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Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers

1
Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
2
Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, China
3
Department of Engineering Physics, Tsinghua University, Beijing 100084, China
4
Pohang Accelerator Laboratory, Pohang 37673, Korea
*
Authors to whom correspondence should be addressed.
These authors contributed equally.
Int. J. Mol. Sci. 2019, 20(8), 1943; https://doi.org/10.3390/ijms20081943
Received: 25 March 2019 / Revised: 17 April 2019 / Accepted: 19 April 2019 / Published: 20 April 2019
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Abstract

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. View Full-Text
Keywords: non-cryogenic structure; HIV-1 integrase; protein dynamics; XFELs non-cryogenic structure; HIV-1 integrase; protein dynamics; XFELs
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Park, J.-H.; Yun, J.-H.; Shi, Y.; Han, J.; Li, X.; Jin, Z.; Kim, T.; Park, J.; Park, S.; Liu, H.; Lee, W. Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers. Int. J. Mol. Sci. 2019, 20, 1943.

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