Eintrag weiter verarbeiten
Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism
Gespeichert in:
| Zeitschriftentitel: | International Journal of Molecular Sciences |
|---|---|
| Personen und Körperschaften: | , , , , , , , , |
| In: | International Journal of Molecular Sciences, 19, 2018, 11, S. 3524 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
MDPI AG
|
| Schlagwörter: |
| author_facet |
Hu, Guodong Yu, Xiu Bian, Yunqiang Cao, Zanxia Xu, Shicai Zhao, Liling Ji, Baohua Wang, Wei Wang, Jihua Hu, Guodong Yu, Xiu Bian, Yunqiang Cao, Zanxia Xu, Shicai Zhao, Liling Ji, Baohua Wang, Wei Wang, Jihua |
|---|---|
| author |
Hu, Guodong Yu, Xiu Bian, Yunqiang Cao, Zanxia Xu, Shicai Zhao, Liling Ji, Baohua Wang, Wei Wang, Jihua |
| spellingShingle |
Hu, Guodong Yu, Xiu Bian, Yunqiang Cao, Zanxia Xu, Shicai Zhao, Liling Ji, Baohua Wang, Wei Wang, Jihua International Journal of Molecular Sciences Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism Inorganic Chemistry Organic Chemistry Physical and Theoretical Chemistry Computer Science Applications Spectroscopy Molecular Biology General Medicine Catalysis |
| author_sort |
hu, guodong |
| spelling |
Hu, Guodong Yu, Xiu Bian, Yunqiang Cao, Zanxia Xu, Shicai Zhao, Liling Ji, Baohua Wang, Wei Wang, Jihua 1422-0067 MDPI AG Inorganic Chemistry Organic Chemistry Physical and Theoretical Chemistry Computer Science Applications Spectroscopy Molecular Biology General Medicine Catalysis http://dx.doi.org/10.3390/ijms19113524 <jats:p>ToxIN is a triangular structure formed by three protein toxins (ToxNs) and three specific noncoding RNA antitoxins (ToxIs). To respond to stimuli, ToxI is preferentially degraded, releasing the ToxN. Thus, the dynamic character is essential in the normal function interactions between ToxN and ToxI. Here, equilibrated molecular dynamics (MD) simulations were performed to study the stability of ToxN and ToxI. The results indicate that ToxI adjusts the conformation of 3′ and 5′ termini to bind to ToxN. Steered molecular dynamics (SMD) simulations combined with the recently developed thermodynamic integration in 3nD (TI3nD) method were carried out to investigate ToxN unbinding from the ToxIN complex. The potentials of mean force (PMFs) and atomistic pictures suggest the unbinding mechanism as follows: (1) dissociation of the 5′ terminus from ToxN, (2) missing the interactions involved in the 3′ terminus of ToxI without three nucleotides (G31, A32, and A33), (3) starting to unfold for ToxI, (4) leaving the binding package of ToxN for three nucleotides of ToxI, (5) unfolding of ToxI. This work provides information on the structure-function relationship at the atomistic level, which is helpful for designing new potent antibacterial drugs in the future.</jats:p> Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism International Journal of Molecular Sciences |
| doi_str_mv |
10.3390/ijms19113524 |
| facet_avail |
Online Free |
| finc_class_facet |
Chemie und Pharmazie Physik Informatik Biologie |
| format |
ElectronicArticle |
| fullrecord |
blob:ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMzM5MC9pam1zMTkxMTM1MjQ |
| id |
ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMzM5MC9pam1zMTkxMTM1MjQ |
| institution |
DE-D275 DE-Bn3 DE-Brt1 DE-Zwi2 DE-D161 DE-Gla1 DE-Zi4 DE-15 DE-Pl11 DE-Rs1 DE-105 DE-14 DE-Ch1 DE-L229 |
| imprint |
MDPI AG, 2018 |
| imprint_str_mv |
MDPI AG, 2018 |
| issn |
1422-0067 |
| issn_str_mv |
1422-0067 |
| language |
English |
| mega_collection |
MDPI AG (CrossRef) |
| match_str |
hu2018atomisticanalysisoftoxnandtoxicomplexunbindingmechanism |
| publishDateSort |
2018 |
| publisher |
MDPI AG |
| recordtype |
ai |
| record_format |
ai |
| series |
International Journal of Molecular Sciences |
| source_id |
49 |
| title |
Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| title_unstemmed |
Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| title_full |
Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| title_fullStr |
Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| title_full_unstemmed |
Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| title_short |
Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| title_sort |
atomistic analysis of toxn and toxi complex unbinding mechanism |
| topic |
Inorganic Chemistry Organic Chemistry Physical and Theoretical Chemistry Computer Science Applications Spectroscopy Molecular Biology General Medicine Catalysis |
| url |
http://dx.doi.org/10.3390/ijms19113524 |
| publishDate |
2018 |
| physical |
3524 |
| description |
<jats:p>ToxIN is a triangular structure formed by three protein toxins (ToxNs) and three specific noncoding RNA antitoxins (ToxIs). To respond to stimuli, ToxI is preferentially degraded, releasing the ToxN. Thus, the dynamic character is essential in the normal function interactions between ToxN and ToxI. Here, equilibrated molecular dynamics (MD) simulations were performed to study the stability of ToxN and ToxI. The results indicate that ToxI adjusts the conformation of 3′ and 5′ termini to bind to ToxN. Steered molecular dynamics (SMD) simulations combined with the recently developed thermodynamic integration in 3nD (TI3nD) method were carried out to investigate ToxN unbinding from the ToxIN complex. The potentials of mean force (PMFs) and atomistic pictures suggest the unbinding mechanism as follows: (1) dissociation of the 5′ terminus from ToxN, (2) missing the interactions involved in the 3′ terminus of ToxI without three nucleotides (G31, A32, and A33), (3) starting to unfold for ToxI, (4) leaving the binding package of ToxN for three nucleotides of ToxI, (5) unfolding of ToxI. This work provides information on the structure-function relationship at the atomistic level, which is helpful for designing new potent antibacterial drugs in the future.</jats:p> |
| container_issue |
11 |
| container_start_page |
0 |
| container_title |
International Journal of Molecular Sciences |
| container_volume |
19 |
| format_de105 |
Article, E-Article |
| format_de14 |
Article, E-Article |
| format_de15 |
Article, E-Article |
| format_de520 |
Article, E-Article |
| format_de540 |
Article, E-Article |
| format_dech1 |
Article, E-Article |
| format_ded117 |
Article, E-Article |
| format_degla1 |
E-Article |
| format_del152 |
Buch |
| format_del189 |
Article, E-Article |
| format_dezi4 |
Article |
| format_dezwi2 |
Article, E-Article |
| format_finc |
Article, E-Article |
| format_nrw |
Article, E-Article |
| _version_ |
1792328826105102342 |
| geogr_code |
not assigned |
| last_indexed |
2024-03-01T12:59:27.79Z |
| geogr_code_person |
not assigned |
| openURL |
url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fvufind.svn.sourceforge.net%3Agenerator&rft.title=Atomistic+Analysis+of+ToxN+and+ToxI+Complex+Unbinding+Mechanism&rft.date=2018-11-09&genre=article&issn=1422-0067&volume=19&issue=11&pages=3524&jtitle=International+Journal+of+Molecular+Sciences&atitle=Atomistic+Analysis+of+ToxN+and+ToxI+Complex+Unbinding+Mechanism&aulast=Wang&aufirst=Jihua&rft_id=info%3Adoi%2F10.3390%2Fijms19113524&rft.language%5B0%5D=eng |
| SOLR | |
| _version_ | 1792328826105102342 |
| author | Hu, Guodong, Yu, Xiu, Bian, Yunqiang, Cao, Zanxia, Xu, Shicai, Zhao, Liling, Ji, Baohua, Wang, Wei, Wang, Jihua |
| author_facet | Hu, Guodong, Yu, Xiu, Bian, Yunqiang, Cao, Zanxia, Xu, Shicai, Zhao, Liling, Ji, Baohua, Wang, Wei, Wang, Jihua, Hu, Guodong, Yu, Xiu, Bian, Yunqiang, Cao, Zanxia, Xu, Shicai, Zhao, Liling, Ji, Baohua, Wang, Wei, Wang, Jihua |
| author_sort | hu, guodong |
| container_issue | 11 |
| container_start_page | 0 |
| container_title | International Journal of Molecular Sciences |
| container_volume | 19 |
| description | <jats:p>ToxIN is a triangular structure formed by three protein toxins (ToxNs) and three specific noncoding RNA antitoxins (ToxIs). To respond to stimuli, ToxI is preferentially degraded, releasing the ToxN. Thus, the dynamic character is essential in the normal function interactions between ToxN and ToxI. Here, equilibrated molecular dynamics (MD) simulations were performed to study the stability of ToxN and ToxI. The results indicate that ToxI adjusts the conformation of 3′ and 5′ termini to bind to ToxN. Steered molecular dynamics (SMD) simulations combined with the recently developed thermodynamic integration in 3nD (TI3nD) method were carried out to investigate ToxN unbinding from the ToxIN complex. The potentials of mean force (PMFs) and atomistic pictures suggest the unbinding mechanism as follows: (1) dissociation of the 5′ terminus from ToxN, (2) missing the interactions involved in the 3′ terminus of ToxI without three nucleotides (G31, A32, and A33), (3) starting to unfold for ToxI, (4) leaving the binding package of ToxN for three nucleotides of ToxI, (5) unfolding of ToxI. This work provides information on the structure-function relationship at the atomistic level, which is helpful for designing new potent antibacterial drugs in the future.</jats:p> |
| doi_str_mv | 10.3390/ijms19113524 |
| facet_avail | Online, Free |
| finc_class_facet | Chemie und Pharmazie, Physik, Informatik, Biologie |
| format | ElectronicArticle |
| format_de105 | Article, E-Article |
| format_de14 | Article, E-Article |
| format_de15 | Article, E-Article |
| format_de520 | Article, E-Article |
| format_de540 | Article, E-Article |
| format_dech1 | Article, E-Article |
| format_ded117 | Article, E-Article |
| format_degla1 | E-Article |
| format_del152 | Buch |
| format_del189 | Article, E-Article |
| format_dezi4 | Article |
| format_dezwi2 | Article, E-Article |
| format_finc | Article, E-Article |
| format_nrw | Article, E-Article |
| geogr_code | not assigned |
| geogr_code_person | not assigned |
| id | ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMzM5MC9pam1zMTkxMTM1MjQ |
| imprint | MDPI AG, 2018 |
| imprint_str_mv | MDPI AG, 2018 |
| institution | DE-D275, DE-Bn3, DE-Brt1, DE-Zwi2, DE-D161, DE-Gla1, DE-Zi4, DE-15, DE-Pl11, DE-Rs1, DE-105, DE-14, DE-Ch1, DE-L229 |
| issn | 1422-0067 |
| issn_str_mv | 1422-0067 |
| language | English |
| last_indexed | 2024-03-01T12:59:27.79Z |
| match_str | hu2018atomisticanalysisoftoxnandtoxicomplexunbindingmechanism |
| mega_collection | MDPI AG (CrossRef) |
| physical | 3524 |
| publishDate | 2018 |
| publishDateSort | 2018 |
| publisher | MDPI AG |
| record_format | ai |
| recordtype | ai |
| series | International Journal of Molecular Sciences |
| source_id | 49 |
| spelling | Hu, Guodong Yu, Xiu Bian, Yunqiang Cao, Zanxia Xu, Shicai Zhao, Liling Ji, Baohua Wang, Wei Wang, Jihua 1422-0067 MDPI AG Inorganic Chemistry Organic Chemistry Physical and Theoretical Chemistry Computer Science Applications Spectroscopy Molecular Biology General Medicine Catalysis http://dx.doi.org/10.3390/ijms19113524 <jats:p>ToxIN is a triangular structure formed by three protein toxins (ToxNs) and three specific noncoding RNA antitoxins (ToxIs). To respond to stimuli, ToxI is preferentially degraded, releasing the ToxN. Thus, the dynamic character is essential in the normal function interactions between ToxN and ToxI. Here, equilibrated molecular dynamics (MD) simulations were performed to study the stability of ToxN and ToxI. The results indicate that ToxI adjusts the conformation of 3′ and 5′ termini to bind to ToxN. Steered molecular dynamics (SMD) simulations combined with the recently developed thermodynamic integration in 3nD (TI3nD) method were carried out to investigate ToxN unbinding from the ToxIN complex. The potentials of mean force (PMFs) and atomistic pictures suggest the unbinding mechanism as follows: (1) dissociation of the 5′ terminus from ToxN, (2) missing the interactions involved in the 3′ terminus of ToxI without three nucleotides (G31, A32, and A33), (3) starting to unfold for ToxI, (4) leaving the binding package of ToxN for three nucleotides of ToxI, (5) unfolding of ToxI. This work provides information on the structure-function relationship at the atomistic level, which is helpful for designing new potent antibacterial drugs in the future.</jats:p> Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism International Journal of Molecular Sciences |
| spellingShingle | Hu, Guodong, Yu, Xiu, Bian, Yunqiang, Cao, Zanxia, Xu, Shicai, Zhao, Liling, Ji, Baohua, Wang, Wei, Wang, Jihua, International Journal of Molecular Sciences, Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism, Inorganic Chemistry, Organic Chemistry, Physical and Theoretical Chemistry, Computer Science Applications, Spectroscopy, Molecular Biology, General Medicine, Catalysis |
| title | Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| title_full | Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| title_fullStr | Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| title_full_unstemmed | Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| title_short | Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| title_sort | atomistic analysis of toxn and toxi complex unbinding mechanism |
| title_unstemmed | Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism |
| topic | Inorganic Chemistry, Organic Chemistry, Physical and Theoretical Chemistry, Computer Science Applications, Spectroscopy, Molecular Biology, General Medicine, Catalysis |
| url | http://dx.doi.org/10.3390/ijms19113524 |