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Prakash A, Li Z, Chirasani VR, Rasquinha JA, Valentin NH, Hubbard GB, Yin G, Dohlman HG, Campbell SL. Molecular and Functional Profiling of Gαi as an Intracellular pH Sensor. RESEARCH SQUARE 2024:rs.3.rs-4203924. [PMID: 38746411 PMCID: PMC11092800 DOI: 10.21203/rs.3.rs-4203924/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Heterotrimeric G proteins (Gα, Gβ and Gγ) act downstream of G-protein-coupled receptors (GPCRs) to mediate signaling pathways that regulate various physiological processes and human disease conditions. Previously, human Gαi and its yeast homolog Gpa1 have been reported to function as intracellular pH sensors, yet the pH sensing capabilities of Gαi and the underlying mechanism remain to be established. Herein, we identify a pH sensing network within Gαi, and evaluate the consequences of pH modulation on the structure and stability of the G-protein. We find that changes over the physiological pH range significantly alter the structure and stability of Gαi-GDP, with the protein undergoing a disorder-to-order transition as the pH is raised from 6.8 to 7.5. Further, we find that modulation of intracellular pH in HEK293 cells regulates Gαi-Gβγ release. Identification of key residues in the pH-sensing network allowed the generation of low pH mimetics that attenuate Gαi-Gβγ release. Our findings, taken together, indicate that pH-dependent structural changes in Gαi alter the agonist-mediated Gβγ dissociation necessary for proper signaling.
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Affiliation(s)
- Ajit Prakash
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zijian Li
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Venkata R. Chirasani
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juhi A. Rasquinha
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie H. Valentin
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Garrett B. Hubbard
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Henrik G. Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sharon L. Campbell
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Freindorf M, Delgado AAA, Kraka E. CO bonding in hexa‐ and pentacoordinate carboxy‐neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study. J Comput Chem 2022. [DOI: 10.1002/jcc.26973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marek Freindorf
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | | | - Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
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Abstract
The use of neutron protein crystallography (NPX) is expanding rapidly, with most structures determined in the last decade. This growth is stimulated by a number of developments, spanning from the building of new NPX beamlines to the availability of improved software for structure refinement. The main bottleneck preventing structural biologists from adding NPX to the suite of methods commonly used is the large volume of the individual crystals required for a successful experiment. A survey of deposited NPX structures in the Protein Data Bank shows that about two-thirds came from crystals prepared using vapor diffusion, while batch and dialysis-based methods all-together contribute to most of the remaining one-third. This chapter explains the underlying principles of these protein crystallization methods and provides practical examples that may help others to successfully prepare large crystals for NPX.
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Kovalevsky A, Gerlits O, Beltran K, Weiss KL, Keen DA, Blakeley MP, Louis JM, Weber IT. Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease. Methods Enzymol 2020; 634:257-279. [PMID: 32093836 DOI: 10.1016/bs.mie.2019.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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.
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Affiliation(s)
- Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, United States
| | - Kaira Beltran
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, United States
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot, United Kingdom
| | | | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, United States
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, GA, United States; Department of Chemistry, Georgia State University, Atlanta, GA, United States
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Svejdal RR, Dickinson ER, Sticker D, Kutter JP, Rand KD. Thiol-ene Microfluidic Chip for Performing Hydrogen/Deuterium Exchange of Proteins at Subsecond Time Scales. Anal Chem 2018; 91:1309-1317. [DOI: 10.1021/acs.analchem.8b03050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rasmus R. Svejdal
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Eleanor R. Dickinson
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Drago Sticker
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
- Microscale Analytical Systems Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jörg P. Kutter
- Microscale Analytical Systems Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Kasper D. Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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Neutron macromolecular crystallography. Emerg Top Life Sci 2018; 2:39-55. [DOI: 10.1042/etls20170083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/12/2017] [Accepted: 12/19/2017] [Indexed: 01/02/2023]
Abstract
Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biological processes and drug-binding. In the last ca. 5 years, new beamlines have come online at reactor neutron sources, such as BIODIFF at Heinz Maier-Leibnitz Zentrum and IMAGINE at Oak Ridge National Laboratory (ORNL), and at spallation neutron sources, such as MaNDi at ORNL and iBIX at the Japan Proton Accelerator Research Complex. In addition, significant improvements have been made to existing beamlines, such as LADI-III at the Institut Laue-Langevin. The new and improved instrumentations are allowing sub-mm3 crystals to be regularly used for data collection and permitting the study of larger systems (unit-cell edges >100 Å). Owing to this increase in capacity and capability, many more studies have been performed and for a wider range of macromolecules, including enzymes, signalling proteins, transport proteins, sugar-binding proteins, fluorescent proteins, hormones and oligonucleotides; of the 126 structures deposited in the Protein Data Bank, more than half have been released since 2013 (65/126, 52%). Although the overall number is still relatively small, there are a growing number of examples for which neutron macromolecular crystallography has provided the answers to questions that otherwise remained elusive.
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Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme. Nat Commun 2017; 8:955. [PMID: 29038582 PMCID: PMC5643538 DOI: 10.1038/s41467-017-01060-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/15/2017] [Indexed: 11/13/2022] Open
Abstract
Enzymes dependent on pyridoxal 5′-phosphate (PLP, the active form of vitamin B6) perform a myriad of diverse chemical transformations. They promote various reactions by modulating the electronic states of PLP through weak interactions in the active site. Neutron crystallography has the unique ability of visualizing the nuclear positions of hydrogen atoms in macromolecules. Here we present a room-temperature neutron structure of a homodimeric PLP-dependent enzyme, aspartate aminotransferase, which was reacted in situ with α-methylaspartate. In one monomer, the PLP remained as an internal aldimine with a deprotonated Schiff base. In the second monomer, the external aldimine formed with the substrate analog. We observe a deuterium equidistant between the Schiff base and the C-terminal carboxylate of the substrate, a position indicative of a low-barrier hydrogen bond. Quantum chemical calculations and a low-pH room-temperature X-ray structure provide insight into the physical phenomena that control the electronic modulation in aspartate aminotransferase. Pyridoxal 5’-phosphate (PLP) is a ubiquitous co factor for diverse enzymes, among them aspartate aminotransferase. Here the authors use neutron crystallography, which allows the visualization of the positions of hydrogen atoms, and computation to characterize the catalytic mechanism of the enzyme.
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Chen JCH, Unkefer CJ. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography. IUCRJ 2017; 4:72-86. [PMID: 28250943 PMCID: PMC5331467 DOI: 10.1107/s205225251601664x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002-2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallo-graphy in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.
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Affiliation(s)
- Julian C.-H. Chen
- Bioscience Division, Protein Crystallography Station, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Clifford J. Unkefer
- Bioscience Division, Protein Crystallography Station, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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