1
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Hua Y, Strauss M, Fisher S, Mauser MFX, Manchet P, Smacchia M, Geyer P, Shayeghi A, Pfeffer M, Eggenweiler TH, Daly S, Commandeur J, Mayor M, Arndt M, Šolomek T, Köhler V. Giving the Green Light to Photochemical Uncaging of Large Biomolecules in High Vacuum. JACS AU 2023; 3:2790-2799. [PMID: 37885583 PMCID: PMC10598566 DOI: 10.1021/jacsau.3c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
The isolation of biomolecules in a high vacuum enables experiments on fragile species in the absence of a perturbing environment. Since many molecular properties are influenced by local electric fields, here we seek to gain control over the number of charges on a biopolymer by photochemical uncaging. We present the design, modeling, and synthesis of photoactive molecular tags, their labeling to peptides and proteins as well as their photochemical validation in solution and in the gas phase. The tailored tags can be selectively cleaved off at a well-defined time and without the need for any external charge-transferring agents. The energy of a single or two green photons can already trigger the process, and it is soft enough to ensure the integrity of the released biomolecular cargo. We exploit differences in the cleavage pathways in solution and in vacuum and observe a surprising robustness in upscaling the approach from a model system to genuine proteins. The interaction wavelength of 532 nm is compatible with various biomolecular entities, such as oligonucleotides or oligosaccharides.
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Affiliation(s)
- Yong Hua
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Marcel Strauss
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Sergey Fisher
- Van’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Martin F. X. Mauser
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Pierre Manchet
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Martina Smacchia
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Philipp Geyer
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Armin Shayeghi
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Michael Pfeffer
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Tim Henri Eggenweiler
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Steven Daly
- MS
Vision, Televisieweg
40, 1322 AM Almere, The Netherlands
| | - Jan Commandeur
- MS
Vision, Televisieweg
40, 1322 AM Almere, The Netherlands
| | - Marcel Mayor
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
- Institute
for Nanotechnology (INT), Karlsruhe Institute
of Technology (KIT), P.O. Box 3640, DE-76021 Karlsruhe Eggenstein-Leopoldshafen, Germany
- Lehn Institute
of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510274, P. R. China
| | - Markus Arndt
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Tomáš Šolomek
- Van’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Valentin Köhler
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
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2
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Zhou M, Jiao L, Xu S, Xu Y, Du M, Zhang X, Kong X. A novel method for photon unfolding spectroscopy of protein ions in the gas phase. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:043003. [PMID: 35489914 DOI: 10.1063/5.0080040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
In this study, a new experimental method for photon unfolding spectroscopy of protein ions based on a Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer was developed. The method of short-time Fourier transform has been applied here to obtain decay curves of target ions trapped in the cell of the FT ICR mass spectrometer. Based on the decay constants, the collision cross sections (CCSs) of target ions were calculated using the energetic hard-sphere model. By combining a tunable laser to the FT ICR mass spectrometer, the changes of CCSs of the target ions were recorded as a function of the wavelengths; thus, the photon isomerization spectrum was obtained. As one example, the photon isomerization spectrum of [Cyt c + 13H]13+ was recorded as the decay constants relative to the applied wavelengths of the laser in the 410-480 nm range. The spectrum shows a maximum at 426 nm, where an unfolded structure induced by a 4 s irradiation can be deduced. The strong peak at 426 nm was also observed for another ion of [Cyt c + 15H]15+, although some difference at 410 nm between the two spectra was found at the same time. This novel method can be expanded to ultraviolet or infrared region, making the experimental study of wavelength-dependent photon-induced structural variation of a variety of organic or biological molecules possible.
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Affiliation(s)
- Min Zhou
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Luyang Jiao
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Shiyin Xu
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Yicheng Xu
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Mengying Du
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Xianyi Zhang
- School of Physics and Electronic Information, Anhui Normal University, Wuhu 241000, China
| | - Xianglei Kong
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
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3
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Gas-phase heme structure of the singly charged cytochrome c anion produced by IR-laser ablation of a droplet beam. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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4
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Kitazaki A, Hasegawa T, Asami H, Kohno JY. Chemical denaturation of gas-phase albumin ions studied by photoelectron detachment yield spectroscopy and infrared laser ablation of droplet beams. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Asami H, Kitazaki A, Kawauchi N, Kohno JY. Gas-Phase Resonance Raman Spectroscopy Combined with IR-Laser Ablation of a Droplet Beam: Local Structural Analysis of Myoglobin. J Phys Chem A 2020; 124:9464-9469. [PMID: 33124826 DOI: 10.1021/acs.jpca.0c08058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gas phase spectroscopy is a powerful tool for examining fundamental chemical structures and properties free from solvent molecules. We developed a gas-phase resonance Raman spectroscopy combined with IR-laser ablation of a droplet beam, which allowed us to elucidate local structures around chromophores in gas-phase proteins and DNAs. To demonstrate the potential of this approach, we applied this method to myoglobin, one of the heme proteins, and elucidated its structures in the gas phase and in aqueous solution. The experimental spectra are compared with calculated spectra of stable heme structures for the structural determination. These results show the oxidation/spin states of the Fe atom in myoglobin in the gas phase and were compared with the aqueous solution from the obtained resonant Raman spectra. The present method gives an important tool to investigate the gas-phase structure of large biomolecules.
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Affiliation(s)
- Hiroya Asami
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Akihiro Kitazaki
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Norishi Kawauchi
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Jun-Ya Kohno
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
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6
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Mitochondrial absorption of short wavelength light drives primate blue retinal cones into glycolysis which may increase their pace of aging. Vis Neurosci 2019; 36:E007. [PMID: 31199213 DOI: 10.1017/s0952523819000063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Photoreceptors have high energy demands and densely packed mitochondria through which light passes before phototransduction. Old world primates including humans have three cone photoreceptor types mediating color vision with short (S blue), medium (M green), and long (L red) wavelength sensitivities. However, S-cones are enigmatic. They comprise <10% of the total cone population, their responses saturate early, and they are susceptible in aging and disease. Here, we show that primate S-cones actually have few mitochondria and are fueled by glycolysis, not by mitochondrial respiration. Glycolysis has a limited ability to sustain activity, potentially explaining early S-cone saturation. Mitochondria act as optical filters showing reduced light transmission at 400-450 nm where S-cones are most sensitive (420 nm). This absorbance is likely to arise in a mitochondrial porphyrin that absorbs strongly in the Soret band. Hence, reducing mitochondria will improve S-cone sensitivity but result in increased glycolysis as an alternative energy source, potentially increasing diabetic vulnerability due to restricted glucose access. Further, glycolysis carries a price resulting in premature functional decline as seen in aged S-cones. Soret band absorption may also impact on mitochondrial rich M and L cones by reducing sensitivity at the lower end of their spectral sensitivity range resulting in increased differentiation from S-cone responses. These data add to the list of unique characteristic of S-cones and may also explain aspects of their vulnerability.
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Daly S, Porrini M, Rosu F, Gabelica V. Electronic spectroscopy of isolated DNA polyanions. Faraday Discuss 2019; 217:361-382. [DOI: 10.1039/c8fd00207j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We address whether action spectroscopy could be used to investigate structural changes in gas-phase biomolecule (e.g. nucleic acid) ions, owing to changes in the environments of their chromophores, while taking advantage of the additional spectrometric separation of complex mixtures.
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Affiliation(s)
- Steven Daly
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle
- Université de Bordeaux
- Inserm & CNRS (ARNA, U1212, UMR5320)
- IECB
- 33607 Pessac
| | - Massimiliano Porrini
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle
- Université de Bordeaux
- Inserm & CNRS (ARNA, U1212, UMR5320)
- IECB
- 33607 Pessac
| | - Frédéric Rosu
- Institut Européen de Chimie et Biologie
- Université de Bordeaux
- CNRS & Inserm (IECB, UMS3033, US001)
- 33607 Pessac
- France
| | - Valérie Gabelica
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle
- Université de Bordeaux
- Inserm & CNRS (ARNA, U1212, UMR5320)
- IECB
- 33607 Pessac
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8
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Kulesza AJ, Titov E, Daly S, Włodarczyk R, Megow J, Saalfrank P, Choi CM, MacAleese L, Antoine R, Dugourd P. Excited States of Xanthene Analogues: Photofragmentation and Calculations by CC2 and Time-Dependent Density Functional Theory. Chemphyschem 2016; 17:3129-3138. [DOI: 10.1002/cphc.201600650] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Alexander Jan Kulesza
- Univ Lyon; Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière; F-69622 Lyon France
| | - Evgenii Titov
- Universität Potsdam, Institut für Chemie; Karl-Liebknecht-Straße 24-25, Haus 25 D-14476 Potsdam Germany
| | - Steven Daly
- Univ Lyon; Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière; F-69622 Lyon France
| | - Radosław Włodarczyk
- Universität Potsdam, Institut für Chemie; Karl-Liebknecht-Straße 24-25, Haus 25 D-14476 Potsdam Germany
| | - Jörg Megow
- Universität Potsdam, Institut für Chemie; Karl-Liebknecht-Straße 24-25, Haus 25 D-14476 Potsdam Germany
| | - Peter Saalfrank
- Universität Potsdam, Institut für Chemie; Karl-Liebknecht-Straße 24-25, Haus 25 D-14476 Potsdam Germany
| | - Chang Min Choi
- Univ Lyon; Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière; F-69622 Lyon France
| | - Luke MacAleese
- Univ Lyon; Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière; F-69622 Lyon France
| | - Rodolphe Antoine
- Univ Lyon; Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière; F-69622 Lyon France
| | - Philippe Dugourd
- Univ Lyon; Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière; F-69622 Lyon France
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9
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Ferrand L, Soorkia S, Grégoire G, Broquier M, Soep B, Shafizadeh N. Bonding of heme Fe(III) with dioxygen: observation and characterization of an incipient bond. Phys Chem Chem Phys 2016; 17:25693-9. [PMID: 26059068 DOI: 10.1039/c5cp01585e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
While ferrous heme (Fe(II)) within hemoproteins binds dioxygen efficiently, it has not yet been possible to observe the analog complex with ferric heme (Fe(III)). We present the first observation and characterization of the latter complex in a cooled ion trap. The bond formation enthalpy of ferric heme-O2 has been derived from the Van't Hoff equation by means of temperature dependent measurements. The binding energy of the [heme Fe(III)-O2](+) ionic complex is rather strong as compared to that of [heme Fe(III)-N2](+), showing the formation of an incipient Fe-O bond, which is confirmed by the electronic absorption spectra of the two complexes. This first observation of the [heme Fe(III)-O2](+) complex lays the basis for the precise description of its electronic states.
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Affiliation(s)
- Léa Ferrand
- ISMO, Univ Paris-Sud, CNRS UMR 8214, bat 210 Univ Paris-Sud 91405, Orsay Cedex, France.
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10
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Drink E, Dugourd P, Dumont E, Aronssohn N, Antoine R, Loison C. Optical properties of prodigiosin and obatoclax: action spectroscopy and theoretical calculations. Phys Chem Chem Phys 2016; 17:25946-55. [PMID: 26120608 DOI: 10.1039/c5cp01498k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prodiginine molecules (prodigiosin and obatoclax) are well-known pH-chromic dyes with promising anti-tumor properties. They present multiple tautomeric and rotameric forms. The protonation state and the structure of such flexible ligands in interaction with a protein are crucial to understand and to model the protein's biological activities. The determination of the protonation state via UV/vis absorption is possible if the ligand spectra of the neutral and protonated states are sufficiently different, and also if we can eliminate other factors potentially impacting the spectrum. Upon measuring the absorption spectra of the ligand in solution, varying solvents and pH values, we have determined that the optical properties of prodigiosin and obatoclax depend on the protonation state and not on the solvent permittivity constant. In parallel, action spectroscopy (using tunable lasers coupled to ion traps) in the gas phase of protonated and sodiated prodigiosin and obatoclax molecules has been performed to evaluate the sensitivity of the charge and the conformational state to their optical properties free of solvent. The spectra are interpreted using computational simulations of molecular structures and electronic excitations. The excitation energies are only slightly sensitive to various isomerizations, and may be used to distinguish between protonated and deprotonated states, even in the presence of a sodium counter-ion.
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Affiliation(s)
- Evangeline Drink
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne cedex, France.
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11
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Antoine R, Lemoine J, Dugourd P. Electron photodetachment dissociation for structural characterization of synthetic and bio-polymer anions. MASS SPECTROMETRY REVIEWS 2014; 33:501-22. [PMID: 24285407 DOI: 10.1002/mas.21402] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 12/21/2012] [Accepted: 01/08/2013] [Indexed: 05/25/2023]
Abstract
Tandem mass spectrometry (MS-MS) is a generic term evoking techniques dedicated to structural analysis, detection or quantification of molecules based on dissociation of a precursor ion into fragments. Searching for the most informative fragmentation patterns has led to the development of a vast array of activation modes that offer complementary ion reactivity and dissociation pathways. Collisional activation of ions using atoms, molecules or surface resulting in unimolecular dissociation of activated ions still plays a key role in tandem mass spectrometry. The discovery of electron capture dissociation (ECD) and then the development of other electron-ion or ion/ion reaction methods, constituted a significant breakthrough, especially for structural analysis of large biomolecules. Similarly, photon activation opened promising new frontiers in ion fragmentation owing to the ability of tightly controlled internal energy deposition and easy implementation on commercial instruments. Ion activation by photons includes slow heating methods such as infrared multiple photon dissociation (IRMPD) and black-body infrared radiative dissociation (BIRD) and higher energy methods like ultra-violet photodissociation (UVPD) and electron photo detachment dissociation (EPD). EPD occurs after UV irradiation of multiply negatively charged ions resulting in the formation of oxidized radical anions. The present paper reviews the hypothesis regarding the mechanisms of electron photo-detachment, radical formation and direct or activated dissociation pathways that support the observation of odd and even electron product ions. Finally, the value of EPD as a complementary structural analysis tool is illustrated through selected examples of synthetic polymers, oligonucleotides, polypeptides, lipids, and polysaccharides.
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Affiliation(s)
- Rodolphe Antoine
- University of Lyon, F-69622, Lyon, France; CNRS et Université Lyon 1, UMR5306, Institut Lumière Matière, Villeurbanne, France
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12
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Dunbar RC. Spectroscopy of Metal-Ion Complexes with Peptide-Related Ligands. Top Curr Chem (Cham) 2014; 364:183-223. [DOI: 10.1007/128_2014_578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Wyer JA, Jørgensen AV, Møller Pedersen B, Brøndsted Nielsen S. Gas-phase spectroscopy of ferric heme-NO complexes. Chemphyschem 2013; 14:4109-13. [PMID: 24166979 DOI: 10.1002/cphc.201300843] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Indexed: 11/10/2022]
Abstract
Weakly bound complexes between ferric heme cations and NO were synthesised in the gas phase from ion-molecule reactions, and their absorption measured based on photodissociation yields. The Soret band, which serves as an important marker band for heme-protein spectroscopy, is maximal at 357±5 nm and significantly blue-shifted compared to ferric heme nitrosyl proteins (maxima between 408 and 422 nm). This is in stark contrast to the Q-band absorption where the protein microenvironment is nearly innocent in perturbing the electronic structure of the porphyrin macrocycle. Photodissociation is primarily through loss of NO. In contrast to the Q-band region, two-photon absorption was seen in the Soret band despite NO loss only requiring ∼1 eV. A model based on intersystem crossing to a long-lived triplet state where a barrier has to be surmounted is suggested. Finally, we summarise the measured absorption maxima of heme and its complexes with amino acids and NO.
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Affiliation(s)
- Jean A Wyer
- Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C (Denmark), Fax: (+45) 8612 0740.
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14
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Wyer JA, Brøndsted Nielsen S. Absorption by Isolated Ferric Heme Nitrosyl Cations In Vacuo. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206213] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15
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Wyer JA, Brøndsted Nielsen S. Absorption by Isolated Ferric Heme Nitrosyl Cations In Vacuo. Angew Chem Int Ed Engl 2012; 51:10256-60. [DOI: 10.1002/anie.201206213] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Indexed: 11/12/2022]
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