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Dali A, Gabler T, Sebastiani F, Furtmüller PG, Becucci M, Hofbauer S, Smulevich G. Entrance channels to coproheme in coproporphyrin ferrochelatase probed by exogenous imidazole binding. J Inorg Biochem 2024; 260:112681. [PMID: 39146673 DOI: 10.1016/j.jinorgbio.2024.112681] [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: 05/17/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/17/2024]
Abstract
Iron insertion into porphyrins is an essential step in heme biosynthesis. In the coproporphyrin-dependent pathway, specific to monoderm bacteria, this reaction is catalyzed by the monomeric enzyme coproporphyrin ferrochelatase. In addition to the mechanistic details of the metalation of the porphyrin, the identification of the substrate access channel for ferrous iron to the active site is important to fully understand this enzymatic system. In fact, whether the iron reaches the active site from the distal or the proximal porphyrin side is still under debate. In this study we have thoroughly addressed this question in Listeria monocytogenes coproporphyrin ferrochelatase by X-ray crystallography, steady-state and pre-steady-state imidazole ligand binding studies, together with a detailed spectroscopic characterization using resonance Raman and UV-vis absorption spectroscopies in solution. Analysis of the X-ray structures of coproporphyrin ferrochelatase-coproporphyrin III crystals soaked with ferrous iron shows that iron is present on both sides of the porphyrin. The kinetic and spectroscopic study of imidazole binding to coproporphyrin ferrochelatase‑iron coproporphyrin III clearly indicates the presence of two possible binding sites in this monomeric enzyme that influence each other, which is confirmed by the observed cooperativity at steady-state and a biphasic behavior in the pre-steady-state experiments. The current results are discussed in the context of the entire heme biosynthetic pathway and pave the way for future studies focusing on protein-protein interactions.
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Affiliation(s)
- Andrea Dali
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Thomas Gabler
- BOKU University, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Paul G Furtmüller
- BOKU University, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy; The European Laboratory for Non-Linear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino (FI), Italy.
| | - Stefan Hofbauer
- BOKU University, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria.
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy; INSTM Research Unit of Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy.
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2
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Yanagisawa S, Kamei T, Shimada A, Gladyck S, Aras S, Hüttemann M, Grossman LI, Kubo M. Resonance Raman spectral analysis of the heme site structure of cytochrome c oxidase with its positive regulator CHCHD2. J Inorg Biochem 2024; 260:112673. [PMID: 39094247 DOI: 10.1016/j.jinorgbio.2024.112673] [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: 05/14/2024] [Revised: 07/10/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024]
Abstract
Cytochrome c oxidase (CcO) reduces O2, pumps protons in the mitochondrial respiratory chain, and is essential for oxygen consumption in the cell. The coiled-coil-helix-coiled-coil-helix domain-containing 2 (CHCHD2; also known as mitochondrial nuclear retrograde regulator 1 [MNRR1], Parkinson's disease 22 [PARK22] and aging-associated gene 10 protein [AAG10]) is a protein that binds to CcO from the intermembrane space and positively regulates the activity of CcO. Despite the importance of CHCHD2 in mitochondrial function, the mechanism of action of CHCHD2 and structural information regarding its binding to CcO remain unknown. Here, we utilized visible resonance Raman spectroscopy to investigate the structural changes around the hemes in CcO in the reduced and CO-bound states upon CHCHD2 binding. We found that CHCHD2 has a significant impact on the structure of CcO in the reduced state. Mapping of the heme peripheries that result in Raman spectral changes in the structure of CcO highlighted helices IX and X near the hemes as sites where CHCHD2 takes action. Part of helix IX is exposed in the intermembrane space, whereas helix X, located between both hemes, may play a key role in proton uptake to a proton-loading site in the reduced state for proton pumping. Taken together, our results suggested that CHCHD2 binds near helix IX and induces a structural change in helix X, accelerating proton uptake.
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Affiliation(s)
| | - Takuto Kamei
- Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Atsuhiro Shimada
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Stephanie Gladyck
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Siddhesh Aras
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Lawrence I Grossman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Minoru Kubo
- Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan.
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3
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Abramczyk H, Surmacki JM, Kopeć M. A Novel HER2 Protein Identification Methodology in Breast Cancer Cells Using Raman Spectroscopy and Raman Imaging: An Analytical Validation Study. J Med Chem 2024; 67:17629-17639. [PMID: 39305290 DOI: 10.1021/acs.jmedchem.4c01591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2024]
Abstract
Conventional assays such as immunohistochemistry (IHC) and in situ hybridization (ISH) used in clinical procedures for quantification of the human epidermal growth factor receptor-2 (HER2) status in breast cancer have many limitations. In the current study, we have used HER2 expression in a broad range of breast cancer phenotypes to explore the potential utility of a novel immunodetection technique using Raman spectroscopy and Raman imaging combined with artificial intelligence models. The correlations between the Raman method and conventional HER2 testing methodologies (IHC and ISH) have been tested. Raman measurements showed a strong linear correlation (p = 0.05, R2=0,9816) with IHC analysis in the studied breast cell lines: MCF-10A, MCF-7, MDA-MB-231, HTB-30 (SK-BR-3), and AU-565 represent normal, nontumorigenic epithelial cells, triple-positive breast carcinoma, and triple-negative breast cancer cell lines. Analytic testing of Raman spectroscopy and Raman imaging demonstrated that this method may offer advantages over the currently used diagnostic methodologies.
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Affiliation(s)
- Halina Abramczyk
- Laboratory of Laser Molecular Spectroscopy, Department of Chemistry, Institute of Applied Radiation Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590Lodz, Poland
| | - Jakub Maciej Surmacki
- Laboratory of Laser Molecular Spectroscopy, Department of Chemistry, Institute of Applied Radiation Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590Lodz, Poland
| | - Monika Kopeć
- Laboratory of Laser Molecular Spectroscopy, Department of Chemistry, Institute of Applied Radiation Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590Lodz, Poland
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4
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Schweitzer-Stenner R. Probing the versatility of cytochrome c by spectroscopic means: A Laudatio on resonance Raman spectroscopy. J Inorg Biochem 2024; 259:112641. [PMID: 38901065 DOI: 10.1016/j.jinorgbio.2024.112641] [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: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Over the last 50 years resonance Raman spectroscopy has become an invaluable tool for the exploration of chromophores in biological macromolecules. Among them, heme proteins and metal complexes have attracted considerable attention. This interest results from the fact that resonance Raman spectroscopy probes the vibrational dynamics of these chromophores without direct interference from the surrounding. However, the indirect influence via through-bond and through-space chromophore-protein interactions can be conveniently probed and analyzed. This review article illustrates this point by focusing on class 1 cytochrome c, a comparatively simple heme protein generally known as electron carrier in mitochondria. The article demonstrates how through selective excitation of resonance Raman active modes information about the ligation, the redox state and the spin state of the heme iron can be obtained from band positions in the Raman spectra. The investigation of intensities and depolarization ratios emerged as tools for the analysis of in-plane and out-of-plane deformations of the heme macrocycle. The article further shows how resonance Raman spectroscopy was used to characterize partially unfolded states of oxidized cytochrome c. Finally, it describes its use for exploring structural changes due to the protein's binding to anionic surfaces like cardiolipin containing membranes.
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5
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Schelvis JPM, Chen Z, Messina MA, Catalano J. Effect of CO binding to P450 BM3 F393 mutants on electron density distribution in the heme cofactor. J Inorg Biochem 2024; 259:112660. [PMID: 39002177 DOI: 10.1016/j.jinorgbio.2024.112660] [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: 03/31/2024] [Revised: 06/04/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024]
Abstract
Resonance Raman spectroscopy has been performed on a set of cytochrome P450 BM3 heme domains in which mutation of the highly conserved Phe393 induces significant variation in heme iron reduction potential. In previous work [Chen, Z., Ost, T.W.B., and Schelvis, J.P.M. (2004) Biochemistry 43, 1798-1808], a correlation between heme vinyl conformation and the heme iron reduction potential indicated a steric control by the protein over the distribution of electron density in the reduced heme cofactor. The current study aims to monitor changes in electron density on the ferrous heme cofactor following CO binding. In addition, ferric-NO complexes have been studied to investigate potential changes to the proximal Cys400 thiolate. We find that binding of CO to the ferrous heme domains results in a reorientation of the vinyl groups to a largely out-of-plane conformation, the extent of which correlates with the size of the residue at position 393. We conclude that FeII dπ back bonding to the CO ligand largely takes away the need for conjugation of the vinyl groups with the porphyrin ring to accommodate FeII dπ back bonding to the porphyrin ligand. The ferrous-CO and ferric-NO data are consistent with a small decrease in σ-electron donation from the proximal Cys400 thiolate in the F393A mutant and, to a lesser extent, the F393H mutant, potentially due to a small increase in hydrogen bonding to the proximal ligand. Phe393 seems strategically placed to preserve robust σ-electron donation to the heme iron and to fine-tune its electron density by limiting vinyl group rotation.
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Affiliation(s)
- Johannes P M Schelvis
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA.
| | - Zhucheng Chen
- School of Life Sciences, Tsinghua University, Beijing, China.
| | - Marisa A Messina
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA.
| | - Jaclyn Catalano
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA.
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6
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Migdalski M, Czepiel J, Moskal P, Birczyńska-Zych M, Kucharska M, Biesiada G, Stokłosa A, Garlicki A, Wesełucha-Birczyńska A. Raman and resonance Raman spectroscopic study of red blood cells in patients diagnosed with malaria. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 325:125037. [PMID: 39217961 DOI: 10.1016/j.saa.2024.125037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/31/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
Raman spectroscopy was used to study erythrocytes collected from patients diagnosed with malaria at the University Hospital in Kraków and from healthy volunteers. A laser line with a wavelength of 442 nm was used to induce the Raman resonance of haem, while a laser with a wavelength of 785 nm was used for the normal Raman effect. The results were analysed using Principal Component Analysis. For the 442 nm laser line, analysis of the entire spectral range (3200 cm-1 to 300 cm-1) showed satisfactory separation of Raman spectra for healthy cells from infected cells, which was significantly improved in the 1500 cm-1-1200 cm-1 spectral range. For the 785 nm laser line, some separation was observed in each range studied, but the best results were achieved over the full spectral range. Plasmodium-derived nucleic acids and phosphodiester vibrations were observed at excitation lines of 442 nm and 785 nm, respectively.
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Affiliation(s)
- Mateusz Migdalski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Jacek Czepiel
- Department of Infectious and Tropical Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688 Kraków, Poland; Department of Infectious Diseases, The University Hospital in Kraków, Jakubowskiego 2, 30-688 Kraków, Poland
| | - Paulina Moskal
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Malwina Birczyńska-Zych
- Department of Infectious and Tropical Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688 Kraków, Poland; Department of Infectious Diseases, The University Hospital in Kraków, Jakubowskiego 2, 30-688 Kraków, Poland
| | - Martyna Kucharska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Grażyna Biesiada
- Department of Infectious and Tropical Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688 Kraków, Poland; Department of Infectious Diseases, The University Hospital in Kraków, Jakubowskiego 2, 30-688 Kraków, Poland
| | - Agnieszka Stokłosa
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Aleksander Garlicki
- Department of Infectious and Tropical Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688 Kraków, Poland; Department of Infectious Diseases, The University Hospital in Kraków, Jakubowskiego 2, 30-688 Kraków, Poland
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7
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Gao X, Ishikawa H, Mizuno M, Mizutani Y. Cooperative Protein Dynamics of Heterotetrameric Hemoglobin from Scapharca inaequivalvis. J Phys Chem B 2024; 128:7558-7567. [PMID: 39072557 DOI: 10.1021/acs.jpcb.4c03917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Hemoglobins achieve cooperative oxygen binding by diverse strategies based on different assemblies of globin subunits. Heterotetrameric hemoglobin from Scapharca inaequivalvis (HbII) consists of two AB-dimers, whose structure closely resembles that of homodimeric hemoglobin from the same organism (HbI). Herein, we investigated the structural dynamics of HbII following carbon monoxide (CO) dissociation using time-resolved resonance Raman (RR) spectroscopy. The observed spectra showed that the heme structure of the transient dissociated form of HbII was similar to that of HbI; however, the transition from the transient dissociated form to the equilibrium unligated form was faster for HbII than for HbI. Furthermore, the dependence of the time-resolved spectra on the yield of CO dissociation revealed that the transition became faster as the number of dissociated ligands increased from one to four. The positive correlation between the rate constants and number of dissociated ligands indicates that the structural transition of HbII following CO dissociation is cooperative.
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Affiliation(s)
- Xiang Gao
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Haruto Ishikawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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8
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Dali A, Sebastiani F, Gabler T, Frattini G, Moreno DM, Estrin DA, Becucci M, Hofbauer S, Smulevich G. Proximal ligand tunes active site structure and reactivity in bacterial L. monocytogenes coproheme ferrochelatase. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124120. [PMID: 38479228 DOI: 10.1016/j.saa.2024.124120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/21/2024] [Accepted: 03/03/2024] [Indexed: 04/02/2024]
Abstract
Ferrochelatases catalyze the insertion of ferrous iron into the porphyrin during the heme b biosynthesis pathway, which is fundamental for both prokaryotes and eukaryotes. Interestingly, in the active site of ferrochelatases, the proximal ligand coordinating the porphyrin iron of the product is not conserved, and its catalytic role is still unclear. Here we compare the L. monocytogenes bacterial coproporphyrin ferrochelatase native enzyme together with selected variants, where the proximal Tyr residue was replaced by a His (i.e. the most common ligand in heme proteins), a Met or a Phe (as in human and actinobacterial ferrochelatases, respectively), in their Fe(III), Fe(II) and Fe(II)-CO adduct forms. The study of the active site structure and the activity of the proteins in solution has been performed by UV-vis electronic absorption and resonance Raman spectroscopies, biochemical characterization, and classical MD simulations. All the mutations alter the H-bond interactions between the iron porphyrin propionate groups and the protein, and induce effects on the activity, depending on the polarity of the proximal ligand. The overall results confirm that the weak or non-existing coordination of the porphyrin iron by the proximal residue is essential for the binding of the substrate and the release of the final product.
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Affiliation(s)
- Andrea Dali
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Thomas Gabler
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Gianfranco Frattini
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Diego M Moreno
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes, 2160 Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, Buenos Aires, Argentina
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy.
| | - Stefan Hofbauer
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria.
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy; INSTM Research Unit of Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy.
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9
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Kopeć M, Borek-Dorosz A, Jarczewska K, Barańska M, Abramczyk H. The role of cardiolipin and cytochrome c in mitochondrial metabolism of cancer cells determined by Raman imaging: in vitro study on the brain glioblastoma U-87 MG cell line. Analyst 2024; 149:2697-2708. [PMID: 38506099 DOI: 10.1039/d4an00015c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
In this paper, we present Raman imaging as a non-invasive approach for studying changes in mitochondrial metabolism caused by cardiolipin-cytochrome c interactions. We investigated the effect of mitochondrial dysregulation on cardiolipin (CL) and cytochrome c (Cyt c) interactions for a brain cancer cell line (U-87 MG). Mitochondrial metabolism was monitored by checking the intensities of the Raman bands at 750 cm-1, 1126 cm-1, 1310 cm-1, 1337 cm-1, 1444 cm-1 and 1584 cm-1. The presented results indicate that under pathological conditions, the content and redox status of Cyt c in mitochondria can be used as a Raman marker to characterize changes in cellular metabolism. This work provides evidence that cardiolipin-cytochrome c interactions are crucial for mitochondrial energy homeostasis by controlling the redox status of Cyt c in the electron transport chain, switching from disabling Cyt c reduction and enabling peroxidase activity. This paper provides experimental support for the hypothesis of how cardiolipin-cytochrome c interactions regulate electron transfer in the respiratory chain, apoptosis and mROS production in mitochondria.
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Affiliation(s)
- Monika Kopeć
- Lodz University of Technology, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Wroblewskiego 15, 93-590 Lodz, Poland.
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Krakow, Poland
| | | | - Karolina Jarczewska
- Lodz University of Technology, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Wroblewskiego 15, 93-590 Lodz, Poland.
| | - Małgorzata Barańska
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Krakow, Poland
| | - Halina Abramczyk
- Lodz University of Technology, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Wroblewskiego 15, 93-590 Lodz, Poland.
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10
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Xu G, Li W, Xie H, Zhu J, Song L, Tang J, Miao Y, Han XX. In Situ Monitoring of Membrane Protein Electron Transfer via Surface-Enhanced Resonance Raman Spectroscopy. Anal Chem 2024; 96:6-11. [PMID: 38132829 DOI: 10.1021/acs.analchem.3c04700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
In situ analysis of membrane protein-ligand interactions under physiological conditions is of significance for both fundamental and applied science, but it is still a big challenge due to the limits in sensitivity and selectivity. Here, we demonstrate the potential of surface-enhanced resonance Raman spectroscopy (SERRS) for the investigation of membrane protein-protein interactions. Lipid biolayers are successfully coated on silver nanoparticles through electrostatic interactions, and a highly sensitive and biomimetic membrane platform is obtained in vitro. Self-assembly and immobilization of the reduced cytochrome b5 on the coated membrane are achieved and protein native biological functions are preserved. Owing to resonance effect, the Raman fingerprint of the immobilized cytochrome b5 redox center is selectively enhanced, allowing for in situ and real-time monitoring of the electron transfer process between cytochrome b5 and their partners, cytochrome c and myoglobin. This study provides a sensitive analytical approach for membrane proteins and paves the way for in situ exploration of their structural basis and functions.
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Affiliation(s)
- Guangyang Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Wei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Han Xie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Jinyu Zhu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Li Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Jinping Tang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Yu Miao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Xiao Xia Han
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
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11
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De Simone G, di Masi A, Pasquadibisceglie A, Coletta A, Sebastiani F, Smulevich G, Coletta M, Ascenzi P. Nitrobindin versus myoglobin: A comparative structural and functional study. J Inorg Biochem 2024; 250:112387. [PMID: 37914583 DOI: 10.1016/j.jinorgbio.2023.112387] [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: 04/12/2023] [Revised: 09/20/2023] [Accepted: 09/24/2023] [Indexed: 11/03/2023]
Abstract
Most hemoproteins display an all-α-helical fold, showing the classical three on three (3/3) globin structural arrangement characterized by seven or eight α-helical segments that form a sandwich around the heme. Over the last decade, a completely distinct class of heme-proteins called nitrobindins (Nbs), which display an all-β-barrel fold, has been identified and characterized from both structural and functional perspectives. Nbs are ten-stranded anti-parallel all-β-barrel heme-proteins found across the evolutionary ladder, from bacteria to Homo sapiens. Myoglobin (Mb), commonly regarded as the prototype of monomeric all-α-helical globins, is involved along with the oligomeric hemoglobin (Hb) in diatomic gas transport, storage, and sensing, as well as in the detoxification of reactive nitrogen and oxygen species. On the other hand, the function(s) of Nbs is still obscure, even though it has been postulated that they might participate to O2/NO signaling and metabolism. This function might be of the utmost importance in poorly oxygenated tissues, such as the eye's retina, where a delicate balance between oxygenation and blood flow (regulated by NO) is crucial. Dysfunction in this balance is associated with several pathological conditions, such as glaucoma and diabetic retinopathy. Here a detailed comparison of the structural, spectroscopic, and functional properties of Mb and Nbs is reported to shed light on the similarities and differences between all-α-helical and all-β-barrel heme-proteins.
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Affiliation(s)
| | | | | | | | - Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | | | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, 00146 Roma, Italy.
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12
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Iritani Y, Ishikawa H, Mizuno M, Mizutani Y. Heme Pocket Structure and Its Functional Implications in an Ancestral Globin Protein. Biochemistry 2023; 62:2727-2737. [PMID: 37647623 DOI: 10.1021/acs.biochem.3c00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Proteins have undergone evolutionary processes to achieve optimal stability, increased functionality, and novel functions. Comparative analysis of existent and ancestral proteins provides insights into the factors that influence protein stability and function. Ancestral sequence reconstruction allows us to deduce the amino acid sequences of ancestral proteins. Here, we present the structural and functional characteristics of an ancestral protein, AncMH, reconstructed to be the last common ancestor of hemoglobins and myoglobins. Our findings reveal that AncMH harbors heme and that the heme binds oxygen. Furthermore, we demonstrate that the ferrous heme in AncMH is pentacoordinated, similar to that of human adult hemoglobin and horse myoglobin. A detailed comparison of the heme pocket structure indicates that the heme pocket in AncMH is more similar to that of hemoglobin than that of myoglobin. However, the autoxidation of AncMH is faster than that of both hemoglobin and myoglobin. Collectively, our results suggest that ancestral proteins of hemoglobins and myoglobins evolved in steps, including the hexa- to pentacoordination transition, followed by stabilization of the oxygen-bound form.
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Affiliation(s)
- Yu Iritani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Haruto Ishikawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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13
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Abramczyk H, Surmacki JM, Kopeć M, Jarczewska K, Romanowska-Pietrasiak B. Hemoglobin and cytochrome c. reinterpreting the origins of oxygenation and oxidation in erythrocytes and in vivo cancer lung cells. Sci Rep 2023; 13:14731. [PMID: 37679473 PMCID: PMC10485004 DOI: 10.1038/s41598-023-41858-z] [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: 03/17/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023] Open
Abstract
Maintaining life (respiration), cell death (apoptosis), oxygen transport and immunity are main biological functions of heme containing proteins. These functions are controlled by the axial ligands and the redox status of the iron ion (oscillations between Fe2+ and Fe3+) in the heme group. This paper aims to evaluate the current state of knowledge on oxidation and oxygenation effects in heme proteins. We determined the redox status of the iron ion in whole blood (without and with anticoagulant), hemoglobin in erythrocytes, in isolated cytochrome c and cytochrome c in mitochondria of the human lung cancer cells using UV-VIS electronic absorption spectroscopy, Raman spectroscopy and Raman imaging. Here we discussed the mechanism responsible for the Q electronic absorption band spectral behavior, i.e., its splitting, and its change in extinction coefficient, as well as vibrational modifications upon oxygenation and oxidation. We compared the redox status of heme in hemoglobin of human erythrocytes and cytochrome c in mitochondria of human lung cancer cells. Presented results allow simultaneous identification of oxy- and deoxy-Hb, where 1547 and 1604 cm-1 vibrations correspond to deoxygenated hemoglobin, while 1585 and 1638 cm-1 correspond to oxyhemoglobin, respectively. Our results extend knowledge of oxidation and oxygenation effects in heme proteins. We demonstrated experimentally the mechanism of electronic-vibrational coupling for the Q band splitting. Presented results extend knowledge on oxidation and oxygenation effects in heme proteins and provide evidence that both processes are strongly coupled. We showed that retinoic acid affects the redox state of heme in cytochrome c in mitochondria. The change of the redox status of cytochrome c in mitochondria from the oxidized form to the reduced form has very serious consequences in dysfunction of mitochondria resulting in inhibition of respiration, apoptosis and cytokine induction.
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Affiliation(s)
- Halina Abramczyk
- Faculty of Chemistry, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Wroblewskiego 15, 93-590, Lodz, Poland.
| | - Jakub Maciej Surmacki
- Faculty of Chemistry, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Wroblewskiego 15, 93-590, Lodz, Poland
| | - Monika Kopeć
- Faculty of Chemistry, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Wroblewskiego 15, 93-590, Lodz, Poland
| | - Karolina Jarczewska
- Faculty of Chemistry, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Wroblewskiego 15, 93-590, Lodz, Poland
| | - Beata Romanowska-Pietrasiak
- Oncological Surgery Department, Medical Genetics Department, Copernicus Provincial Multidisciplinary Centre of Oncology and Traumatology in Lodz, Pabianicka 62, 93-513, Lodz, Poland
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14
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Domes R, Frosch T. Molecular Interactions Identified by Two-Dimensional Analysis-Detailed Insight into the Molecular Interactions of the Antimalarial Artesunate with the Target Structure β-Hematin by Means of 2D Raman Correlation Spectroscopy. Anal Chem 2023; 95:12719-12731. [PMID: 37586701 PMCID: PMC10469332 DOI: 10.1021/acs.analchem.3c01415] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
A thorough understanding of the interaction of endoperoxide antimalarial agents with their biological target structures is of utmost importance for the tailored design of future efficient antimalarials. Detailed insights into molecular interactions between artesunate and β-hematin were derived with a combination of resonance Raman spectroscopy, two-dimensional correlation analysis, and density functional theory calculations. Resonance Raman spectroscopy with three distinct laser wavelengths enabled the specific excitation of different chromophore parts of β-hematin. The resonance Raman spectra of the artesunate-β-hematin complexes were thoroughly analyzed with the help of high-resolution and highly sensitive two-dimensional correlation spectroscopy. Spectral changes in the peak properties were found with increasing artesunate concentration. Changes in the low-frequency, morphology-sensitive Raman bands indicated a loss in crystallinity of the drug-target complexes. Differences in the high-wavenumber region were assigned to increased distortions of the planarity of the structure of the target molecule due to the appearance of various coexisting alkylation species. Evidence for the appearance of high-valent ferryl-oxo species could be observed with the help of differences in the peak properties of oxidation-state sensitive Raman modes. To support those findings, the relaxed ground-state structures of ten possible covalent mono- and di-meso(Cm)-alkylated hematin-dihydroartemisinyl complexes were calculated using density functional theory. A very good agreement with the experimental peak properties was achieved, and the out-of-plane displacements along the lowest-frequency normal coordinates were investigated by normal coordinate structural decomposition analysis. The strongest changes in all data were observed in vibrations with a high participation of Cm-parts of β-hematin.
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Affiliation(s)
- Robert Domes
- Leibniz
Institute of Photonic Technology, Albert Einstein Strasse 9, D-07745 Jena, Germany
| | - Torsten Frosch
- Biophotonics and
Biomedical Engineering Group, Technical
University Darmstadt, Merckstraße 25, 64283 Darmstadt, Germany
- Leibniz
Institute of Photonic Technology, Albert Einstein Strasse 9, D-07745 Jena, Germany
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15
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Palermo JC, Colombo MC, Scocozza MF, Murgida DH, Estrin DA, Bari SE. Reduction of metmyoglobin by inorganic disulfide species. J Inorg Biochem 2023; 245:112256. [PMID: 37244768 DOI: 10.1016/j.jinorgbio.2023.112256] [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: 03/27/2023] [Revised: 05/03/2023] [Accepted: 05/11/2023] [Indexed: 05/29/2023]
Abstract
The mechanism of the metal centered reduction of metmyoglobin (MbFeIII) by inorganic disulfide species has been studied by combined spectroscopic and kinetic analyses, under argon atmosphere. The process is kinetically characterized by biexponential time traces, for variable ratios of excess disulfide to protein, in the pH interval 6.6-8.0. Using UV-vis and resonance Raman spectroscopies, we observed that MbFeIII is converted into a low spin hexacoordinated ferric complex, tentatively assigned as MbFeIII(HSS-)/MbFeIII(SS2-), in an initial fast step. The complex is slowly converted into a pentacoordinated ferrous form, assigned as MbFeII according to the resonance Raman records. The reduction is a pH-dependent process, but independent of the initial disulfide concentration, suggesting the unimolecular decomposition of the intermediate complex following a reductive homolysis. We estimated the rate of the fast formation of the complex at pH 7.4 (kon = 3.7 × 103 M-1 s-1), and a pKa2 = 7.5 for the equilibrium MbFeIII(HSS-)/MbFeIII(SS2-). Also, we estimated the rate for the slow reduction at the same pH (kred = 10-2 s-1). A reaction mechanism compliant with the experimental results is proposed. This mechanistic study provides a differential kinetic signature for the reactions of disulfide compared to sulfide species on metmyoglobin, which may be considered in other hemeprotein systems.
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Affiliation(s)
- Juan Cruz Palermo
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Melisa Carllinni Colombo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina
| | - Magalí F Scocozza
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina
| | - Daniel H Murgida
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina
| | - Darío A Estrin
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina
| | - Sara E Bari
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina.
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16
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Sebastiani F, Dali A, Alonso de Armiño DJ, Campagni L, Patil G, Becucci M, Hofbauer S, Estrin DA, Smulevich G. The role of the distal cavity in carbon monoxide stabilization in the coproheme decarboxylase enzyme from C. diphtheriae. J Inorg Biochem 2023; 245:112243. [PMID: 37196412 DOI: 10.1016/j.jinorgbio.2023.112243] [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: 03/03/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/19/2023]
Abstract
This work focuses on the carbon monoxide adducts of the wild-type and selected variants of the coproheme decarboxylase from actinobacterial Corynebacterium diphtheriae complexed with coproheme, monovinyl monopropionyl deuteroheme (MMD), and heme b. The UV - vis and resonance Raman spectroscopies together with the molecular dynamics simulations clearly show that the wild-type coproheme-CO adduct is characterized by two CO conformers, one hydrogen-bonded to the distal H118 residue and the other showing a weak polar interaction with the distal cavity. Instead, upon conversion to heme b, i.e. after decarboxylation of propionates 2 and 4 and rotation by 90o of the porphyrin ring inside the cavity, CO probes a less polar environment. In the absence of the H118 residue, both coproheme and heme b complexes form only the non-H-bonded CO species. The unrotated MMD-CO adduct as observed in the H118F variant, confirms that decarboxylation of propionate 2 only, does not affect the heme cavity. The rupture of both the H-bonds involving propionates 2 and 4 destabilizes the porphyrin inside the cavity with the subsequent formation of a CO adduct in an open conformation. In addition, in this work we present data on CO binding to reversed heme b, obtained by hemin reconstitution of the H118A variant, and to heme d, obtained by addition of an excess of hydrogen peroxide. The results will be discussed and compared with those reported for the representatives of the firmicute clade.
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Affiliation(s)
- Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy
| | - Andrea Dali
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy
| | - Diego Javier Alonso de Armiño
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Lorenzo Campagni
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy
| | - Gaurav Patil
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, Vienna A-1190, Austria
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy.
| | - Stefan Hofbauer
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, Vienna A-1190, Austria.
| | - Dario A Estrin
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina; Universidad de Buenos Aires, Departamento de Quimica Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina.
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy; INSTM Research Unit of Firenze, via della Lastruccia 3, Sesto Fiorentino I-50019, Italy.
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17
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Jing Y, Usai R, Liu Y, Kincaid JR. Revealing substrate-induced structural changes in active site of human CYP51 in the presence of its physiological substrates. J Inorg Biochem 2023; 242:112167. [PMID: 36870163 PMCID: PMC10082466 DOI: 10.1016/j.jinorgbio.2023.112167] [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: 12/13/2022] [Revised: 02/01/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023]
Abstract
The human sterol 14α-demethylases (CYP51, CYP is an abbreviation for cytochrome P450) catalyze three-step oxidative removal of 14α-methyl group of lanosterol by first forming an alcohol, then an aldehyde, and finally conducting a CC bond cleavage reaction. This present study utilizes a combination of Resonance Raman spectroscopy and Nanodisc technology to probe the active site structure of CYP51 in the presence of its hydroxylase and lyase substrates. Ligand-binding induced partial low-to-high-spin conversion is observed by applying electronic absorption spectroscopy and Resonance Raman (RR) spectroscopy. This low degree of spin conversion of CYP51 is contributed by the retention of the water ligand coordinated to the heme iron as well as direct interaction between the hydroxyl group of lyase substrate and the iron center. No significant changes in active site structure are found between detergent-stabilized CYP51 and nanodisc-incorporated CYP51, nevertheless, it is demonstrated that nanodisc-incorporated assemblies provide much more well-defined active site RR spectroscopic responses, which induces a larger conversion from low-to-high-spin state in presence of the substrates. Moreover, a positive polar environment around the exogenous diatomic ligand is detected, providing insight into the mechanism of this essential CC bond cleavage reaction.
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Affiliation(s)
- Yuanqi Jing
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Remigio Usai
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Yilin Liu
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA.
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
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18
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Zhang R, Wang P, Chen J, Tian Y, Gao J. Age estimation of bloodstains based on Raman spectroscopy and chemometrics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 290:122284. [PMID: 36592590 DOI: 10.1016/j.saa.2022.122284] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/04/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
The accurate estimation of the bloodstain age, which is one of the important biological evidence of crime scene, can provide a lot of information related to crime. How to extract the information quickly and accurately from bloodstains without damage has been a focused problem. In this study, a bloodstains age estimation method based on Raman spectroscopy and chemometrics was developed. As many as 11 simulated environments based on different temperature and humidity were constructed in the method, and bloodstains of three species including human were studied. The influence of environmental factors such as temperature and humidity on the variation of Raman spectral peaks during the aging process of bloodstains was analyzed using the e-index fitting. When the humidity was kept constant, the increase of temperature generally promoted the changes of the spectral peaks. When the temperature was kept constant, the increase of humidity generally slowed the changes of spectral peaks. These works provide data support for the further development of Raman spectroscopy for bloodstain age estimation and could accelerate its application in actual scenes.
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Affiliation(s)
- Rui Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Peng Wang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
| | - Jiansheng Chen
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Yubing Tian
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Jing Gao
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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19
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Valianti VK, Tselios C, Pinakoulaki E. Reversible thermally induced spin crossover in the myoglobin-nitrito adduct directly monitored by resonance Raman spectroscopy. RSC Adv 2023; 13:9020-9025. [PMID: 36950070 PMCID: PMC10025812 DOI: 10.1039/d3ra00225j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/12/2023] [Indexed: 03/24/2023] Open
Abstract
Myoglobin has been demonstrated to function as a nitrite reductase to produce nitric oxide during hypoxia. One of the most intriguing aspects of the myoglobin/nitrite interactions revealed so far is the unusual O-binding mode of nitrite to the ferric heme iron, although conflicting data have been reported for the electronic structure of this complex also raising the possibility of linkage isomerism. In this work, we applied resonance Raman spectroscopy in a temperature-dependent approach to investigate the binding of nitrite to ferric myoglobin and the properties of the formed adduct from ambient to low temperatures (293 K to 153 K). At ambient temperature the high spin state of the ferric heme Fe-O-N[double bond, length as m-dash]O species is present and upon decreasing the temperature the low spin state is populated, demonstrating that a thermally-induced spin crossover phenomenon takes place analogous to what has been observed in many transition metal complexes. The observed spin crossover is fully reversible and is not due to linkage isomerism, since the O-binding mode is retained upon the spin transition. The role of the heme pocket environment in controlling the nitrite binding mode and spin transition is discussed.
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Affiliation(s)
| | - Charalampos Tselios
- Department of Chemistry, University of Cyprus 2109 Aglantzia Cyprus
- Department of Chemical Engineering, Cyprus University of Technology Lemesos Cyprus
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20
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Targeting erythrocyte-mediated hypoxia to alleviate lung injury induced by pyrrolizidine alkaloids. Arch Toxicol 2023; 97:819-829. [PMID: 36639515 DOI: 10.1007/s00204-023-03443-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
Pyrrolizidine alkaloids (PAs) are widely distributed natural toxins and have been extensively studied for their hepatotoxicity. However, PA-induced pulmonary toxicity remains less studied regarding the initiating mechanism and treatment approaches. Our previous study demonstrated the formation of pyrrole-hemoglobin adducts after PA exposure in vivo, which is suspected to affect the oxygen-carrying capacity of erythrocytes [red blood cells (RBCs)] consequently. The present study aimed to investigate the effects of PAs on the oxygen-carrying capacity of RBCs and the potential of targeting RBC-mediated hypoxia to alleviate PA-induced lung injury. First, rats were treated with retrorsine (RTS) or monocrotaline (MCT) intravenously at 0.2 mmol/kg. The results of Raman spectrometry analysis on blood samples revealed both RTS and MCT significantly reduced the oxygen-carrying capacity of RBCs. Further, MCT (0.2 mmol/kg) was orally given to the rats with or without pretreatment with two doses of erythropoietin (Epo, 500 IU/kg/dose every other day), an RBC-stimulating agent. Biochemical and histological results showed pretreatment with Epo effectively reduced the cardiopulmonary toxicity induced by MCT. These findings provide the first evidence that adduction on hemoglobin, and the resulting RBC damage and impaired oxygen-carrying capacity, are the major initiating mechanism underlying PA-induced pulmonary arterial hypertension (PAH), while targeting the RBC damage is a potential therapeutic approach for PA-induced lung injury.
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21
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Sebastiani F, Baroni C, Patil G, Dali A, Becucci M, Hofbauer S, Smulevich G. The Role of the Hydrogen Bond Network in Maintaining Heme Pocket Stability and Protein Function Specificity of C. diphtheriae Coproheme Decarboxylase. Biomolecules 2023; 13:235. [PMID: 36830604 PMCID: PMC9953210 DOI: 10.3390/biom13020235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Monoderm bacteria accumulate heme b via the coproporphyrin-dependent biosynthesis pathway. In the final step, in the presence of two molecules of H2O2, the propionate groups of coproheme at positions 2 and 4 are decarboxylated to form vinyl groups by coproheme decarboxylase (ChdC), in a stepwise process. Decarboxylation of propionate 2 produces an intermediate that rotates by 90° inside the protein pocket, bringing propionate 4 near the catalytic tyrosine, to allow the second decarboxylation step. The active site of ChdCs is stabilized by an extensive H-bond network involving water molecules, specific amino acid residues, and the propionate groups of the porphyrin. To evaluate the role of these H-bonds in the pocket stability and enzyme functionality, we characterized, via resonance Raman and electronic absorption spectroscopies, single and double mutants of the actinobacterial pathogen Corynebacterium diphtheriae ChdC complexed with coproheme and heme b. The selective elimination of the H-bond interactions between propionates 2, 4, 6, and 7 and the polar residues of the pocket allowed us to establish the role of each H-bond in the catalytic reaction and to follow the changes in the interactions from the substrate to the product.
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Affiliation(s)
- Federico Sebastiani
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Chiara Baroni
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Gaurav Patil
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Andrea Dali
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Maurizio Becucci
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
- INSTM Research Unit of Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
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22
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GLB-3: A resilient, cysteine-rich, membrane-tethered globin expressed in the reproductive and nervous system of Caenorhabditis elegans. J Inorg Biochem 2023; 238:112063. [PMID: 36370505 DOI: 10.1016/j.jinorgbio.2022.112063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/05/2022]
Abstract
The popular genetic model organism Caenorhabditis elegans (C. elegans) encodes 34 globins, whereby the few that are well-characterized show divergent properties besides the typical oxygen carrier function. Here, we present a biophysical characterization and expression analysis of C. elegans globin-3 (GLB-3). GLB-3 is predicted to exist in two isoforms and is expressed in the reproductive and nervous system. Knockout of this globin causes a 99% reduction in fertility and reduced motility. Spectroscopic analysis reveals that GLB-3 exists as a bis-histidyl-ligated low-spin form in both the ferrous and ferric heme form. A function in binding of diatomic gases is excluded on the basis of the slow CO-binding kinetics. Unlike other globins, GLB-3 is also not capable of reacting with H2O2, H2S, and nitrite. Intriguingly, not only does GLB-3 contain a high number of cysteine residues, it is also highly stable under harsh conditions (pH = 2 and high concentrations of H2O2). The resilience diminishes when the N- and C-terminal extensions are removed. Redox potentiometric measurements reveal a slightly positive redox potential (+8 ± 19 mV vs. SHE), suggesting that the heme iron may be able to oxidize cysteines. Electron paramagnetic resonance shows that formation of an intramolecular disulphide bridge, involving Cys70, affects the heme-pocket region. The results suggest an involvement of the globin in (cysteine) redox chemistry.
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Lima AMF, Daniel CR, Pacheco MTT, de Brito PL, Silveira L. Discrimination of leukemias and non-leukemic cancers in blood serum samples of children and adolescents using a Raman spectral model. Lasers Med Sci 2022; 38:22. [PMID: 36564570 PMCID: PMC9789313 DOI: 10.1007/s10103-022-03681-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 11/08/2022] [Indexed: 12/25/2022]
Abstract
This study aimed to identify the differences presented in the Raman spectrum of blood serum from normal subjects compared to leukemic and non-leukemic subjects and the differences between the leukemics and non-leukemics, correlating the spectral differences with the biomolecules. Serum samples from children and adolescents were subjected to Raman spectroscopy (830 nm, laser power 350 mW; n = 566 spectra, being 72 controls, 269 leukemics, and 225 non-leukemics). Exploratory analysis based on principal component analysis (PCA) of the serum sample's spectra was performed. Classification models based on partial least squares discriminant analysis (PLS-DA) were developed to classify the spectra into normal, leukemic, and non-leukemic, as well as to discriminate spectra of leukemic from non-leukemic. The exploratory analysis showed principal components with peaks related to amino acids, proteins, lipids, and carotenoids. The spectral differences between normal, leukemic, and non-leukemic showed features assigned to proteins (serum features), amino acids, and carotenoids. The PLS-DA model classified the spectra of the normal group versus leukemic and non-leukemic groups with accuracy of 66%, sensitivity of 99%, and specificity of 57%. The PLS-DA discriminated the spectra of the leukemic and non-leukemic groups with accuracy of 67%, sensitivity of 72%, and specificity of 60%. The study showed that Raman spectroscopy is a technique that may be used for the biochemical differentiation of leukemias and other types of cancer in serum samples of children and adolescents. Nevertheless, building an extensive data library of Raman spectra from serum samples of controls, leukemics, and non-leukemics of different age groups is necessary to understand the findings better.
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Affiliation(s)
- Ana Mara Ferreira Lima
- Universidade Anhembi Morumbi-UAM, Rua Casa do Ator, 275, São Paulo, SP, 04546-001, Brazil
| | - Camila Ribeiro Daniel
- Universidade Anhembi Morumbi-UAM, Rua Casa do Ator, 275, São Paulo, SP, 04546-001, Brazil
| | - Marcos Tadeu Tavares Pacheco
- Universidade Anhembi Morumbi-UAM, Rua Casa do Ator, 275, São Paulo, SP, 04546-001, Brazil
- Center for Innovation, Technology, and Education-CITÉ, Parque Tecnológico de São José Dos Campos, Estr. Dr. Altino Bondensan, 500, São José dos Campos, SP, 12247-016, Brazil
| | - Pedro Luiz de Brito
- Centro de Tratamento Infantojuvenil Fabiana Macedo de Morais-CTFM, Grupo de Assistência à Criança com Câncer-GACC, Av. Possidônio José de Freitas, 1200, São José dos Campos, SP, 12244-010, Brazil
| | - Landulfo Silveira
- Universidade Anhembi Morumbi-UAM, Rua Casa do Ator, 275, São Paulo, SP, 04546-001, Brazil.
- Center for Innovation, Technology, and Education-CITÉ, Parque Tecnológico de São José Dos Campos, Estr. Dr. Altino Bondensan, 500, São José dos Campos, SP, 12247-016, Brazil.
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Schweitzer-Stenner R. Heme-Protein Interactions and Functional Relevant Heme Deformations: The Cytochrome c Case. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248751. [PMID: 36557884 PMCID: PMC9781506 DOI: 10.3390/molecules27248751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Heme proteins are known to perform a plethora of biologically important functions. This article reviews work that has been conducted on various class I cytochrome c proteins over a period of nearly 50 years. The article focuses on the relevance of symmetry-lowering heme-protein interactions that affect the function of the electron transfer protein cytochrome c. The article provides an overview of various, mostly spectroscopic studies that explored the electronic structure of the heme group in these proteins and how it is affected by symmetry-lowering deformations. In addition to discussing a large variety of spectroscopic studies, the article provides a theoretical framework that should enable a comprehensive understanding of the physical chemistry that underlies the function not only of cytochrome c but of all heme proteins.
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Heme-bound tyrosine vibrations in hemoglobin M: Resonance Raman, crystallography, and DFT calculation. Biophys J 2022; 121:2767-2780. [PMID: 35689380 DOI: 10.1016/j.bpj.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/23/2022] [Accepted: 06/03/2022] [Indexed: 11/22/2022] Open
Abstract
Hemoglobins M (Hbs M) are human hemoglobin variants in which either the α or β subunit contains a ferric heme in the α2β2 tetramer. Though the ferric subunit cannot bind O2, it regulates O2 affinity of its counterpart ferrous subunit. We have investigated resonance Raman spectra of two Hbs, M Iwate (α87His → tyrosine [Tyr]) and M Boston (α58His → Tyr), having tyrosine as a heme axial ligand at proximal and distal positions, respectively, that exhibit unassigned resonance Raman bands arising from ferric (not ferrous) hemes at 899 and 876 cm-1. Our quantum chemical calculations using density functional theory on Fe-porphyrin models with p-cresol and/or 4-methylimidazole showed that the unassigned bands correspond to the breathing-like modes of Fe3+-bound Tyr and are sensitive to the Fe-O-C(Tyr) angle. Based on the frequencies of the Raman bands, the Fe-O-C(Tyr) angles of Hbs M Iwate and M Boston were predicted to be 153.5° and 129.2°, respectively. Consistent with this prediction, x-ray crystallographic analysis showed that the Fe-O-C(Tyr) angles of Hbs M Iwate and M Boston in the T quaternary structure were 153.6° and 134.6°, respectively. It also showed a similar Fe-O bond length (1.96 and 1.97 Å) and different tilting angles.
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Dey C, Roy M, Dey SG. Insights from Self-Assembled Aggregates of Amyloid β Peptides on Gold Surfaces. ACS OMEGA 2022; 7:9973-9983. [PMID: 35382274 PMCID: PMC8973063 DOI: 10.1021/acsomega.1c06056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/24/2022] [Indexed: 06/12/2023]
Abstract
Amyloid β (Aβ) peptides mutated at different positions using a cysteine moiety assemble on Au electrodes using the thiol functionality of cysteine. Self-assembled monolayers (SAMs) of Aβ on Au surfaces can act as abiological platforms that allow the mimicking of fibrils and oligomeric Aβ via the formation of controlled large and small peptide aggregates. These Aβ constructs bind with heme and Cu and exhibit different reactivities. These abiological platforms can also be used to investigate potential drugs that can interact with heme and Cu-Aβ. SAM formation of Aβ mutants allows the study of different morphology and structure as well as behavior changes on binding with different metals and cytochrome c (Cyt c). This review provides a detailed insight into the structure and reactivities of various Aβ aggregated on Au electrodes mimicking the cell membrane.
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27
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Redox state changes of mitochondrial cytochromes in brain and breast cancers by Raman spectroscopy and imaging. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132134] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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28
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Bose D, Aggarwal S, Das D, Narayana C, Chakrabarti A. Erythroid spectrin binding modulates peroxidase and catalase activity of heme proteins. IUBMB Life 2022; 74:474-487. [DOI: 10.1002/iub.2607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/27/2022] [Accepted: 02/08/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Dipayan Bose
- Crystallography & Molecular Biology Division Saha Institute of Nuclear Physics Kolkata India
- Homi Bhabha National Institute Mumbai India
| | - Shantanu Aggarwal
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research Bengaluru India
| | - Debashree Das
- Crystallography & Molecular Biology Division Saha Institute of Nuclear Physics Kolkata India
| | - Chandrabhas Narayana
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research Bengaluru India
| | - Abhijit Chakrabarti
- Crystallography & Molecular Biology Division Saha Institute of Nuclear Physics Kolkata India
- Homi Bhabha National Institute Mumbai India
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Singha A, Mittra K, Dey A. Synthetic heme dioxygen adducts: electronic structure and reactivity. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2021.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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30
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Valle-Altamirano RG, Baratto MC, Badillo-Ramírez I, Gasteazoro F, Pogni R, Saniger JM, Valderrama B. Identification of Fe( iii)–OH species as a catalytic intermediate in plant peroxidases at high H 2O 2 concentration. NEW J CHEM 2022. [DOI: 10.1039/d1nj04837f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The structure for compound III formed after exposure of plant heme peroxidases to excess H2O2 seems to be a hydroxylated form, providing new evidence for understanding the structural basis of the substrate-induced suicidal behavior of these enzymes.
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Affiliation(s)
- Rodolfo G. Valle-Altamirano
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Maria Camilla Baratto
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Isidro Badillo-Ramírez
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Francisco Gasteazoro
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
| | - Rebecca Pogni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - José M. Saniger
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Brenda Valderrama
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
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Volkov VV, McMaster J, Aizenberg J, Perry CC. Mapping blood biochemistry by Raman spectroscopy at the cellular level. Chem Sci 2021; 13:133-140. [PMID: 35059161 PMCID: PMC8694331 DOI: 10.1039/d1sc05764b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/01/2021] [Indexed: 11/21/2022] Open
Abstract
We report how Raman difference imaging provides insight on cellular biochemistry in vivo as a function of sub-cellular dimensions and the cellular environment. We show that this approach offers a sensitive diagnostic to address blood biochemistry at the cellular level. We examine Raman microscopic images of the distribution of the different hemoglobins in both healthy (discocyte) and unhealthy (echinocyte) blood cells and interpret these images using pre-calculated, accurate pre-resonant Raman tensors for scattering intensities specific to hemoglobins. These tensors are developed from theoretical calculations of models of the oxy, deoxy and met forms of heme benchmarked against the experimental visible spectra of the corresponding hemoglobins. The calculations also enable assignments of the electronic transitions responsible for the colour of blood: these are mainly ligand to metal charge transfer transitions. We assign the electronic transitions responsible for the colour of blood and present a Raman imaging diagnostic approach for individual blood cells.![]()
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Affiliation(s)
- Victor V Volkov
- Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University. Clifton Lane Nottingham NG11 8NS UK +44 (0)115 8486695
| | - Jonathan McMaster
- School of Chemistry, Faculty of Science, The University of Nottingham Nottingham NG7 2RD UK
| | - Joanna Aizenberg
- John A. Poulson School of Engineering and Applied Sciences, Harvard University 29 Oxford Street Cambridge MA 02138 USA
| | - Carole C Perry
- Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University. Clifton Lane Nottingham NG11 8NS UK +44 (0)115 8486695
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32
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Patterson DC, Liu Y, Das S, Yennawar NH, Armache JP, Kincaid JR, Weinert EE. Heme-Edge Residues Modulate Signal Transduction within a Bifunctional Homo-Dimeric Sensor Protein. Biochemistry 2021; 60:3801-3812. [PMID: 34843212 DOI: 10.1021/acs.biochem.1c00581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bifunctional enzymes, which contain two domains with opposing enzymatic activities, are widely distributed in bacteria, but the regulatory mechanism(s) that prevent futile cycling are still poorly understood. The recently described bifunctional enzyme, DcpG, exhibits unusual heme properties and is surprisingly able to differentially regulate its two cyclic dimeric guanosine monophosphate (c-di-GMP) metabolic domains in response to heme gaseous ligands. Mutagenesis of heme-edge residues was used to probe the heme pocket and resulted in decreased O2 dissociation kinetics, identifying roles for these residues in modulating DcpG gas sensing. In addition, the resonance Raman spectra of the DcpG wild type and heme-edge mutants revealed that the mutations alter the heme electrostatic environment, vinyl group conformations, and spin state population. Using small-angle X-ray scattering and negative stain electron microscopy, the heme-edge mutations were demonstrated to cause changes to the protein conformation, which resulted in altered signaling transduction and enzyme kinetics. These findings provide insights into molecular interactions that regulate DcpG gas sensing as well as mechanisms that have evolved to control multidomain bacterial signaling proteins.
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Affiliation(s)
- Dayna C Patterson
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yilin Liu
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Sayan Das
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Emily E Weinert
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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33
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Takamura A, Ozawa T. Recent advances of vibrational spectroscopy and chemometrics for forensic biological analysis. Analyst 2021; 146:7431-7449. [PMID: 34813634 DOI: 10.1039/d1an01637g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biological materials found at a crime scene are crucially important evidence for forensic investigation because they provide contextual information about a crime and can be linked to the donor-individuals through combination with DNA analysis. Applications of vibrational spectroscopy to forensic biological analysis have been emerging because of its advantageous characteristics such as the non-destructivity, rapid measurement, and quantitative evaluation, compared to most current methods based on histological observation or biochemical techniques. This review presents an overview of recent developments in vibrational spectroscopy for forensic biological analysis. We also emphasize chemometric techniques, which can elicit reliable and advanced analytical outputs from highly complex spectral data from forensic biological materials. The analytical subjects addressed herein include body fluids, hair, soft tissue, bones, and bioagents. Promising applications for various analytical purposes in forensic biology are presented. Simultaneously, future avenues of study requiring further investigation are discussed.
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Affiliation(s)
- Ayari Takamura
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. .,RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Takeaki Ozawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Structure-function characterization of the mono- and diheme forms of MhuD, a noncanonical heme oxygenase from Mycobacterium tuberculosis. J Biol Chem 2021; 298:101475. [PMID: 34883099 PMCID: PMC8801480 DOI: 10.1016/j.jbc.2021.101475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/29/2022] Open
Abstract
MhuD is a noncanonical heme oxygenase (HO) from Mycobacterium tuberculosis (Mtb) that catalyzes unique heme degradation chemistry distinct from canonical HOs, generating mycobilin products without releasing carbon monoxide. Its crucial role in the Mtb heme uptake pathway has identified MhuD as an auspicious drug target. MhuD is capable of binding either one or two hemes within a single active site, but only the monoheme form was previously reported to be enzymatically active. Here we employed resonance Raman (rR) spectroscopy to examine several factors proposed to impact the reactivity of mono- and diheme MhuD, including heme ruffling, heme pocket hydrophobicity, and amino acid–heme interactions. We determined that the distal heme in the diheme MhuD active site has negligible effects on both the planarity of the His-coordinated heme macrocycle and the strength of the Fe-NHis linkage relative to the monoheme form. Our rR studies using isotopically labeled hemes unveiled unexpected biomolecular dynamics for the process of heme binding that converts MhuD from mono- to diheme form, where the second incoming heme replaces the first as the His75-coordinated heme. Ferrous CO-ligated diheme MhuD was found to exhibit multiple Fe-C-O conformers, one of which contains catalytically predisposed H-bonding interactions with the distal Asn7 residue identical to those in the monoheme form, implying that it is also enzymatically active. This was substantiated by activity assays and MS product analysis that confirmed the diheme form also degrades heme to mycobilins, redefining MhuD’s functional paradigm and further expanding our understanding of its role in Mtb physiology.
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Gout J, Meuris F, Desbois A, Dorlet P. In vitro coordination of Fe-protoheme with amyloid β is non-specific and exhibits multiple equilibria. J Inorg Biochem 2021; 227:111664. [PMID: 34955310 DOI: 10.1016/j.jinorgbio.2021.111664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
In addition to copper and zinc, heme is thought to play a role in Alzheimer's disease and its metabolism is strongly affected during the course of this disease. Amyloid β, the peptide associated with Alzheimer's disease, was shown to bind heme in vitro with potential catalytic activity linked to oxidative stress. To date, there is no direct determination of the structure of this complex. In this work, we studied the binding mode of heme to amyloid β in different conditions of pH and redox state by using isotopically labelled peptide in combination with advanced magnetic and vibrational spectroscopic methods. Our results show that the interaction between heme and amyloid β leads to a variety of species in equilibrium. The formation of these species seems to depend on many factors suggesting that the binding site is neither very strong nor highly specific. In addition, our data do not support the currently accepted model where a water molecule is bound to the ferric heme as sixth ligand. They also exclude structural models mimicking a peroxidatic site in the amyloid β-Fe-protoheme complexes.
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Affiliation(s)
- Jérôme Gout
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Laboratoire Stress Oxydant et Détoxication, Gif-sur-Yvette, France
| | - Floriane Meuris
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Laboratoire Stress Oxydant et Détoxication, Gif-sur-Yvette, France
| | - Alain Desbois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Laboratoire Stress Oxydant et Détoxication, Gif-sur-Yvette, France.
| | - Pierre Dorlet
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France; Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Laboratoire Stress Oxydant et Détoxication, Gif-sur-Yvette, France.
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36
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Ex Vivo Vibration Spectroscopic Analysis of Colorectal Polyps for the Early Diagnosis of Colorectal Carcinoma. Diagnostics (Basel) 2021; 11:diagnostics11112048. [PMID: 34829393 PMCID: PMC8621094 DOI: 10.3390/diagnostics11112048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/25/2021] [Accepted: 10/31/2021] [Indexed: 02/01/2023] Open
Abstract
Colorectal cancer is one of the most common and often fatal cancers in humans, but it has the highest chance of a cure if detected at an early precancerous stage. Carcinogenesis in the colon begins as an uncontrolled growth forming polyps. Some of these polyps can finally be converted to colon cancer. Early diagnosis of adenomatous polyps is the main approach for screening and preventing colorectal cancer, and vibration spectroscopy can be used for this purpose. This work is focused on evaluating FTIR and Raman spectroscopy as a tool in the ex vivo analysis of colorectal polyps, which could be important for the early diagnosis of colorectal carcinoma. Multivariate analyses (PCA and LDA) were used to assist the spectroscopic discrimination of normal colon tissue, as well as benign and malignant colon polyps. The spectra demonstrated evident differences in the characteristic bands of the main tissue constituents, i.e., proteins, nucleic acids, lipids, polysaccharides, etc. Suitable models for discriminating the three mentioned diagnostic groups were proposed based on multivariate analyses of the spectroscopic data. LDA classification was especially successful in the case of a combined set of 55 variables from the FTIR, FT Raman and dispersion Raman spectra. This model can be proposed for ex vivo colorectal cancer diagnostics in combination with the colonoscopic extraction of colon polyps for further testing. This pilot study is a precursor for the further evaluation of the diagnostic potential for the simultaneous in vivo application of colonoscopic Raman probes.
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Fleitas-Salazar N, Pedroso-Santana S, Silva-Campa E, Angulo-Molina A, Toledo JR, Riera R, Pedroza-Montero M. Raman spectroscopy and silver nanoparticles for efficient detection of membrane proteins in living cells. NANOTECHNOLOGY 2021; 32:495101. [PMID: 34450614 DOI: 10.1088/1361-6528/ac21ee] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
Molecular fingerprints revealed by Raman techniques show great potential for biomedical applications, like disease diagnostic through Raman detection of tumor markers and other molecules in the cell membrane. However, SERS substrates used in membrane molecule studies produce enhanced Raman spectra of high variability and challenging band assignments that limit their application. In this work, these drawbacks are addressed to detect membrane-associated hemoglobin (Hbm) in human erythrocytes through Raman spectroscopy. These cells are incubated with silver nanoparticles (AgNPs) in PBS before Raman measurements. Our results showed that AgNPs form large aggregates in PBS that adhered to the erythrocyte membrane, which enhances Raman scattering by molecules around the membrane, like Hbm. Also, deoxyHb markers may allow Hbmdetection in Raman spectra of oxygenated erythrocytes (oxyRBCs). Raman spectra of oxyRBCs incubated with AgNPs showed enhanced deoxyHb signals with good spectral reproducibility, supporting the Hbmdetection through deoxyHb markers. Instead, Raman spectra of oxyRBCs showed oxyHb bands associated with free cytoplasmic hemoglobin. Other factors influencing Raman detection of membrane proteins are discussed, like bothz-position and dimension of the sample volume. The results encourage membrane protein studies in living cells using Raman spectroscopy, leading to the characterization and diagnostic of different pathologies through a non-invasive technique.
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Affiliation(s)
- Noralvis Fleitas-Salazar
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
- Departamento de Investigación en Física, Universidad de Sonora, Hermosillo 83000, Mexico
| | - Seidy Pedroso-Santana
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
- Departamento de Investigación en Física, Universidad de Sonora, Hermosillo 83000, Mexico
| | - Erika Silva-Campa
- Departamento de Investigación en Física, Universidad de Sonora, Hermosillo 83000, Mexico
| | - Aracely Angulo-Molina
- Departamento de Investigación en Física, Universidad de Sonora, Hermosillo 83000, Mexico
| | - Jorge R Toledo
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Raul Riera
- Departamento de Investigación en Física, Universidad de Sonora, Hermosillo 83000, Mexico
| | - Martin Pedroza-Montero
- Departamento de Investigación en Física, Universidad de Sonora, Hermosillo 83000, Mexico
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Zhou J, Zhou PL, Shen Q, Ahmed SA, Pan XT, Liu HL, Ding XL, Li J, Wang K, Xia XH. Probing Multidimensional Structural Information of Single Molecules Transporting through a Sub-10 nm Conical Plasmonic Nanopore by SERS. Anal Chem 2021; 93:11679-11685. [PMID: 34415740 DOI: 10.1021/acs.analchem.1c00875] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Probing the orientation and oxygenation state of single molecules (SMs) is of great importance for understanding the advanced structure of individual molecules. Here, we manipulate molecules transporting through the hot spot of a sub-10 nm conical gold nanopore and acquire the multidimensional structural information of the SMs by surface enhanced Raman scattering (SERS) detection. The sub-10 nm size and conical shape of the plasmonic nanopore guarantee its high detection sensitivity. SERS spectra show a high correlation with the orientations of small-sized single rhodamine 6G (R6G) during transport. Meanwhile, SERS spectra of a single hemoglobin (Hb) reveal both the vertical/parallel orientations of the porphyrin ring and oxygenated/deoxygenated states of Hb. The present study provides a new strategy for bridging the primary sequence and the advanced structure of SMs.
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Affiliation(s)
- Juan Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Pan-Ling Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qi Shen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Saud Asif Ahmed
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiao-Tong Pan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hai-Ling Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xin-Lei Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jian Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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39
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Diz V, Bieza SA, Oviedo Rouco S, Estrin DA, Murgida DH, Bari SE. Reactivity of inorganic sulfide species towards a pentacoordinated heme model system. J Inorg Biochem 2021; 220:111459. [PMID: 33894504 DOI: 10.1016/j.jinorgbio.2021.111459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 02/07/2023]
Abstract
The reactivity of inorganic sulfide towards ferric bis(N-acetyl)- microperoxidase 11 in sodium dodecyl sulfate has been explored by means of visible absorption and resonance Raman spectroscopies. The reaction has been previously studied in buffered solutions at neutral pH and in the presence of excess sulfide, revealing the formation of a moderately stable hexacoordinated low spin ferric sulfide complex that yields the ferrous form in the hour's timescale. In the surfactant solution, instead, the ferrous form is rapidly formed. The spectroscopic characterization of the heme structure in the surfactant milieu revealed the stabilization of a major ferric mono-histidyl high spin heme, which may be ascribed to out of plane distortions prompting the detachment of the axially ligated water molecule, thus leading to a differential reactivity. The ferric bis(N-acetyl)- microperoxidase 11 in sodium dodecyl sulfate provides a model for pentacoordinated heme platforms with an imidazole-based ligand.
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Affiliation(s)
- Virginia Diz
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina
| | - Silvina A Bieza
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Santiago Oviedo Rouco
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Darío A Estrin
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Daniel H Murgida
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Sara E Bari
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina.
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40
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Verma T, Majumdar S, Yadav S, Ahmed SM, Umapathy S, Nandi D. Cell-free hemoglobin is a marker of systemic inflammation in mouse models of sepsis: a Raman spectroscopic study. Analyst 2021; 146:4022-4032. [PMID: 34032232 DOI: 10.1039/d1an00066g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sepsis is a life-threatening condition caused by heightened host immune responses post infection. Despite intensive research, most of the existing diagnostic methods remain non-specific, labour-intensive, time-consuming or are not sensitive enough for rapid and timely diagnosis of the onset and progression of sepsis. The present work was undertaken to explore the potential of Raman spectroscopy to identify the biomarkers of sepsis in a label-free and minimally invasive manner using different mouse models of inflammation. The sera of BALB/c mice infected with Salmonella Typhimurium reveal extensive hemolysis, as indicated by the Raman bands that are characteristic of the porphyrin ring of hemoglobin (668, 743, 1050, 1253 and 1397 cm-1) which increase in a kinetic manner. These markers are also observed in a lipopolysaccharide-induced endotoxic shock model, but not in a thioglycollate-induced sterile peritonitis model. These data demonstrate that hemolysis is a signature of systemic, but not localised, inflammation. To further validate our observations, sepsis was induced in the nitric oxide synthase 2 (Nos2-/-) deficient strain which is more sensitive to infection. Interestingly, Nos2-/- mice exhibit a higher degree of hemolysis than C57BL/6 mice. Sepsis-induced hemolysis was also confirmed using resonance Raman spectroscopy with 442 nm excitation which demonstrated a pronounced increase in the resonant Raman bands at 670 and 1350 cm-1 in sera of the infected mice. This is the first study to identify inflammation-induced hemolysis in mouse models of sepsis using Raman spectral signatures for hemoglobin. The possible implications of this method in detecting hemolysis in different inflammatory pathologies, such as the ongoing COVID-19 pandemic, are discussed.
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Affiliation(s)
- Taru Verma
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India.
| | - Shamik Majumdar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Shikha Yadav
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Syed Moiz Ahmed
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Siva Umapathy
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India. and Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
| | - Dipankar Nandi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India. and Department of Biochemistry, Indian Institute of Science, Bangalore, India
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41
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Dybas J, Chiura T, Marzec KM, Mak PJ. Probing Heme Active Sites of Hemoglobin in Functional Red Blood Cells Using Resonance Raman Spectroscopy. J Phys Chem B 2021; 125:3556-3565. [PMID: 33787265 PMCID: PMC8154613 DOI: 10.1021/acs.jpcb.1c01199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
The UV–vis absorption, Raman
imaging, and resonance Raman
(rR) spectroscopy methods were employed to study cyanohemoglobin (HbCN)
adducts inside living functional red blood cells (RBCs). The cyanide
ligands are especially optically sensitive probes of the active site
environment of heme proteins. The rR studies of HbCN and its isotopic
analogues (13CN–, C15N–, and 13C15N–), as well as a careful deconvolution of spectral data, revealed
that the ν(Fe–CN) stretching, δ(Fe–CN) bending,
and ν(C≡N) stretching modes occur at 454, 382, and 2123
cm–1, respectively. Interestingly, while the ν(Fe–CN)
modes exhibit the same frequencies in both the isolated and RBC-enclosed
hemoglobin molecules, small frequency differences are observed in
the δ(Fe–CN) bending modes and the values of their isotopic
shifts. These studies show that even though the overall tilted conformation
of the Fe–C≡N fragment in the isolated HbCN is preserved
in the HbCN enclosed within living cells, there is a small difference
in the degree of distortion of the Fe–C≡N fragment.
The slight changes in the ligand geometry can be reasonably attributed
to the high ordering and tight packing of Hb molecules inside RBCs.
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Affiliation(s)
- Jakub Dybas
- Chemistry Department, Saint Louis University, 3501 Laclede Avenue, Saint Louis 63103, Missouri, United States.,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzyńskiego Str., Krakow 30-348, Poland
| | - Tapiwa Chiura
- Chemistry Department, Saint Louis University, 3501 Laclede Avenue, Saint Louis 63103, Missouri, United States
| | - Katarzyna M Marzec
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzyńskiego Str., Krakow 30-348, Poland
| | - Piotr J Mak
- Chemistry Department, Saint Louis University, 3501 Laclede Avenue, Saint Louis 63103, Missouri, United States
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42
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El Khoury Y, Le Breton G, Cunha AV, Jansen TLC, van Wilderen LJGW, Bredenbeck J. Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c. J Chem Phys 2021; 154:124201. [PMID: 33810651 DOI: 10.1063/5.0039969] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.
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Affiliation(s)
- Youssef El Khoury
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Guillaume Le Breton
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ana V Cunha
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Luuk J G W van Wilderen
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
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43
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Hammerschmid D, Germani F, Drusin SI, Fagnen C, Schuster CD, Hoogewijs D, Marti MA, Venien-Bryan C, Moens L, Van Doorslaer S, Sobott F, Dewilde S. Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens. Comput Struct Biotechnol J 2021; 19:1874-1888. [PMID: 33995893 PMCID: PMC8076648 DOI: 10.1016/j.csbj.2021.03.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Globin-coupled sensors (GCS) usually consist of three domains: a sensor/globin, a linker, and a transmitter domain. The globin domain (GD), activated by ligand binding and/or redox change, induces an intramolecular signal transduction resulting in a response of the transmitter domain. Depending on the nature of the transmitter domain, GCSs can have different activities and functions, including adenylate and di-guanylate cyclase, histidine kinase activity, aerotaxis and/or oxygen sensing function. The gram-negative delta-proteobacterium Geobacter sulfurreducens expresses a protein with a GD covalently linked to a four transmembrane domain, classified, by sequence similarity, as GCS (GsGCS). While its GD is fully characterized, not so its transmembrane domain, which is rarely found in the globin superfamily. In the present work, GsGCS was characterized spectroscopically and by native ion mobility-mass spectrometry in combination with cryo-electron microscopy. Although lacking high resolution, the oligomeric state and the electron density map were valuable for further rational modeling of the full-length GsGCS structure. This model demonstrates that GsGCS forms a transmembrane domain-driven tetramer with minimal contact between the GDs and with the heme groups oriented outward. This organization makes an intramolecular signal transduction less likely. Our results, including the auto-oxidation rate and redox potential, suggest a potential role for GsGCS as redox sensor or in a membrane-bound e-/H+ transfer. As such, GsGCS might act as a player in connecting energy production to the oxidation of organic compounds and metal reduction. Database searches indicate that GDs linked to a four or seven helices transmembrane domain occur more frequently than expected.
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Key Words
- AfGcHK, Anaeromyxobacter sp. Fw109-5 GcHK
- AsFRMF, Ascaris suum FRMF-amide receptor
- AvGReg, Azotobacter vinilandii Greg
- BpGReg, Bordetella pertussis Greg
- BsHemAT, Bacillus subtilis HemAT
- CCS, collision cross section
- CIU, collision-induced unfolding
- CMC, critical micelle concentration
- CV, cyclic voltammetry
- CeGLB26, Caenorhabditis elegans globin 26
- CeGLB33, Caenorhabditis elegans globin 33
- CeGLB6, Caenorhabditis elegans globin 6
- DDM, n-dodecyl-β-d-maltoside
- DPV, differential pulse voltammetry
- EcDosC, Escherichia coli Dos with DGC activity
- FMRF, H-Phe-Met-Arg-Phe-NH2 neuropeptide
- GCS, globin-coupled sensor
- GD, globin domain
- GGDEF, Gly-Gly-Asp-Glu-Phe motive
- Gb, globin
- Geobacter sulfurreducens
- GintHb, hemoglobin from Gasterophilus intestinalis
- Globin-coupled sensor
- GsGCS, Geobacter sulfurreducens GCS
- GsGCS162, GD of GsGCS
- IM-MS, ion mobility-mass spectrometry
- LmHemAC, Leishmania major HemAC
- MaPgb, Methanosarcina acetivorans protoglobin
- MtTrHbO, Mycobacterium tuberculosis truncated hemoglobin O
- NH4OAc, ammonium acetate
- OG, n-octyl-β-d-glucopyranoside
- PDE, phosphodiesterase
- PcMb, Physether catodon myoglobin
- PccGCS, Pectobacterium carotivorum GCS
- PsiE, phosphate-starvation-inducible E
- RR, resonance Raman
- SCE, saturated calomel electrode
- SHE, standard hydrogen electrode
- SaktrHb, Streptomyces avermitilis truncated hemoglobin-antibiotic monooxygenase
- SwMb, myoglobin from sperm whale
- TD, Transmitter domain
- TmD, Transmembrane domain
- Transmembrane domain
- Transmembrane-coupled globins
- mNgb, mouse neuroglobin
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Affiliation(s)
- Dietmar Hammerschmid
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Francesca Germani
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Salvador I. Drusin
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Charline Fagnen
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Claudio D. Schuster
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - David Hoogewijs
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System, University of Fribourg, Switzerland
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Catherine Venien-Bryan
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Luc Moens
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Sabine Van Doorslaer
- Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom
| | - Sylvia Dewilde
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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44
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Dai X, Fu W, Chi H, Mesias VSD, Zhu H, Leung CW, Liu W, Huang J. Optical tweezers-controlled hotspot for sensitive and reproducible surface-enhanced Raman spectroscopy characterization of native protein structures. Nat Commun 2021; 12:1292. [PMID: 33637710 PMCID: PMC7910584 DOI: 10.1038/s41467-021-21543-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 01/27/2021] [Indexed: 01/05/2023] Open
Abstract
Surface-enhanced Raman spectroscopy (SERS) has emerged as a powerful tool to detect biomolecules in aqueous environments. However, it is challenging to identify protein structures at low concentrations, especially for the proteins existing in an equilibrium mixture of various conformations. Here, we develop an in situ optical tweezers-coupled Raman spectroscopy to visualize and control the hotspot between two Ag nanoparticle-coated silica beads, generating tunable and reproducible SERS enhancements with single-molecule level sensitivity. This dynamic SERS detection window is placed in a microfluidic flow chamber to detect the passing-by proteins, which precisely characterizes the structures of three globular proteins without perturbation to their native states. Moreover, it directly identifies the structural features of the transient species of alpha-synuclein among its predominant monomers at physiological concentration of 1 μM by reducing the ensemble averaging. Hence, this SERS platform holds the promise to resolve the structural details of dynamic, heterogeneous, and complex biological systems.
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Affiliation(s)
- Xin Dai
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Laboratory for Synthetic Chemistry and Chemical Biology, Health@InnoHK, Hong Kong Science Park, Hong Kong, China
| | - Wenhao Fu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Huanyu Chi
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Vince St Dollente Mesias
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hongni Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Cheuk Wai Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Wei Liu
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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45
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Kruse F, Nguyen AD, Dragelj J, Heberle J, Hildebrandt P, Mroginski MA, Weidinger IM. A Resonance Raman Marker Band Characterizes the Slow and Fast Form of Cytochrome c Oxidase. J Am Chem Soc 2021; 143:2769-2776. [PMID: 33560128 DOI: 10.1021/jacs.0c10767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cytochrome c oxidase (CcO) in its as-isolated form is known to exist in a slow and fast form, which differ drastically in their ability to bind oxygen and other ligands. While preparation methods have been established that yield either the fast or the slow form of the protein, the underlying structural differences have not been identified yet. Here, we have performed surface enhanced resonance Raman (SERR) spectroscopy of CcO immobilized on electrodes in both forms. SERR spectra obtained in resonance with the heme a3 metal-to-ligand charge transfer (MLCT) transition at 650 nm displayed a sharp vibrational band at 748 or 750 cm-1 when the protein was in its slow or fast form, respectively. DFT calculations identified the band as a mode of the His-419 ligand that is sensitive to the oxygen ligand and the protonation state of Tyr-288 within the binuclear complex. Potential-dependent SERR spectroscopy showed a redox-induced change of this band around 525 mV versus Ag/AgCl exclusively for the fast form, which coincides with the redox potential of the Tyr-O/Tyr-O- transition. Our data points to a peroxide ligand in the resting state of CcO for both forms. The observed frequencies and redox sensitivities of the Raman marker band suggest that a radical Tyr-288 is present in the fast form and a protonated Tyr-288 in the slow form.
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Affiliation(s)
- Fabian Kruse
- Department of Chemistry and Food Chemistry, Technische Universität Dresden, 01069 Dresden, Germany
| | - Anh Duc Nguyen
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Jovan Dragelj
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Joachim Heberle
- Freie Universität Berlin, Department of Physics, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
| | - Peter Hildebrandt
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Inez M Weidinger
- Department of Chemistry and Food Chemistry, Technische Universität Dresden, 01069 Dresden, Germany
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46
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Pal I, Roy M, Dey SG. Interaction of ApoMyoglobin with Heme-hIAPP complex. J Inorg Biochem 2020; 216:111348. [PMID: 33450674 DOI: 10.1016/j.jinorgbio.2020.111348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
Human Islet Amyloid Polypeptide (hIAPP) or amylin, can bind heme and the resultant complexes are prone to generate partially reduced oxygen species (PROS). The formation of PROS and the related oxidative stress highlight the importance of Heme-hIAPP in the onset and development of Type 2 Diabetes mellitus (T2Dm) in humans. In this study, the interaction of Heme-hIAPP with apomyoglobin (ApoMb) has been investigated using a combination of spectroscopic and electrophoresis techniques. Absorption, resonance Raman data and gel electrophoresis results confirm that ApoMb can uptake heme from Heme-hIAPP and constitute a six-coordinate high-spin ferric heme active site identical to that of myoglobin (Mb). The heme transfer reaction has two distinct kinetic steps. A possible mechanism of this reaction involves heme transfer to the apoprotein in the first step followed by a reorganisation of the protein chain to form the active site of native Mb. Increase in the pH of the reaction medium enhances the rate of the second step of heme transfer. This possibly corresponds to the deprotonation of a propionate side chain of the heme moiety at high pH which facilitates secondary interactions with the conserved distal Lys45 residue of horse heart Mb. Additionally, ApoMb sequesters ligand bound heme from Heme-hIAPP. After the heme transfer reaction, the amount of PROS formed by Heme-hIAPP complex diminishes significantly. This not only potentially diminishes heme-induced toxicity in the pancreatic β-cells but also produces Mb which has well-documented functions throughout the respiratory system and can thereby likely reduce the risks associated with T2Dm.
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Affiliation(s)
- Ishita Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
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47
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López-Castaños KA, Ortiz-Frade LA, Méndez E, Quiroga-González E, González-Fuentes MA, Méndez-Albores A. Indirect Quantification of Glyphosate by SERS Using an Incubation Process With Hemin as the Reporter Molecule: A Contribution to Signal Amplification Mechanism. Front Chem 2020; 8:612076. [PMID: 33392153 PMCID: PMC7775572 DOI: 10.3389/fchem.2020.612076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/30/2020] [Indexed: 02/03/2023] Open
Abstract
The indirect determination of the most used herbicide worldwide, glyphosate, was achieved by the SERS technique using hemin chloride as the reporter molecule. An incubation process between hemin and glyphosate solutions was required to obtain a reproducible Raman signal on SERS substrates consisting of silicon decorated with Ag nanoparticles (Si-AgNPs). At 780 nm of excitation wavelength, SERS spectra from hemin solutions do not show extra bands in the presence of glyphosate. However, the hemin bands increase in intensity as a function of glyphosate concentration. This allows the quantification of the herbicide using as marker band the signal associated with the ring breathing mode of pyridine at 745 cm-1. The linear range was from 1 × 10-10 to 1 × 10-5 M and the limit of detection (LOD) was 9.59 × 10-12 M. This methodology was successfully applied to the quantification of the herbicide in honey. From Raman experiments with and without silver nanoparticles, it was possible to state that the hemin is the species responsible for the absorption in the absence or the presence of the herbicide via vinyl groups. Likewise, when the glyphosate concentration increases, a subtle increase occurs in the planar orientation of the vinyl group at position 2 in the porphyrin ring of hemin over the silver surface, favoring the reduction of the molecule. The total Raman signal of the hemin-glyphosate incubated solutions includes a maximized electromagnetic contribution by the use of the appropriate laser excitation, and chemical contributions related to charge transfer between silver and hemin, and from resonance properties of Raman scattering of hemin. Incubation of the reporter molecule with the analyte before the conjugation with the SERS substrate has not been explored before and could be extrapolated to other reporter-analyte systems that depend on a binding equilibrium process.
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Affiliation(s)
| | - Luis A. Ortiz-Frade
- Centro de Investigación y Desarrollo Tecnológico en Electroquímica (CIDETEQ), Pedro Escobedo, Mexico
| | - Erika Méndez
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | | | | | - Alia Méndez-Albores
- Centro de Química-ICUAP, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
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48
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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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49
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Takahashi S, Nambu S, Matsui T, Fujii H, Ishikawa H, Mizutani Y, Tsumoto K, Ikeda-Saito M. Unique Electronic Structures of the Highly Ruffled Hemes in Heme-Degrading Enzymes of Staphylococcus aureus, IsdG and IsdI, by Resonance Raman and Electron Paramagnetic Resonance Spectroscopies. Biochemistry 2020; 59:3918-3928. [PMID: 32988197 DOI: 10.1021/acs.biochem.0c00731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Staphylococcus aureus uses IsdG and IsdI to convert heme into a mixture of staphylobilin isomers, 15-oxo-β-bilirubin and 5-oxo-δ-bilirubin, formaldehyde, and iron. The highly ruffled heme found in the heme-IsdI and IsdG complexes has been proposed to be responsible for the unique heme degradation products. We employed resonance Raman (RR) and electron paramagnetic resonance (EPR) spectroscopies to examine the coordination and electronic structures of heme bound to IsdG and IsdI. Heme complexed to IsdG and IsdI is coordinated by a neutral histidine. The trans ligand is hydroxide in the ferric alkaline form of both proteins. In the ferric neutral form at pH 6.0, heme is six-coordinated with water as the sixth ligand for IsdG and is in the mixture of the five-coordinated and six-coordinated species for IsdI. In the ferrous CO-bound form, CO is strongly hydrogen bonded with a distal residue. The marker lines, ν2 and ν3, appear at frequencies that are distinct from other proteins having planar hemes. The EPR spectra for the ferric hydroxide and cyanide states might be explained by assuming the thermal mixing of the d-electron configurations, (dxy)2(dxz,dyz)3 and (dxz,dyz)4(dxy)1. The fraction for the latter becomes larger for the ferric cyanide form. In the ferric neutral state at pH 6.0, the quantum mechanical mixing of the high and intermediate spin configurations might explain the peculiar frequencies of ν2 and ν3 in the RR spectra. The heme ruffling imposed by IsdG and IsdI gives rise to unique electronic structures of heme, which are expected to modulate the first and subsequent steps of the heme oxygenation.
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Affiliation(s)
- Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan
| | - Shusuke Nambu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan
| | - Toshitaka Matsui
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan
| | - Hiroshi Fujii
- Graduate School of Humanities and Sciences, Nara Women's University, Kitauoyanishi, Nara 630-8506, Japan.,Department of Chemistry, Biology, and Environmental Science, Nara Women's University, Kitauoyanishi, Nara 630-8506, Japan
| | - Haruto Ishikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masao Ikeda-Saito
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan.,BIOCEV, First Faculty of Medicine, Charles University, 252 50 Vestec, Czech Republic
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50
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Dybas J, Bokamper MJ, Marzec KM, Mak PJ. Probing the structure-function relationship of hemoglobin in living human red blood cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 239:118530. [PMID: 32498028 DOI: 10.1016/j.saa.2020.118530] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/14/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
Hemoglobin (Hb) is a key component of respiratory system and as such plays important role in human physiology. The studies of Hb's structure and functions are usually performed on cell-free protein; however, it has been shown that there are functionally relevant differences between isolated Hb and Hb present inside red blood cells (RBCs). It is clear that new experimental approaches are needed to understand the origin of these differences and to gain insight into the structure-function relationship of Hb within intact living cells. In this work we present a novel application of Resonance Raman spectroscopy to study heme active site of different forms of human Hb within living RBCs using laser excitation lines in resonance with their Soret absorption bands. These studies revealed that there are no significant changes in the disposition of the Fe-O-O fragment or the Fe-NHis linkage for Hb molecules enclosed in RBCs and these in free isolated states. However, some changes in the orientation of the heme vinyl groups were observed which might account for the differences in the protein activity and ligand affinity. This work highlights importance of protein-based studies and presents a new opportunity to translate these results to physiological cell systems.
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Affiliation(s)
- Jakub Dybas
- Saint Louis University, Chemistry Department, 3501 Laclede Ave., 63103 Saint Louis, MO, United States; Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), 14 Bobrzyńskiego Str., 30-348 Krakow, Poland
| | - Matthew J Bokamper
- Saint Louis University, Chemistry Department, 3501 Laclede Ave., 63103 Saint Louis, MO, United States
| | - Katarzyna M Marzec
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), 14 Bobrzyńskiego Str., 30-348 Krakow, Poland.
| | - Piotr J Mak
- Saint Louis University, Chemistry Department, 3501 Laclede Ave., 63103 Saint Louis, MO, United States.
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