title: Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.
abstract: Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.
authors.affiliation: Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Oksana
authors.initials: O
authors.lastname: Gerlits
authors.affiliation: UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Troy
authors.initials: T
authors.lastname: Wymore
authors.affiliation: Solid State Physics Division, BARC, Trombay, Mumbai, 400085, India.
authors.forename: Amit
authors.initials: A
authors.lastname: Das
authors.affiliation: Departments of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA.
authors.forename: Chen-Hsiang
authors.initials: CH
authors.lastname: Shen
authors.affiliation: UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Jerry M
authors.initials: JM
authors.lastname: Parks
authors.affiliation: UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
authors.affiliation: Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Weiss
authors.affiliation: ISIS Facility, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK.
authors.forename: David A
authors.initials: DA
authors.lastname: Keen
authors.affiliation: Large-Scale Structures Group, Institut Laue Langevin, 71 avenue des Martyrs - CS 20156, 38042, Grenoble Cedex 9, France.
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Blakeley
authors.affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Louis
authors.affiliation: Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Langan
authors.affiliation: Departments of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA.
authors.forename: Irene T
authors.initials: IT
authors.lastname: Weber
authors.affiliation: Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. kovalevskyay@ornl.gov.
authors.forename: Andrey
authors.identifier: http://orcid.org/0000-0003-4459-9142
authors.initials: A
authors.lastname: Kovalevsky
mesh_terms: D020134:Catalytic Domain; D003461:Crystallography / Q000379:methods*; D016333:HIV Protease / Q000737:chemistry / Q000378:metabolism*; D011522:Protons; D011789:Quantum Theory; D055672:Static Electricity; D013379:Substrate Specificity
chemical_list: D011522:Protons; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1
keywords: QM/MM modeling; aspartic protease; enzymes; neutron crystallography; proton transfer