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Asundi AS, Noonikara-Poyil A, Phan VQH, Dias HVR, Sarangi R. Understanding Copper(I)-Ethylene Bonding Using Cu K-Edge X-ray Absorption Spectroscopy. Inorg Chem 2023; 62:19298-19311. [PMID: 37963391 DOI: 10.1021/acs.inorgchem.3c02904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Copper plays many important roles in ethylene chemistry, thus generating significant interest in understanding the structures, bonding, and properties of copper(I)-ethylene complexes. In this work, the ethylene binding characteristics of a series of isolable Cu(I)-ethylene compounds supported by a systematic set of fluorinated and nonfluorinated bis- and tris(pyrazolyl)borate and the related bis(pyrazolyl)methane ligands have been investigated. Through a combination of X-ray absorption spectroscopy and quantum chemical calculations, we characterize their geometric and electronic structures and the role that fluorinated ligands play in lowering the electron density at Cu sites. Such ligands increase the ethylene-to-Cu σ-donor interaction and, correspondingly, decrease the Cu-to-ethylene π back-bonding. This latter interaction leads to a partial vacancy in the Cu 3d level, which manifests experimentally as a low-energy feature in the Cu K pre-edge, allowing for its direct observation and comparison within a series of Cu(I) compounds. The pre-edge feature is reproduced by TD-DFT calculations, and its energy position and total intensity are used to quantitatively probe Cu-ethylene bonding. The variations in the Cu electronic structure influence the stability and overall ethylene bonding strength of these compounds, ultimately showing how substituents on the supporting ligands have a notable effect on their physical and chemical properties.
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Affiliation(s)
- Arun S Asundi
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Anurag Noonikara-Poyil
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Vo Quang Huy Phan
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, United States
| | - H V Rasika Dias
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Ritimukta Sarangi
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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Azhar BJ, Abbas S, Aman S, Yamburenko MV, Chen W, Müller L, Uzun B, Jewell DA, Dong J, Shakeel SN, Groth G, Binder BM, Grigoryan G, Schaller GE. Basis for high-affinity ethylene binding by the ethylene receptor ETR1 of Arabidopsis. Proc Natl Acad Sci U S A 2023; 120:e2215195120. [PMID: 37253004 PMCID: PMC10266040 DOI: 10.1073/pnas.2215195120] [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: 09/06/2022] [Accepted: 04/14/2023] [Indexed: 06/01/2023] Open
Abstract
The gaseous hormone ethylene is perceived in plants by membrane-bound receptors, the best studied of these being ETR1 from Arabidopsis. Ethylene receptors can mediate a response to ethylene concentrations at less than one part per billion; however, the mechanistic basis for such high-affinity ligand binding has remained elusive. Here we identify an Asp residue within the ETR1 transmembrane domain that plays a critical role in ethylene binding. Site-directed mutation of the Asp to Asn results in a functional receptor that has a reduced affinity for ethylene, but still mediates ethylene responses in planta. The Asp residue is highly conserved among ethylene receptor-like proteins in plants and bacteria, but Asn variants exist, pointing to the physiological relevance of modulating ethylene-binding kinetics. Our results also support a bifunctional role for the Asp residue in forming a polar bridge to a conserved Lys residue in the receptor to mediate changes in signaling output. We propose a new structural model for the mechanism of ethylene binding and signal transduction, one with similarities to that found in a mammalian olfactory receptor.
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Affiliation(s)
- Beenish J. Azhar
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
- Department of Biochemistry, Quaid-i-azam University, Islamabad45320, Pakistan
| | - Safdar Abbas
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
- Department of Biochemistry, Quaid-i-azam University, Islamabad45320, Pakistan
| | - Sitwat Aman
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
| | | | - Wei Chen
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
| | - Lena Müller
- Institute of Biochemical Plant Physiology, Heinrich Heine University Düsseldorf,40225Düsseldorf, Germany
| | - Buket Uzun
- Institute of Biochemical Plant Physiology, Heinrich Heine University Düsseldorf,40225Düsseldorf, Germany
| | - David A. Jewell
- Department of Computer Science, Dartmouth College, Hanover, NH03755
| | - Jian Dong
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
| | - Samina N. Shakeel
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
- Department of Biochemistry, Quaid-i-azam University, Islamabad45320, Pakistan
| | - Georg Groth
- Institute of Biochemical Plant Physiology, Heinrich Heine University Düsseldorf,40225Düsseldorf, Germany
| | - Brad M. Binder
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN37996
| | - Gevorg Grigoryan
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
- Department of Computer Science, Dartmouth College, Hanover, NH03755
| | - G. Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755
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Cutsail G, Schott-Verdugo S, Müller L, DeBeer S, Groth G, Gohlke H. Spectroscopic and QM/MM studies of the Cu(I) binding site of the plant ethylene receptor ETR1. Biophys J 2022; 121:3862-3873. [PMID: 36086818 PMCID: PMC9674993 DOI: 10.1016/j.bpj.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/17/2022] [Accepted: 09/06/2022] [Indexed: 11/15/2022] Open
Abstract
Herein, we present, to our knowledge, the first spectroscopic characterization of the Cu(I) active site of the plant ethylene receptor ETR1. The x-ray absorption (XAS) and extended x-ray absorption fine structure (EXAFS) spectroscopies presented here establish that ETR1 has a low-coordinate Cu(I) site. The EXAFS resolves a mixed first coordination sphere of N/O and S scatterers at distances consistent with potential histidine and cysteine residues. This finding agrees with the coordination of residues C65 and H69 to the Cu(I) site, which are critical for ethylene activity and well conserved. Furthermore, the Cu K-edge XAS and EXAFS of ETR1 exhibit spectroscopic changes upon addition of ethylene that are attributed to modifications in the Cu(I) coordination environment, suggestive of ethylene binding. Results from umbrella sampling simulations of the proposed ethylene binding helix of ETR1 at a mixed quantum mechanics/molecular mechanics level agree with the EXAFS fit distance changes upon ethylene binding, particularly in the increase of the distance between H69 and Cu(I), and yield binding energetics comparable with experimental dissociation constants. The observed changes in the copper coordination environment might be the triggering signal for the transmission of the ethylene response.
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Affiliation(s)
- George Cutsail
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany; Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, Essen, Germany
| | - Stephan Schott-Verdugo
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Bioinformatics), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Lena Müller
- Institut für Biochemische Pflanzenphysiologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Georg Groth
- Institut für Biochemische Pflanzenphysiologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Bioinformatics), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany; Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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Mehara J, Watson BT, Noonikara-Poyil A, Zacharias AO, Roithová J, Rasika Dias HV. Binding Interactions in Copper, Silver and Gold π-Complexes. Chemistry 2022; 28:e202103984. [PMID: 35076112 PMCID: PMC9305286 DOI: 10.1002/chem.202103984] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Indexed: 12/14/2022]
Abstract
The copper(I), silver(I), and gold(I) metals bind π‐ligands by σ‐bonding and π‐back bonding interactions. These interactions were investigated using bidentate ancillary ligands with electron donating and withdrawing substituents. The π‐ligands span from ethylene to larger terminal and internal alkenes and alkynes. Results of X‐ray crystallography, NMR, and IR spectroscopy and gas phase experiments show that the binding energies increase in the order Ag<Cu<Au and the binding energies are slightly higher for alkynes than for alkenes. Modulation of the electron density at the metal using substituents on the ancillary ligands shows that the π‐back bonding interaction plays a dominant role for the binding in the copper and gold complexes.
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Affiliation(s)
- Jaya Mehara
- Department of Spectroscopy and Catalysis, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen (The, Netherlands
| | - Brandon T Watson
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Anurag Noonikara-Poyil
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Adway O Zacharias
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Jana Roithová
- Department of Spectroscopy and Catalysis, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen (The, Netherlands
| | - H V Rasika Dias
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas, 76019, USA
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Joy S, Periyasamy G. Binding mode of 1-methylcyclopropene, an ethylene antagonist in various copper models. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2019.112662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Structural Model of the ETR1 Ethylene Receptor Transmembrane Sensor Domain. Sci Rep 2019; 9:8869. [PMID: 31222090 PMCID: PMC6586836 DOI: 10.1038/s41598-019-45189-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/03/2019] [Indexed: 01/14/2023] Open
Abstract
The structure, mechanism of action and copper stoichiometry of the transmembrane sensor domain of the plant ethylene receptor ETR1 and homologs have remained elusive, hampering the understanding on how the perception of the plant hormone ethylene is transformed into a downstream signal. We generated the first structural model of the transmembrane sensor domain of ETR1 by integrating ab initio structure prediction and coevolutionary information. To refine and independently validate the model, we determined protein-related copper stoichiometries on purified receptor preparations and explored the helix arrangement by tryptophan scanning mutagenesis. All-atom molecular dynamics simulations of the dimeric model reveal how ethylene can bind proximal to the copper ions in the receptor, illustrating the initial stages of the ethylene perception process.
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A systematic examination of ligand basicity effects on bonding in palladium(0)- and palladium(II)-ethylene complexes. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Greene C, Grudzien PK, York JT. Binding and electrophilic activation of ethylene by zinc(II), cadmium(II), and mercury(II) complexes: A theoretical investigation. J Organomet Chem 2017. [DOI: 10.1016/j.jorganchem.2017.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Light KM, Wisniewski JA, Vinyard WA, Kieber-Emmons MT. Perception of the plant hormone ethylene: known-knowns and known-unknowns. J Biol Inorg Chem 2016; 21:715-28. [DOI: 10.1007/s00775-016-1378-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 07/19/2016] [Indexed: 12/18/2022]
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Halbert S, Gérard H. A computational study of the effects of ancillary ligands on copper(i)–ethylene interaction. NEW J CHEM 2015. [DOI: 10.1039/c5nj00546a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural and electronic calculations on a ligand database are used to quantify the influence of the ancillary ligands and coordination mode on the electronic structure of Cu(i) ethylene complexes.
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Affiliation(s)
- Stéphanie Halbert
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR 7616
- Laboratoire de Chimie Théorique
- Paris
| | - Hélène Gérard
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR 7616
- Laboratoire de Chimie Théorique
- Paris
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