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Girard E, Lopes P, Spoerner M, Dhaussy AC, Prangé T, Kalbitzer HR, Colloc'h N. High Pressure Promotes Binding of the Allosteric Inhibitor Zn 2+-Cyclen in Crystals of Activated H-Ras. Chemistry 2024; 30:e202400304. [PMID: 38647362 DOI: 10.1002/chem.202400304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
In this work, we experimentally investigate the potency of high pressure to drive a protein toward an excited state where an inhibitor targeted for this state can bind. Ras proteins are small GTPases cycling between active GTP-bound and inactive GDP-bound states. Various states of GTP-bound Ras in active conformation coexist in solution, amongst them, state 2 which binds to effectors, and state 1, weakly populated at ambient conditions, which has a low affinity for effectors. Zn2+-cyclen is an allosteric inhibitor of Ras protein, designed to bind specifically to the state 1. In H-Ras(wt).Mg2+.GppNHp crystals soaked with Zn2+-cyclen, no binding could be observed, as expected in the state 2 conformation which is the dominant state at ambient pressure. Interestingly, Zn2+-cyclen binding is observed at 500 MPa pressure, close to the nucleotide, in Ras protein that is driven by pressure to a state 1 conformer. The unknown binding mode of Zn2+-cyclen to H-Ras can thus be fully characterized in atomic details. As a more general conjunction from our study, high pressure x-ray crystallography turns out to be a powerful method to induce transitions allowing drug binding in proteins that are in low-populated conformations at ambient conditions, enabling the design of specific inhibitors.
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Affiliation(s)
- Eric Girard
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | - Pedro Lopes
- Institute for Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Michael Spoerner
- Institute for Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | | | - Thierry Prangé
- CiTCoM, CNRS, Faculté de Pharmacie, Université de Paris-Cité, Paris, France
| | - Hans Robert Kalbitzer
- Institute for Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Nathalie Colloc'h
- ISTCT UMR6030, Centre Cyceron, CNRS - Université de Caen Normandie - Normandie Université, Caen, France
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP. Commun Biol 2024; 7:59. [PMID: 38216663 PMCID: PMC10786866 DOI: 10.1038/s42003-023-05609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/20/2023] [Indexed: 01/14/2024] Open
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature versus. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Altogether, our work indicates that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY, 10016, USA
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY, 10016, USA.
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Colloc'h N, Dhaussy AC, Girard E. Exploring the structural dynamics of proteins by pressure perturbation using macromolecular crystallography. Methods Enzymol 2023; 688:349-381. [PMID: 37748831 DOI: 10.1016/bs.mie.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
High pressure is a convenient thermodynamic parameter to probe the dynamics of proteins as it is intimately related to volume which is essential for protein function. To be biologically active, a protein fluctuates between different substates. Pressure perturbation can promote some hidden substates by modifying the population between them. High pressure macromolecular crystallography (HPMX) is a perfect tool to capture and to characterize such substates at a molecular level providing new insights on protein dynamics. The present chapter describes the use of the diamond anvil cell to perform HPMX experiments. It also provides tips on sample preparation and optimal data collection as well as on efficient analysis of the resulting high-pressure structures.
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Affiliation(s)
- Nathalie Colloc'h
- Imagerie et stratégies thérapeutiques pour les cancers et tissus cérébraux (ISTCT), CNRS Université de Caen Normandie, Centre Cyceron, Caen, France
| | | | - Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.538097. [PMID: 37205580 PMCID: PMC10187168 DOI: 10.1101/2023.05.02.538097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature vs. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes novel interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Together, our work argues that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY 10016
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY 10016
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Prangé T, Carpentier P, Dhaussy AC, van der Linden P, Girard E, Colloc'h N. Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization. Acta Crystallogr D Struct Biol 2022; 78:162-173. [DOI: 10.1107/s2059798321012134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022] Open
Abstract
The stability of the tetrameric enzyme urate oxidase in complex with excess of 8-azaxanthine was investigated either under high hydrostatic pressure per se or under a high pressure of argon. The active site is located at the interface of two subunits, and the catalytic activity is directly related to the integrity of the tetramer. This study demonstrates that applying pressure to a protein–ligand complex drives the thermodynamic equilibrium towards ligand saturation of the complex, revealing a new binding site. A transient dimeric intermediate that occurs during the pressure-induced dissociation process was characterized under argon pressure and excited substates of the enzyme that occur during the catalytic cycle can be trapped by pressure. Comparison of the different structures under pressure infers an allosteric role of the internal hydrophobic cavity in which argon is bound, since this cavity provides the necessary flexibility for the active site to function.
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Girard E, Lopes P, Spoerner M, Dhaussy AC, Prangé T, Kalbitzer HR, Colloc'h N. Equilibria between conformational states of the Ras oncogene protein revealed by high pressure crystallography. Chem Sci 2022; 13:2001-2010. [PMID: 35308861 PMCID: PMC8848853 DOI: 10.1039/d1sc05488k] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/12/2022] [Indexed: 01/04/2023] Open
Abstract
In this work, we experimentally investigate the allosteric transitions between conformational states on the Ras oncogene protein using high pressure crystallography. Ras protein is a small GTPase involved in central regulatory processes occurring in multiple conformational states. Ras acts as a molecular switch between active GTP-bound, and inactive GDP-bound states, controlling essential signal transduction pathways. An allosteric network of interactions between the effector binding regions and the membrane interacting regions is involved in Ras cycling. The conformational states which coexist simultaneously in solution possess higher Gibbs free energy than the ground state. Equilibria between these states can be shifted by applying pressure favouring conformations with lower partial molar volume, and has been previously analyzed by high-pressure NMR spectroscopy. High-pressure macromolecular crystallography (HPMX) is a powerful tool perfectly complementary to high-pressure NMR, allowing characterization at the molecular level with a high resolution the different allosteric states involved in the Ras cycling. We observe a transition above 300 MPa in the crystal leading to more stable conformers. Thus, we compare the crystallographic structures of Ras(wt)·Mg2+·GppNHp and Ras(D33K)·Mg2+·GppNHp at various high hydrostatic pressures. This gives insight into per-residue descriptions of the structural plasticity involved in allosteric equilibria between conformers. We have mapped out at atomic resolution the different segments of Ras protein which remain in the ground-state conformation or undergo structural changes, adopting excited-energy conformations corresponding to transient intermediate states. Such in crystallo phase transitions induced by pressure open the possibility to finely explore the structural determinants related to switching between Ras allosteric sub-states without any mutations nor exogenous partners. The equilibria between structural states induced by pressure within the crystal structure of Ras are illustrated with different colors corresponding to different Ras substates.![]()
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Affiliation(s)
- Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Pedro Lopes
- Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
| | - Michael Spoerner
- Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
| | | | - Thierry Prangé
- CiTCoM UMR 8038, CNRS Université de Paris, Faculté de Pharmacie, Paris, France
| | - Hans Robert Kalbitzer
- Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
| | - Nathalie Colloc'h
- ISTCT UMR 6030, CNRS, Université de Caen Normandie, CERVOxy Group, Centre Cyceron, Caen, France
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Prangé T, Girard E, Fourme R, Dhaussy A, Edwards B, Vaishnav A, Patel C, Guy‐Evans H, Hervé G, Evans DR. Pressure‐induced activation of latent dihydroorotase from Aquifex aeolicusas revealed by high pressure protein crystallography. FEBS J 2019; 286:1204-1213. [DOI: 10.1111/febs.14758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/19/2018] [Accepted: 01/15/2019] [Indexed: 01/25/2023]
Affiliation(s)
- Thierry Prangé
- Laboratoire de Cristallographie & RMN biologiques (UMR 8015 CNRS) Paris France
| | - Eric Girard
- CEA CNRS IBS Université Grenoble Alpes France
| | - Roger Fourme
- Synchrotron SOLEIL L'Orme des Merisiers Saint‐Aubin France
| | | | - Brian Edwards
- Department of Biochemistry and Molecular Biology Wayne State University School of Medicine Detroit MI USA
| | - Asmita Vaishnav
- Department of Biochemistry and Molecular Biology Wayne State University School of Medicine Detroit MI USA
| | - Chandni Patel
- Department of Biochemistry and Molecular Biology Wayne State University School of Medicine Detroit MI USA
| | - Hedeel Guy‐Evans
- Department of Chemistry Eastern Michigan University Ypsilanti MI USA
| | - Guy Hervé
- Laboratoire BIOSIPE Sorbonne Université Institut de Biologie Paris Seine Université Pierre et Marie Curie Paris France
| | - David R. Evans
- Department of Biochemistry and Molecular Biology Wayne State University School of Medicine Detroit MI USA
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