Studying the recognition mechanism of TcaR and ssDNA using molecular dynamic simulations
The transcription regulator teicoplanin-associate locus regulator (TcaR) plays a vital role in interfering with ssDNA replication and resisting ssDNA phage invasion. Although recent studies demonstrated that TcaR had strong interaction with ssDNA, the dynamics and interaction mechanism of dimeric Tc...
| Main Authors: | , , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
2020
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| Online Access: | https://hdl.handle.net/10356/142670 |
| _version_ | 1826128624662609920 |
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| author | Fan, Jing-rong Zhang, Hong-xing Mu, Yu-guang Zheng, Qing-chuan |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Fan, Jing-rong Zhang, Hong-xing Mu, Yu-guang Zheng, Qing-chuan |
| author_sort | Fan, Jing-rong |
| collection | NTU |
| description | The transcription regulator teicoplanin-associate locus regulator (TcaR) plays a vital role in interfering with ssDNA replication and resisting ssDNA phage invasion. Although recent studies demonstrated that TcaR had strong interaction with ssDNA, the dynamics and interaction mechanism of dimeric TcaR bound to ssDNA have not been rationalized at the atomic level. In our study, MD simulations combined with MM-GB/SA calculations were employed to study recognition mechanism between TcaR and ssDNA. The results illuminate that electrostatic interaction is the main driving force for the binding process. We put forward that six anchoring residues (Arg70, Arg71, Ser188, Gln191, Arg221 and Arg222) play a vital role in stabilizing the ssDNA by forming strong hydrogen bond and salt bridge interactions. TcaR undergoes the asymmetric conformational changes at the wHTH domain upon binding to ssDNA. This may be attributed to the changing of electrostatic potential, enhanced contacts and salt bridge interaction. The present study provides new insights into the recognition mechanism of TcaR bound to ssDNA, which could contribute to understanding about the multiple TcaR functions in staphylococci enrich our understanding of MarR family. |
| first_indexed | 2024-10-01T07:27:59Z |
| format | Journal Article |
| id | ntu-10356/142670 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T07:27:59Z |
| publishDate | 2020 |
| record_format | dspace |
| spelling | ntu-10356/1426702020-06-26T06:10:20Z Studying the recognition mechanism of TcaR and ssDNA using molecular dynamic simulations Fan, Jing-rong Zhang, Hong-xing Mu, Yu-guang Zheng, Qing-chuan School of Biological Sciences Science::Biological sciences TcaR Recognition Mechanism The transcription regulator teicoplanin-associate locus regulator (TcaR) plays a vital role in interfering with ssDNA replication and resisting ssDNA phage invasion. Although recent studies demonstrated that TcaR had strong interaction with ssDNA, the dynamics and interaction mechanism of dimeric TcaR bound to ssDNA have not been rationalized at the atomic level. In our study, MD simulations combined with MM-GB/SA calculations were employed to study recognition mechanism between TcaR and ssDNA. The results illuminate that electrostatic interaction is the main driving force for the binding process. We put forward that six anchoring residues (Arg70, Arg71, Ser188, Gln191, Arg221 and Arg222) play a vital role in stabilizing the ssDNA by forming strong hydrogen bond and salt bridge interactions. TcaR undergoes the asymmetric conformational changes at the wHTH domain upon binding to ssDNA. This may be attributed to the changing of electrostatic potential, enhanced contacts and salt bridge interaction. The present study provides new insights into the recognition mechanism of TcaR bound to ssDNA, which could contribute to understanding about the multiple TcaR functions in staphylococci enrich our understanding of MarR family. 2020-06-26T06:10:20Z 2020-06-26T06:10:20Z 2017 Journal Article Fan, J., Zhang, H., Mu, Y., & Zheng, Q. (2018). Studying the recognition mechanism of TcaR and ssDNA using molecular dynamic simulations. Journal of Molecular Graphics and Modelling, 80, 67-75. doi:10.1016/j.jmgm.2017.12.001 1093-3263 https://hdl.handle.net/10356/142670 10.1016/j.jmgm.2017.12.001 29324326 2-s2.0-85042022564 80 67 75 en Journal of Molecular Graphics and Modelling © 2017 Elsevier Inc. All rights reserved. |
| spellingShingle | Science::Biological sciences TcaR Recognition Mechanism Fan, Jing-rong Zhang, Hong-xing Mu, Yu-guang Zheng, Qing-chuan Studying the recognition mechanism of TcaR and ssDNA using molecular dynamic simulations |
| title | Studying the recognition mechanism of TcaR and ssDNA using molecular dynamic simulations |
| title_full | Studying the recognition mechanism of TcaR and ssDNA using molecular dynamic simulations |
| title_fullStr | Studying the recognition mechanism of TcaR and ssDNA using molecular dynamic simulations |
| title_full_unstemmed | Studying the recognition mechanism of TcaR and ssDNA using molecular dynamic simulations |
| title_short | Studying the recognition mechanism of TcaR and ssDNA using molecular dynamic simulations |
| title_sort | studying the recognition mechanism of tcar and ssdna using molecular dynamic simulations |
| topic | Science::Biological sciences TcaR Recognition Mechanism |
| url | https://hdl.handle.net/10356/142670 |
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