politzer 80th Birthday Festschrift

Electronic supplementary material

ESM 1

(PDF 3973 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Štěpán, J., Kabelka, I., Koča, J. et al. Behavior of BsoBI endonuclease in the presence and absence of DNA. J Mol Model 24, 22 (2018). https://doi.org/10.1007/s00894-017-3557-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-017-3557-8

Keywords

Search

Navigation