Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease
Abstract Proteins are not static but are flexible molecules that can adopt many different conformations. The HIV-1 protease is an important target for the development of therapies to treat AIDS, due to its critical role in the viral life cycle. We investigated several dynamics studies on the HIV-1 p...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-40818-x |
| _version_ | 1797453275793981440 |
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| author | Mohammad Rahimi Majid Taghdir Farzane Abasi Joozdani |
| author_facet | Mohammad Rahimi Majid Taghdir Farzane Abasi Joozdani |
| author_sort | Mohammad Rahimi |
| collection | DOAJ |
| description | Abstract Proteins are not static but are flexible molecules that can adopt many different conformations. The HIV-1 protease is an important target for the development of therapies to treat AIDS, due to its critical role in the viral life cycle. We investigated several dynamics studies on the HIV-1 protease families to illustrate the significance of examining the dynamic behaviors and molecular motions for an entire understanding of their dynamics-structure–function relationships. Using computer simulations and principal component analysis approaches, the dynamics data obtained revealed that: (i) The flap regions are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease; (ii) There are dynamic structural regions in some proteins that contribute to the biological function and allostery of proteins via appropriate flexibility. These regions are a clear sign of the evolution of conformational dynamics of proteins, which we call dynamozones. The flap regions are one of the most important dynamozones members that are critical for HIV-1 protease function. Due to the existence of other members of dynamozones in different proteins, we propose to consider dynamozones as a footprint of the evolution of the conformational dynamics of proteins. |
| first_indexed | 2024-03-09T15:20:29Z |
| format | Article |
| id | doaj.art-655fa1d90ea842f2a6af3088ecf641d1 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-09T15:20:29Z |
| publishDate | 2023-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-655fa1d90ea842f2a6af3088ecf641d12023-11-26T12:50:39ZengNature PortfolioScientific Reports2045-23222023-08-0113111810.1038/s41598-023-40818-xDynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 proteaseMohammad Rahimi0Majid Taghdir1Farzane Abasi Joozdani2Department of Biophysics, Faculty of Biological Science, Tarbiat Modares UniversityDepartment of Biophysics, Faculty of Biological Science, Tarbiat Modares UniversityDepartment of Biophysics, Faculty of Biological Science, Tarbiat Modares UniversityAbstract Proteins are not static but are flexible molecules that can adopt many different conformations. The HIV-1 protease is an important target for the development of therapies to treat AIDS, due to its critical role in the viral life cycle. We investigated several dynamics studies on the HIV-1 protease families to illustrate the significance of examining the dynamic behaviors and molecular motions for an entire understanding of their dynamics-structure–function relationships. Using computer simulations and principal component analysis approaches, the dynamics data obtained revealed that: (i) The flap regions are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease; (ii) There are dynamic structural regions in some proteins that contribute to the biological function and allostery of proteins via appropriate flexibility. These regions are a clear sign of the evolution of conformational dynamics of proteins, which we call dynamozones. The flap regions are one of the most important dynamozones members that are critical for HIV-1 protease function. Due to the existence of other members of dynamozones in different proteins, we propose to consider dynamozones as a footprint of the evolution of the conformational dynamics of proteins.https://doi.org/10.1038/s41598-023-40818-x |
| spellingShingle | Mohammad Rahimi Majid Taghdir Farzane Abasi Joozdani Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease Scientific Reports |
| title | Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease |
| title_full | Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease |
| title_fullStr | Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease |
| title_full_unstemmed | Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease |
| title_short | Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease |
| title_sort | dynamozones are the most obvious sign of the evolution of conformational dynamics in hiv 1 protease |
| url | https://doi.org/10.1038/s41598-023-40818-x |
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