Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases
Protein intrinsically disordered regions (IDRs) play pivotal roles in molecular recognition and regulatory processes through structural disorder-to-order transitions. To understand and exploit the distinctive functional implications of IDRs and to unravel the underlying molecular mechanisms, structu...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022000174 |
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| author | Carla Guillén-Pingarrón Pedro M. Guillem-Gloria Anjali Soni Gloria Ruiz-Gómez Martina Augsburg Frank Buchholz Massimiliano Anselmi M. Teresa Pisabarro |
| author_facet | Carla Guillén-Pingarrón Pedro M. Guillem-Gloria Anjali Soni Gloria Ruiz-Gómez Martina Augsburg Frank Buchholz Massimiliano Anselmi M. Teresa Pisabarro |
| author_sort | Carla Guillén-Pingarrón |
| collection | DOAJ |
| description | Protein intrinsically disordered regions (IDRs) play pivotal roles in molecular recognition and regulatory processes through structural disorder-to-order transitions. To understand and exploit the distinctive functional implications of IDRs and to unravel the underlying molecular mechanisms, structural disorder-to-function relationships need to be deciphered. The DNA site-specific recombinase system Cre/loxP represents an attractive model to investigate functional molecular mechanisms of IDRs. Cre contains a functionally dispensable disordered N-terminal tail, which becomes indispensable in the evolved Tre/loxLTR recombinase system. The difficulty to experimentally obtain structural information about this tail has so far precluded any mechanistic study on its involvement in DNA recombination. Here, we use in vitro and in silico evolution data, conformational dynamics, AI-based folding simulations, thermodynamic stability calculations, mutagenesis and DNA recombination assays to investigate how evolution and the dynamic behavior of this IDR may determine distinct functional properties. Our studies suggest that partial conformational order in the N-terminal tail of Tre recombinase and its packing to a conserved hydrophobic surface on the protein provide thermodynamic stability. Based on our results, we propose a link between protein stability and function, offering new plausible atom-detailed mechanistic insights into disorder-function relationships. Our work highlights the potential of N-terminal tails to be exploited for regulation of the activity of Cre-like tyrosine-type SSRs, which merits future investigations and could be of relevance in future rational engineering for their use in biotechnology and genomic medicine. |
| first_indexed | 2024-04-11T05:20:23Z |
| format | Article |
| id | doaj.art-67284fa5206f417cb15625c7550bf64d |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:20:23Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-67284fa5206f417cb15625c7550bf64d2022-12-24T04:51:14ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-01209891001Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinasesCarla Guillén-Pingarrón0Pedro M. Guillem-Gloria1Anjali Soni2Gloria Ruiz-Gómez3Martina Augsburg4Frank Buchholz5Massimiliano Anselmi6M. Teresa Pisabarro7Structural Bioinformatics, BIOTEC, TU Dresden, Tatzberg 47-51, 01307 Dresden, GermanyStructural Bioinformatics, BIOTEC, TU Dresden, Tatzberg 47-51, 01307 Dresden, GermanyStructural Bioinformatics, BIOTEC, TU Dresden, Tatzberg 47-51, 01307 Dresden, GermanyStructural Bioinformatics, BIOTEC, TU Dresden, Tatzberg 47-51, 01307 Dresden, GermanyUniversity Carl Gustav Carus and Medical Faculty, UCC, Medical Systems Biology, TU Dresden, Fetscherstrasse 74, Dresden, GermanyUniversity Carl Gustav Carus and Medical Faculty, UCC, Medical Systems Biology, TU Dresden, Fetscherstrasse 74, Dresden, GermanyTheoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany; Corresponding authors.Structural Bioinformatics, BIOTEC, TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany; Corresponding authors.Protein intrinsically disordered regions (IDRs) play pivotal roles in molecular recognition and regulatory processes through structural disorder-to-order transitions. To understand and exploit the distinctive functional implications of IDRs and to unravel the underlying molecular mechanisms, structural disorder-to-function relationships need to be deciphered. The DNA site-specific recombinase system Cre/loxP represents an attractive model to investigate functional molecular mechanisms of IDRs. Cre contains a functionally dispensable disordered N-terminal tail, which becomes indispensable in the evolved Tre/loxLTR recombinase system. The difficulty to experimentally obtain structural information about this tail has so far precluded any mechanistic study on its involvement in DNA recombination. Here, we use in vitro and in silico evolution data, conformational dynamics, AI-based folding simulations, thermodynamic stability calculations, mutagenesis and DNA recombination assays to investigate how evolution and the dynamic behavior of this IDR may determine distinct functional properties. Our studies suggest that partial conformational order in the N-terminal tail of Tre recombinase and its packing to a conserved hydrophobic surface on the protein provide thermodynamic stability. Based on our results, we propose a link between protein stability and function, offering new plausible atom-detailed mechanistic insights into disorder-function relationships. Our work highlights the potential of N-terminal tails to be exploited for regulation of the activity of Cre-like tyrosine-type SSRs, which merits future investigations and could be of relevance in future rational engineering for their use in biotechnology and genomic medicine.http://www.sciencedirect.com/science/article/pii/S2001037022000174Intrinsically disordered protein regionssite-specific DNA recombinaseEvolutionMolecular dynamicsStructural disorderThermodynamic stability |
| spellingShingle | Carla Guillén-Pingarrón Pedro M. Guillem-Gloria Anjali Soni Gloria Ruiz-Gómez Martina Augsburg Frank Buchholz Massimiliano Anselmi M. Teresa Pisabarro Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases Computational and Structural Biotechnology Journal Intrinsically disordered protein regions site-specific DNA recombinase Evolution Molecular dynamics Structural disorder Thermodynamic stability |
| title | Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases |
| title_full | Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases |
| title_fullStr | Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases |
| title_full_unstemmed | Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases |
| title_short | Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases |
| title_sort | conformational dynamics promotes disordered regions from function dispensable to essential in evolved site specific dna recombinases |
| topic | Intrinsically disordered protein regions site-specific DNA recombinase Evolution Molecular dynamics Structural disorder Thermodynamic stability |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022000174 |
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