Dynamical perspective of protein-DNA interaction
The interactions between protein-DNA are essential for various biological activities. In this review, we provide an overview of protein-DNA interactions that emphasizes the importance of dynamical aspects. We divide protein-DNA interactions into two categories: nonspecific and specific and both the...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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De Gruyter
2014-03-01
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| Series: | Biomolecular Concepts |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/bmc-2013-0037 |
| _version_ | 1818587277040812032 |
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| author | Batabyal Subrata Choudhury Susobhan Sao Dilip Mondol Tanumoy Kumar Pal Samir |
| author_facet | Batabyal Subrata Choudhury Susobhan Sao Dilip Mondol Tanumoy Kumar Pal Samir |
| author_sort | Batabyal Subrata |
| collection | DOAJ |
| description | The interactions between protein-DNA are essential for various biological activities. In this review, we provide an overview of protein-DNA interactions that emphasizes the importance of dynamical aspects. We divide protein-DNA interactions into two categories: nonspecific and specific and both the categories would be discussed highlighting some of our relevant work. In the case of nonspecific protein-DNA interaction, solvation studies (picosecond and femtosecond-resolved) explore the role environmental dynamics and change in the micropolarity around DNA molecules upon complexation with histone protein (H1). While exploring the specific protein-DNA interaction at λ-repressor-operator sites interaction, particularly OR1 and OR2, it was observed that the interfacial water dynamics is minimally perturbed upon interaction with DNA, suggesting the labile interface in the protein-DNA complex. Förster resonance energy transfer (FRET) study revealed that the structure of the protein is more compact in repressor-OR2 complex than in the repressor-OR1 complex. Fluorescence anisotropy studies indicated enhanced flexibility of the C-terminal domain of the repressor at fast timescales after complex formation with OR1. The enhanced flexibility and different conformation of the C-terminal domain of the repressor upon complexation with OR1 DNA compared to OR2 DNA were found to have pronounced effect on the rate of photoinduced electron transfer. |
| first_indexed | 2024-12-16T09:06:18Z |
| format | Article |
| id | doaj.art-baac72a782b54b48815aae0d73b0ea0a |
| institution | Directory Open Access Journal |
| issn | 1868-5021 1868-503X |
| language | English |
| last_indexed | 2024-12-16T09:06:18Z |
| publishDate | 2014-03-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Biomolecular Concepts |
| spelling | doaj.art-baac72a782b54b48815aae0d73b0ea0a2022-12-21T22:37:03ZengDe GruyterBiomolecular Concepts1868-50211868-503X2014-03-0151214310.1515/bmc-2013-0037Dynamical perspective of protein-DNA interactionBatabyal Subrata0Choudhury Susobhan1Sao Dilip2Mondol Tanumoy3Kumar Pal Samir4Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, IndiaDepartment of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, IndiaDepartment of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, IndiaDepartment of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, IndiaDepartment of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, IndiaThe interactions between protein-DNA are essential for various biological activities. In this review, we provide an overview of protein-DNA interactions that emphasizes the importance of dynamical aspects. We divide protein-DNA interactions into two categories: nonspecific and specific and both the categories would be discussed highlighting some of our relevant work. In the case of nonspecific protein-DNA interaction, solvation studies (picosecond and femtosecond-resolved) explore the role environmental dynamics and change in the micropolarity around DNA molecules upon complexation with histone protein (H1). While exploring the specific protein-DNA interaction at λ-repressor-operator sites interaction, particularly OR1 and OR2, it was observed that the interfacial water dynamics is minimally perturbed upon interaction with DNA, suggesting the labile interface in the protein-DNA complex. Förster resonance energy transfer (FRET) study revealed that the structure of the protein is more compact in repressor-OR2 complex than in the repressor-OR1 complex. Fluorescence anisotropy studies indicated enhanced flexibility of the C-terminal domain of the repressor at fast timescales after complex formation with OR1. The enhanced flexibility and different conformation of the C-terminal domain of the repressor upon complexation with OR1 DNA compared to OR2 DNA were found to have pronounced effect on the rate of photoinduced electron transfer.https://doi.org/10.1515/bmc-2013-0037different dynamical conformationsmolecular recognitionoperator dnaphotoinduced electron transferprotein-dna interactionsprotein-dna interfaceresonance energy transfersolvation dynamics |
| spellingShingle | Batabyal Subrata Choudhury Susobhan Sao Dilip Mondol Tanumoy Kumar Pal Samir Dynamical perspective of protein-DNA interaction Biomolecular Concepts different dynamical conformations molecular recognition operator dna photoinduced electron transfer protein-dna interactions protein-dna interface resonance energy transfer solvation dynamics |
| title | Dynamical perspective of protein-DNA interaction |
| title_full | Dynamical perspective of protein-DNA interaction |
| title_fullStr | Dynamical perspective of protein-DNA interaction |
| title_full_unstemmed | Dynamical perspective of protein-DNA interaction |
| title_short | Dynamical perspective of protein-DNA interaction |
| title_sort | dynamical perspective of protein dna interaction |
| topic | different dynamical conformations molecular recognition operator dna photoinduced electron transfer protein-dna interactions protein-dna interface resonance energy transfer solvation dynamics |
| url | https://doi.org/10.1515/bmc-2013-0037 |
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