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Title: Chapter Twelve - Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease

Abstract

HIV-1 protease is an essential therapeutic target for the design and development of antiviral inhibitors to treat AIDS. We used room temperature neutron crystallography to accurately determine hydrogen atom positions in several protease complexes with clinical drugs, amprenavir and darunavir. Hydrogen bonding interactions were carefully mapped to provide an unprecedented picture of drug binding to the protease target. We demonstrate that hydrogen atom positions within the enzyme catalytic site can be altered by introducing drug resistant mutations and by protonating surface residues that trigger proton transfer reactions between the catalytic Asp residues and the hydroxyl group of darunavir. When protein perdeuteration is not feasible, we validate the use of initial H/D exchange with unfolded protein and partial deuteration in pure D2O with hydrogenous glycerol to maximize deuterium incorporation into the protein, with no detrimental effects on the growth of quality crystals suitable for neutron diffraction experiments.

Authors:
ORCiD logo [1];  [2];  [2]; ORCiD logo [1];  [3];  [4];  [5];  [6]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Tennessee Wesleyan Univ., Athens, TN (United States)
  3. Science and Technology Facilities Council (STFC), Oxford (United Kingdom). Rutherford Appleton Lab. (RAL)
  4. Inst. Laue-Langevin (ILL), Grenoble (France)
  5. Georgia State Univ., Atlanta, GA (United States)
  6. National Inst. of Health (NIH), Bethesda, MD (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1606039
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Methods in Enzymology
Additional Journal Information:
Journal Volume: 634; Journal Issue: 1; Journal ID: ISSN 0076-6879
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; Human immunodeficiency virus type 1; Acquired immunodeficiency syndrome; HIV-1 protease; Structure-assisted drug design; Clinical protease inhibitor; Neutron crystallography; Protonation state; Proton transfer; Hydrogen bond

Citation Formats

Kovalevsky, Andrii Y., Beltran, Kaira, Gerlits, Oksana, Weiss, Kevin L., Keen, David A., Blakeley, Matthew P., Weber, Irene, and Louis, John M.. Chapter Twelve - Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease. United States: N. p., 2020. Web. https://doi.org/10.1016/bs.mie.2019.12.002.
Kovalevsky, Andrii Y., Beltran, Kaira, Gerlits, Oksana, Weiss, Kevin L., Keen, David A., Blakeley, Matthew P., Weber, Irene, & Louis, John M.. Chapter Twelve - Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease. United States. https://doi.org/10.1016/bs.mie.2019.12.002
Kovalevsky, Andrii Y., Beltran, Kaira, Gerlits, Oksana, Weiss, Kevin L., Keen, David A., Blakeley, Matthew P., Weber, Irene, and Louis, John M.. Sun . "Chapter Twelve - Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease". United States. https://doi.org/10.1016/bs.mie.2019.12.002. https://www.osti.gov/servlets/purl/1606039.
@article{osti_1606039,
title = {Chapter Twelve - Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease},
author = {Kovalevsky, Andrii Y. and Beltran, Kaira and Gerlits, Oksana and Weiss, Kevin L. and Keen, David A. and Blakeley, Matthew P. and Weber, Irene and Louis, John M.},
abstractNote = {HIV-1 protease is an essential therapeutic target for the design and development of antiviral inhibitors to treat AIDS. We used room temperature neutron crystallography to accurately determine hydrogen atom positions in several protease complexes with clinical drugs, amprenavir and darunavir. Hydrogen bonding interactions were carefully mapped to provide an unprecedented picture of drug binding to the protease target. We demonstrate that hydrogen atom positions within the enzyme catalytic site can be altered by introducing drug resistant mutations and by protonating surface residues that trigger proton transfer reactions between the catalytic Asp residues and the hydroxyl group of darunavir. When protein perdeuteration is not feasible, we validate the use of initial H/D exchange with unfolded protein and partial deuteration in pure D2O with hydrogenous glycerol to maximize deuterium incorporation into the protein, with no detrimental effects on the growth of quality crystals suitable for neutron diffraction experiments.},
doi = {10.1016/bs.mie.2019.12.002},
journal = {Methods in Enzymology},
number = 1,
volume = 634,
place = {United States},
year = {2020},
month = {3}
}

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