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Chemical Approach to Biological Safety: Molecular-Level Control of an Integrated Zinc Finger Nuclease. Chembiochem 2017; 19:66-75. [DOI: 10.1002/cbic.201700420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Indexed: 01/20/2023]
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Németh E, Balogh RK, Borsos K, Czene A, Thulstrup PW, Gyurcsik B. Intrinsic protein disorder could be overlooked in cocrystallization conditions: An SRCD case study. Protein Sci 2016; 25:1977-1988. [PMID: 27508941 DOI: 10.1002/pro.3010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/08/2016] [Indexed: 12/21/2022]
Abstract
X-ray diffractometry dominates protein studies, as it can provide 3D structures of these diverse macromolecules or their molecular complexes with interacting partners: substrates, inhibitors, and/or cofactors. Here, we show that under cocrystallization conditions the results could reflect induced protein folds instead of the (partially) disordered original structures. The analysis of synchrotron radiation circular dichroism spectra revealed that the Im7 immunity protein stabilizes the native-like solution structure of unfolded NColE7 nuclease mutants via complex formation. This is consistent with the fact that among the several available crystal structures with its inhibitor or substrate, all NColE7 structures are virtually the same. Our results draw attention to the possible structural consequence of protein modifications, which is often hidden by compensational effects of intermolecular interactions. The growing evidence on the importance of protein intrinsic disorder thus, demands more extensive complementary experiments in solution phase with the unligated form of the protein of interest.
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Affiliation(s)
- Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary.,MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary
| | - Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary
| | - Katalin Borsos
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary
| | - Anikó Czene
- MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary. .,MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary.
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Preorganization of the catalytic Zn2+-binding site in the HNH nuclease motif—A solution study. J Inorg Biochem 2015; 151:143-9. [DOI: 10.1016/j.jinorgbio.2015.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/31/2015] [Accepted: 03/31/2015] [Indexed: 11/18/2022]
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Németh E, Schilli GK, Nagy G, Hasenhindl C, Gyurcsik B, Oostenbrink C. Design of a colicin E7 based chimeric zinc-finger nuclease. J Comput Aided Mol Des 2014; 28:841-50. [PMID: 24952471 PMCID: PMC4104000 DOI: 10.1007/s10822-014-9765-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 06/13/2014] [Indexed: 12/02/2022]
Abstract
Colicin E7 is a natural bacterial toxin. Its nuclease domain (NColE7) enters the target cell and kills it by digesting the nucleic acids. The HNH-motif as the catalytic centre of NColE7 at the C-terminus requires the positively charged N-terminal loop for the nuclease activity-offering opportunities for allosteric control in a NColE7-based artificial nuclease. Accordingly, four novel zinc finger nucleases were designed by computational methods exploiting the special structural features of NColE7. The constructed models were subjected to MD simulations. The comparison of structural stability and functional aspects showed that these models may function as safely controlled artificial nucleases. This study was complemented by random mutagenesis experiments identifying potentially important residues for NColE7 function outside the catalytic region.
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Affiliation(s)
- Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720 Hungary
| | - Gabriella K. Schilli
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720 Hungary
| | - Gábor Nagy
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Christoph Hasenhindl
- Christian Doppler Laboratory for Antibody Engineering, Department of Chemistry, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720 Hungary
- MTA-SzTE Bioinorganic Chemistry Research Group of Hungarian Academy of Sciences, Dóm tér 7, Szeged, 6720 Hungary
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
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Czene A, Tóth E, Németh E, Otten H, Poulsen JCN, Christensen HEM, Rulíšek L, Nagata K, Larsen S, Gyurcsik B. A new insight into the zinc-dependent DNA-cleavage by the colicin E7 nuclease: a crystallographic and computational study. Metallomics 2014; 6:2090-9. [DOI: 10.1039/c4mt00195h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structure of a colicin E7 metallonuclease mutant complemented by QM/MM calculations suggests an alternative catalytic mechanism of Zn2+-containing HNH nucleases.
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Affiliation(s)
- Anikó Czene
- MTA-SZTE Bioinorganic Chemistry Research Group
- H-6720 Szeged, Hungary
| | - Eszter Tóth
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged, Hungary
| | - Eszter Németh
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged, Hungary
| | - Harm Otten
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen, Denmark
| | | | | | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Kyosuke Nagata
- Nagata Special Laboratory
- Faculty of Medicine
- University of Tsukuba
- Tsukuba 305-8575, Japan
| | - Sine Larsen
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen, Denmark
| | - Béla Gyurcsik
- MTA-SZTE Bioinorganic Chemistry Research Group
- H-6720 Szeged, Hungary
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged, Hungary
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