Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers
HIV-1 integrase (HIV-1 IN) is an enzyme produced by the HIV-1 virus that integrates genetic material of the virus into the DNA of infected human cells. HIV-1 IN acts as a key component of the Retroviral Pre-Integration Complex (PIC). Protein dynamics could play an important role during the catalysis...
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doaj-43164a06344c4b1392966590f942c4152020-11-24T21:20:56ZengMDPI AGInternational Journal of Molecular Sciences1422-00672019-04-01208194310.3390/ijms20081943ijms20081943Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron LasersJae-Hyun Park0Ji-Hye Yun1Yingchen Shi2Jeongmin Han3Xuanxuan Li4Zeyu Jin5Taehee Kim6Jaehyun Park7Sehan Park8Haiguang Liu9Weontae Lee10Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, KoreaStructural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, KoreaComplex Systems Division, Beijing Computational Science Research Center, Beijing 100193, ChinaStructural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, KoreaComplex Systems Division, Beijing Computational Science Research Center, Beijing 100193, ChinaStructural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, KoreaStructural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, KoreaPohang Accelerator Laboratory, Pohang 37673, KoreaPohang Accelerator Laboratory, Pohang 37673, KoreaComplex Systems Division, Beijing Computational Science Research Center, Beijing 100193, ChinaStructural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, KoreaHIV-1 integrase (HIV-1 IN) is an enzyme produced by the HIV-1 virus that integrates genetic material of the virus into the DNA of infected human cells. HIV-1 IN acts as a key component of the Retroviral Pre-Integration Complex (PIC). Protein dynamics could play an important role during the catalysis of HIV-1 IN; however, this process has not yet been fully elucidated. X-ray free electron laser (XFEL) together with nuclear magnetic resonance (NMR) could provide information regarding the dynamics during this catalysis reaction. Here, we report the non-cryogenic crystal structure of HIV-1 IN catalytic core domain at 2.5 Å using microcrystals in XFELs. Compared to the cryogenic structure at 2.1 Å using conventional synchrotron crystallography, there was a good agreement between the two structures, except for a catalytic triad formed by Asp64, Asp116, and Glu152 (DDE) and the lens epithelium-derived growth factor binding sites. The helix III region of the 140–153 residues near the active site and the DDE triad show a higher dynamic profile in the non-cryogenic structure, which is comparable to dynamics data obtained from NMR spectroscopy in solution state.https://www.mdpi.com/1422-0067/20/8/1943non-cryogenic structureHIV-1 integraseprotein dynamicsXFELs |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jae-Hyun Park Ji-Hye Yun Yingchen Shi Jeongmin Han Xuanxuan Li Zeyu Jin Taehee Kim Jaehyun Park Sehan Park Haiguang Liu Weontae Lee |
spellingShingle |
Jae-Hyun Park Ji-Hye Yun Yingchen Shi Jeongmin Han Xuanxuan Li Zeyu Jin Taehee Kim Jaehyun Park Sehan Park Haiguang Liu Weontae Lee Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers International Journal of Molecular Sciences non-cryogenic structure HIV-1 integrase protein dynamics XFELs |
author_facet |
Jae-Hyun Park Ji-Hye Yun Yingchen Shi Jeongmin Han Xuanxuan Li Zeyu Jin Taehee Kim Jaehyun Park Sehan Park Haiguang Liu Weontae Lee |
author_sort |
Jae-Hyun Park |
title |
Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers |
title_short |
Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers |
title_full |
Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers |
title_fullStr |
Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers |
title_full_unstemmed |
Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers |
title_sort |
non-cryogenic structure and dynamics of hiv-1 integrase catalytic core domain by x-ray free-electron lasers |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1422-0067 |
publishDate |
2019-04-01 |
description |
HIV-1 integrase (HIV-1 IN) is an enzyme produced by the HIV-1 virus that integrates genetic material of the virus into the DNA of infected human cells. HIV-1 IN acts as a key component of the Retroviral Pre-Integration Complex (PIC). Protein dynamics could play an important role during the catalysis of HIV-1 IN; however, this process has not yet been fully elucidated. X-ray free electron laser (XFEL) together with nuclear magnetic resonance (NMR) could provide information regarding the dynamics during this catalysis reaction. Here, we report the non-cryogenic crystal structure of HIV-1 IN catalytic core domain at 2.5 Å using microcrystals in XFELs. Compared to the cryogenic structure at 2.1 Å using conventional synchrotron crystallography, there was a good agreement between the two structures, except for a catalytic triad formed by Asp64, Asp116, and Glu152 (DDE) and the lens epithelium-derived growth factor binding sites. The helix III region of the 140–153 residues near the active site and the DDE triad show a higher dynamic profile in the non-cryogenic structure, which is comparable to dynamics data obtained from NMR spectroscopy in solution state. |
topic |
non-cryogenic structure HIV-1 integrase protein dynamics XFELs |
url |
https://www.mdpi.com/1422-0067/20/8/1943 |
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