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

Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, China
Department of Engineering Physics, Tsinghua University, Beijing 100084, China
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;
Received: 25 March 2019 / Revised: 17 April 2019 / Accepted: 19 April 2019 / Published: 20 April 2019
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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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