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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] [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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Kostyuk AI, Rapota DD, Morozova KI, Fedotova AA, Jappy D, Semyanov AV, Belousov VV, Brazhe NA, Bilan DS. Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy. Free Radic Biol Med 2024; 217:68-115. [PMID: 38508405 DOI: 10.1016/j.freeradbiomed.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/10/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.
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Affiliation(s)
- Alexander I Kostyuk
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia
| | - Diana D Rapota
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Kseniia I Morozova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna A Fedotova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - David Jappy
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia
| | - Alexey V Semyanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; Sechenov First Moscow State Medical University, Moscow, 119435, Russia; College of Medicine, Jiaxing University, Jiaxing, Zhejiang Province, 314001, China
| | - Vsevolod V Belousov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia; Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia; Life Improvement by Future Technologies (LIFT) Center, Skolkovo, Moscow, 143025, Russia
| | - Nadezda A Brazhe
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Dmitry S Bilan
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia.
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3
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Lin C, Mazor Y, Reppert M. Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis. J Phys Chem B 2024; 128:2266-2280. [PMID: 38442033 DOI: 10.1021/acs.jpcb.3c06488] [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: 03/07/2024]
Abstract
Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.
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Affiliation(s)
- Chientzu Lin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
| | - Yuval Mazor
- School of Molecular Sciences, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
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4
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Brazhe NA, Nikelshparg EI, Baizhumanov AA, Grivennikova VG, Semenova AA, Novikov SM, Volkov VS, Arsenin AV, Yakubovsky DI, Evlyukhin AB, Bochkova ZV, Goodilin EA, Maksimov GV, Sosnovtseva O, Rubin AB. SERS uncovers the link between conformation of cytochrome c heme and mitochondrial membrane potential. Free Radic Biol Med 2023; 196:133-144. [PMID: 36649901 DOI: 10.1016/j.freeradbiomed.2023.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
The balance between the mitochondrial respiratory chain activity and the cell's needs in ATP ensures optimal cellular function. Cytochrome c is an essential component of the electron transport chain (ETC), which regulates ETC activity, oxygen consumption, ATP synthesis and can initiate apoptosis. The impact of conformational changes in cytochrome c on its function is not understood for the lack of access to these changes in intact mitochondria. We have developed a novel sensor that uses unique properties of label-free surface-enhanced Raman spectroscopy (SERS) to identify conformational changes in heme of cytochrome c and to elucidate their role in functioning mitochondria. We have verified that molecule bond vibrations assessed by SERS are a reliable indicator of the heme conformation during changes in the inner mitochondrial membrane potential and ETC activity. We have demonstrated that cytochrome c heme reversibly switches between planar and ruffled conformations in response to the inner mitochondrial membrane potential (ΔΨ) and H+ concentration in the intermembrane space. This regulates the efficiency of the mitochondrial respiratory chain, thus, adjusting the mitochondrial respiration to the cell's consumption of ATP and the overall activity. We have found that under hypertensive conditions cytochrome c heme loses its sensitivity to ΔΨ that can affect the regulation of ETC activity. The ability of the proposed SERS-based sensor to track mitochondrial function opens broad perspectives in cell bioenergetics.
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Affiliation(s)
- Nadezda A Brazhe
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia.
| | - Evelina I Nikelshparg
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia
| | - Adil A Baizhumanov
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia
| | - Vera G Grivennikova
- Department of Biochemistry, Biological Faculty, Moscow State University, 119234, Russia
| | - Anna A Semenova
- Faculty of Materials Sciences, Moscow State University, 119899, Russia
| | - Sergey M Novikov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141701, Russia
| | - Valentyn S Volkov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141701, Russia; GrapheneTek, Skolkovo Innovation Center, Moscow, 121205, Russia
| | - Aleksey V Arsenin
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141701, Russia
| | - Dmitry I Yakubovsky
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141701, Russia
| | - Andrey B Evlyukhin
- Institute of Quantum Optics, Leibniz Universität Hannover, Hannover, 30167, Germany
| | - Zhanna V Bochkova
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia
| | - Eugene A Goodilin
- Faculty of Materials Sciences, Moscow State University, 119899, Russia; Faculty of Chemistry, Moscow State University, 119991, Russia; Kurnakov Institute of General and Inorganic Chemistry RAS, Moscow, 119071, Russia
| | - Georgy V Maksimov
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia; Federal State Autonomous Educational Institution of Higher Education "National Research Technological University "MISiS", Moscow, 119049, Russia
| | - Olga Sosnovtseva
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK, 2200, Denmark.
| | - Andrey B Rubin
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia
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5
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Dahl PJ, Yi SM, Gu Y, Acharya A, Shipps C, Neu J, O’Brien JP, Morzan UN, Chaudhuri S, Guberman-Pfeffer MJ, Vu D, Yalcin SE, Batista VS, Malvankar NS. A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks. SCIENCE ADVANCES 2022; 8:eabm7193. [PMID: 35544567 PMCID: PMC9094664 DOI: 10.1126/sciadv.abm7193] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/28/2022] [Indexed: 06/10/2023]
Abstract
Although proteins are considered as nonconductors that transfer electrons only up to 1 to 2 nanometers via tunneling, Geobacter sulfurreducens transports respiratory electrons over micrometers, to insoluble acceptors or syntrophic partner cells, via nanowires composed of polymerized cytochrome OmcS. However, the mechanism enabling this long-range conduction is unclear. Here, we demonstrate that individual nanowires exhibit theoretically predicted hopping conductance, at rate (>1010 s-1) comparable to synthetic molecular wires, with negligible carrier loss over micrometers. Unexpectedly, nanowires show a 300-fold increase in their intrinsic conductance upon cooling, which vanishes upon deuteration. Computations show that cooling causes a massive rearrangement of hydrogen bonding networks in nanowires. Cooling makes hemes more planar, as revealed by Raman spectroscopy and simulations, and lowers their reduction potential. We find that the protein surrounding the hemes acts as a temperature-sensitive switch that controls charge transport by sensing environmental perturbations. Rational engineering of heme environments could enable systematic tuning of extracellular respiration.
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Affiliation(s)
- Peter J. Dahl
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sophia M. Yi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Yangqi Gu
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Atanu Acharya
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Catharine Shipps
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Jens Neu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - J. Patrick O’Brien
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Uriel N. Morzan
- Department of Chemistry, Yale University, New Haven, CT, USA
| | | | - Matthew J. Guberman-Pfeffer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Dennis Vu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | | | - Nikhil S. Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
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6
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Verma PK, Sawant SD. Unravelling reaction selectivities via bio-inspired porphyrinoid tetradentate frameworks. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Kroneck PMH. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. J Biol Inorg Chem 2021; 27:1-21. [PMID: 34865208 PMCID: PMC8840924 DOI: 10.1007/s00775-021-01921-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2- is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2- to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
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Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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8
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Gonzaga de França Lopes L, Gouveia Júnior FS, Karine Medeiros Holanda A, Maria Moreira de Carvalho I, Longhinotti E, Paulo TF, Abreu DS, Bernhardt PV, Gilles-Gonzalez MA, Cirino Nogueira Diógenes I, Henrique Silva Sousa E. Bioinorganic systems responsive to the diatomic gases O2, NO, and CO: From biological sensors to therapy. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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Fernandes TM, Morgado L, Turner DL, Salgueiro CA. Protein Engineering of Electron Transfer Components from Electroactive Geobacter Bacteria. Antioxidants (Basel) 2021; 10:844. [PMID: 34070486 PMCID: PMC8227773 DOI: 10.3390/antiox10060844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/02/2021] [Accepted: 05/20/2021] [Indexed: 01/02/2023] Open
Abstract
Electrogenic microorganisms possess unique redox biological features, being capable of transferring electrons to the cell exterior and converting highly toxic compounds into nonhazardous forms. These microorganisms have led to the development of Microbial Electrochemical Technologies (METs), which include applications in the fields of bioremediation and bioenergy production. The optimization of these technologies involves efforts from several different disciplines, ranging from microbiology to materials science. Geobacter bacteria have served as a model for understanding the mechanisms underlying the phenomenon of extracellular electron transfer, which is highly dependent on a multitude of multiheme cytochromes (MCs). MCs are, therefore, logical targets for rational protein engineering to improve the extracellular electron transfer rates of these bacteria. However, the presence of several heme groups complicates the detailed redox characterization of MCs. In this Review, the main characteristics of electroactive Geobacter bacteria, their potential to develop microbial electrochemical technologies and the main features of MCs are initially highlighted. This is followed by a detailed description of the current methodologies that assist the characterization of the functional redox networks in MCs. Finally, it is discussed how this information can be explored to design optimal Geobacter-mutated strains with improved capabilities in METs.
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Affiliation(s)
- Tomás M. Fernandes
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
| | - Leonor Morgado
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
| | - David L. Turner
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal;
| | - Carlos A. Salgueiro
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
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10
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Rivera S, Young PG, Hoffer ED, Vansuch GE, Metzler CL, Dunham CM, Weinert EE. Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled Sensors. Inorg Chem 2018; 57:14386-14395. [PMID: 30378421 DOI: 10.1021/acs.inorgchem.8b02584] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In order to respond to external stimuli, bacteria have evolved sensor proteins linking external signals to intracellular outputs that can then regulate downstream pathways and phenotypes. Globin coupled sensor proteins (GCSs) serve to link environmental O2 levels to cellular processes by coupling a heme-containing sensor globin domain to a catalytic output domain. However, the mechanism by which O2 binding activates these proteins is currently unknown. To provide insights into the signaling mechanism, two distinct dimeric complexes of the isolated globin domain of the GCS from Bordetella pertussis ( BpeGlobin) were solved via X-ray crystallography in which differences in ligand-bound states were observed. Both monomers of one dimer contain Fe(II)-O2 states, while the other dimer consists of the Fe(III)-H2O and Fe(II)-O2 states. These data provide the first molecular insights into the heme pocket conformation of the active Fe(II)-O2 form of these enzymes. In addition, heme distortion modes and heme-protein interactions were found to correlate with the ligation state of the globin, suggesting that these conformational changes play a role in O2-dependent signaling. Fourier transform infrared spectroscopy (FTIR) of the full-length GCS from B. pertussis ( BpeGReg) and the closely related GCS from Pectobacterium carotovorum ssp. carotovorum ( PccGCS) confirmed the importance of an ordered water within the heme pocket and two distal residues (Tyr43 and Ser68) as hydrogen-bond donors. Taken together, this work provides mechanistic insights into BpeGReg O2 sensing and the signaling mechanisms of diguanylate cyclase-containing GCS proteins.
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Affiliation(s)
- Shannon Rivera
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Paul G Young
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Eric D Hoffer
- Department of Biochemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Gregory E Vansuch
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Carmen L Metzler
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Christine M Dunham
- Department of Biochemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Emily E Weinert
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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11
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Influence of heme c attachment on heme conformation and potential. J Biol Inorg Chem 2018; 23:1073-1083. [PMID: 30143872 DOI: 10.1007/s00775-018-1603-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
Heme c is characterized by its covalent attachment to a polypeptide. The attachment is typically to a CXXCH motif in which the two Cys form thioether bonds with the heme, "X" can be any amino acid other than Cys, and the His serves as a heme axial ligand. Some cytochromes c, however, contain heme attachment motifs with three or four intervening residues in a CX3CH or CX4CH motif. Here, the impacts of these variations in the heme attachment motif on heme ruffling and electronic structure are investigated by spectroscopically characterizing CX3CH and CX4CH variants of Hydrogenobacter thermophilus cytochrome c552. In addition, a novel CXCH variant is studied. 1H and 13C NMR, EPR, and resonance Raman spectra of the protein variants are analyzed to deduce the extent of ruffling using previously reported relationships between these spectral data and heme ruffling. In addition, the reduction potentials of these protein variants are measured using protein film voltammetry. The CXCH and CX4CH variants are found to have enhanced heme ruffling and lower reduction potentials. Implications of these results for the use of these noncanonical motifs in nature, and for the engineering of novel heme peptide structures, are discussed.
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12
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Chertkova RV, Brazhe NA, Bryantseva TV, Nekrasov AN, Dolgikh DA, Yusipovich AI, Sosnovtseva O, Maksimov GV, Rubin AB, Kirpichnikov MP. New insight into the mechanism of mitochondrial cytochrome c function. PLoS One 2017; 12:e0178280. [PMID: 28562658 PMCID: PMC5451065 DOI: 10.1371/journal.pone.0178280] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 05/10/2017] [Indexed: 11/22/2022] Open
Abstract
We investigate functional role of the P76GTKMIFA83 fragment of the primary structure of cytochrome c. Based on the data obtained by the analysis of informational structure (ANIS), we propose a model of functioning of cytochrome c. According to this model, conformational rearrangements of the P76GTKMIFA83 loop fragment have a significant effect on conformational mobility of the heme. It is suggested that the conformational mobility of cytochrome c heme is responsible for its optimal orientation with respect to electron donor and acceptor within ubiquinol–cytochrome c oxidoreductase (complex III) and cytochrome c oxidase (complex IV), respectively, thus, ensuring electron transfer from complex III to complex IV. To validate the model, we design several mutant variants of horse cytochrome c with multiple substitutions of amino acid residues in the P76GTKMIFA83 sequence that reduce its ability to undergo conformational rearrangements. With this, we study the succinate–cytochrome c reductase and cytochrome c oxidase activities of rat liver mitoplasts in the presence of mutant variants of cytochrome c. The electron transport activity of the mutant variants decreases to different extent. Resonance Raman spectroscopy (RRS) and surface-enhanced Raman spectroscopy (SERS) data demonstrate, that all mutant cytochromes possess heme with the higher degree of ruffling deformation, than that of the wild-type (WT) cytochrome c. The increase in the ruffled deformation of the heme of oxidized cytochromes correlated with the decrease in the electron transport rate of ubiquinol–cytochrome c reductase (complex III). Besides, all mutant cytochromes have lower mobility of the pyrrol rings and methine bridges, than WT cytochrome c. We show that a decrease in electron transport activity in the mutant variants correlates with conformational changes and reduced mobility of heme porphyrin. This points to a significant role of the P76GTKMIFA83 fragment in the electron transport function of cytochrome c.
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Affiliation(s)
- Rita V. Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- * E-mail: (RVC); (NAB)
| | - Nadezda A. Brazhe
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (RVC); (NAB)
| | - Tatiana V. Bryantseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey N. Nekrasov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander I. Yusipovich
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Olga Sosnovtseva
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Georgy V. Maksimov
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Andrei B. Rubin
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
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13
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Sun Y, Benabbas A, Zeng W, Muralidharan S, Boon EM, Champion PM. Kinetic Control of O2 Reactivity in H-NOX Domains. J Phys Chem B 2016; 120:5351-8. [PMID: 27229134 DOI: 10.1021/acs.jpcb.6b03348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transient absorption, resonance Raman, and vibrational coherence spectroscopies are used to investigate the mechanisms of NO and O2 binding to WT Tt H-NOX and its P115A mutant. Vibrational coherence spectra of the oxy complexes provide clear evidence for the enhancement of an iron-histidine mode near 217 cm(-1) following photoexcitation, which indicates that O2 can be dissociated in these proteins. However, the quantum yield of O2 photolysis is low, particularly in the wild type (≲3%). Geminate recombination of O2 and NO in both of these proteins is very fast (∼1.4 × 10(11) s(-1)) and highly efficient. We show that the distal heme pocket of the H-NOX system forms an efficient trap that limits the O2 off-rate and determines the overall affinity. The distal pocket hydrogen bond, which appears to be stronger in the P115A mutant, may help retard the O2 ligand from escaping into the solvent following either photoinduced or thermal dissociation. This, along with a strengthening of the Fe-O2 bond that is correlated with the significant heme ruffing and saddling distortions, explains the unusually high O2 affinity of WT Tt H-NOX and the even higher affinity found in the P115A mutant.
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Affiliation(s)
- Yuhan Sun
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Weiqiao Zeng
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Sandhya Muralidharan
- Department of Chemistry and the Institute of Chemical Biology and Drug Discovery, Stony Brook University , Stony Brook, New York 11794, United States
| | - Elizabeth M Boon
- Department of Chemistry and the Institute of Chemical Biology and Drug Discovery, Stony Brook University , Stony Brook, New York 11794, United States
| | - Paul M Champion
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
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14
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 549] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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15
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Investigations of heme distortion, low-frequency vibrational excitations, and electron transfer in cytochrome c. Proc Natl Acad Sci U S A 2014; 111:6570-5. [PMID: 24753591 DOI: 10.1073/pnas.1322274111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome (cyt) c is an important electron transfer protein. The ruffling deformation of its heme cofactor has been suggested to relate to its electron transfer rate. However, there is no direct experimental evidence demonstrating this correlation. In this work, we studied Pseudomonas aeruginosa cytochrome c551 and its F7A mutant. These two proteins, although similar in their X-ray crystal structure, display a significant difference in their heme out-of-plane deformations, mainly along the ruffling coordinate. Resonance Raman and vibrational coherence measurements also indicate significant differences in ruffling-sensitive modes, particularly the low-frequency γa mode found between ∼50-60 cm(-1). This supports previous assignments of γa as having a large ruffling content. Measurement of the photoreduction kinetics finds an order of magnitude decrease of the photoreduction cross-section in the F7A mutant, which has nearly twice the ruffling deformation as the WT. Additional measurements on cytochrome c demonstrate that heme ruffling is correlated exponentially with the electron transfer rates and suggest that ruffling could play an important role in redox control. A major relaxation of heme ruffling in cytochrome c, upon binding to the mitochondrial membrane, is discussed in this context.
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16
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Mak PJ, Gregory MC, Sligar SG, Kincaid JR. Resonance Raman spectroscopy reveals that substrate structure selectively impacts the heme-bound diatomic ligands of CYP17. Biochemistry 2014; 53:90-100. [PMID: 24328388 PMCID: PMC3922198 DOI: 10.1021/bi4014424] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An important function of steroidogenic cytochromes P450 is the transformation of cholesterol to produce androgens, estrogens, and the corticosteroids. The activities of cytochrome P450c17 (CYP17) are essential in sex hormone biosynthesis, with severe developmental defects being a consequence of deficiency or mutations. The first reaction catalyzed by this multifunctional P450 is the 17α-hydroxylation of pregnenolone (PREG) to 17α-hydroxypregnenolone (17-OH PREG) and progesterone (PROG) to 17α-hydroxyprogesterone (17-OH PROG). The hydroxylated products then either are used for production of corticoids or undergo a second CYP17 catalyzed transformation, representing the first committed step of androgen formation. While the hydroxylation reactions are catalyzed by the well-known Compound I intermediate, the lyase reaction is believed to involve nucleophilic attack of the earlier peroxo- intermediate on the C20-carbonyl. Herein, resonance Raman (rR) spectroscopy reveals that substrate structure does not impact heme structure for this set of physiologically important substrates. On the other hand, rR spectra obtained here for the ferrous CO adducts with these four substrates show that substrates do interact differently with the Fe-C-O fragment, with large differences between the spectra obtained for the samples containing 17-OH PROG and 17-OH PREG, the latter providing evidence for the presence of two Fe-C-O conformers. Collectively, these results demonstrate that individual substrates can differentially impact the disposition of a heme-bound ligand, including dioxygen, altering the reactivity patterns in such a way as to promote preferred chemical conversions, thereby avoiding the profound functional consequences of unwanted side reactions.
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Affiliation(s)
- Piotr J. Mak
- Department of Chemistry, Marquette University, Milwaukee, WI 53233
| | | | - Stephen G. Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801
- Department of Chemistry, University of Illinois, Urbana, IL, 61801
- College of Medicine, University of Illinois, Urbana, IL, 61801
| | - James R. Kincaid
- Department of Chemistry, Marquette University, Milwaukee, WI 53233
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17
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Henriques J, Costa PJ, Calhorda MJ, Machuqueiro M. Charge parametrization of the DvH-c3 heme group: validation using constant-(pH,E) molecular dynamics simulations. J Phys Chem B 2012. [PMID: 23199023 DOI: 10.1021/jp3082134] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We studied the effect of using different heme group charge parametrization methods and schemes (Merz-Kollman, CHELPG, and single- and multiconformational RESP) on the quality of the results produced by the constant-(pH,E) MD method, applied to the redox titration of Desulfovibrio vulgaris Hildenborough cytochrome c(3). These new and more accurate charge sets enabled us to overcome the previously reported dependence of the method's performance on the dielectric constant, ε, assigned to the protein region. In particular, we found a systematic, clear shift of the E(mod) toward more negative values than those previously reported, in agreement with an electrostatics based reasoning. The simulations showed strong coupling between protonating/redox sites. We were also able to capture significant direct and, especially, indirect interactions between hemes, such as those mediated by histidine 67. Our results highlight the importance of having a good quantum description of the system before deriving atomic partial charges for classic force fields.
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Affiliation(s)
- João Henriques
- Centro de Química e Bioquímica and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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18
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Nicoludis JM, Miller ST, Jeffrey PD, Barrett SP, Rablen PR, Lawton TJ, Yatsunyk LA. Optimized end-stacking provides specificity of N-methyl mesoporphyrin IX for human telomeric G-quadruplex DNA. J Am Chem Soc 2012. [PMID: 23181361 DOI: 10.1021/ja3088746] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
N-methyl mesoporphyrin IX (NMM) is exceptionally selective for G-quadruplexes (GQ) relative to duplex DNA and, as such, has found a wide range of applications in biology and chemistry. In addition, NMM is selective for parallel versus antiparallel GQ folds, as was recently demonstrated in our laboratory. Here, we present the X-ray crystal structure of a complex between NMM and human telomeric DNA dAGGG(TTAGGG)(3), Tel22, determined in two space groups, P2(1)2(1)2 and P6, at 1.65 and 2.15 Å resolution, respectively. The former is the highest resolution structure of the human telomeric GQ DNA reported to date. The biological unit contains a Tel22 dimer of 5'-5' stacked parallel-stranded quadruplexes capped on both ends with NMM, supporting the spectroscopically determined 1:1 stoichiometry. NMM is capable of adjusting its macrocycle geometry to closely match that of the terminal G-tetrad required for efficient π-π stacking. The out-of-plane N-methyl group of NMM fits perfectly into the center of the parallel GQ core where it aligns with potassium ions. In contrast, the interaction of the N-methyl group with duplex DNA or antiparallel GQ would lead to steric clashes that prevent NMM from binding to these structures, thus explaining its unique selectivity. On the basis of the biochemical data, binding of NMM to Tel22 does not rely on relatively nonspecific electrostatic interactions, which characterize most canonical GQ ligands, but rather it is hydrophobic in nature. The structural features observed in the NMM-Tel22 complex described here will serve as guidelines for developing new quadruplex ligands that have excellent affinity and precisely defined selectivity.
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Affiliation(s)
- John M Nicoludis
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, Pennsylvania 19081, United States
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19
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Nakamura M, Ikezaki A, Takahashi M. Metal-Porphyrin Orbital Interactions in Paramagnetic Iron Complexes Having Planar and Deformed Porphyrin Ring. J CHIN CHEM SOC-TAIP 2012. [DOI: 10.1002/jccs.201200474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Ukpabi G, Takayama SIJ, Mauk AG, Murphy MEP. Inactivation of the heme degrading enzyme IsdI by an active site substitution that diminishes heme ruffling. J Biol Chem 2012; 287:34179-88. [PMID: 22891243 PMCID: PMC3464526 DOI: 10.1074/jbc.m112.393249] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
IsdG and IsdI are paralogous heme degrading enzymes from the bacterium Staphylococcus aureus. Heme bound by these enzymes is extensively ruffled such that the meso-carbons at the sites of oxidation are distorted toward bound oxygen. In contrast, the canonical heme oxygenase family degrades heme that is bound with minimal distortion. Trp-66 is a conserved heme pocket residue in IsdI implicated in heme ruffling. IsdI variants with Trp-66 replaced with residues having less bulky aromatic and alkyl side chains were characterized with respect to catalytic activity, heme ruffling, and electrochemical properties. The heme degradation activity of the W66Y and W66F variants was approximately half that of the wild-type enzyme, whereas the W66L and W66A variants were inactive. A crystal structure and NMR spectroscopic analysis of the W66Y variant reveals that heme binds to this enzyme with less heme ruffling than observed for wild-type IsdI. The reduction potential of this variant (-96 ± 7 mV versus standard hydrogen electrode) is similar to that of wild-type IsdI (-89 ± 7 mV), so we attribute the diminished activity of this variant to the diminished heme ruffling observed for heme bound to this enzyme and conclude that Trp-66 is required for optimal catalytic activity.
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Affiliation(s)
- Georgia Ukpabi
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3 Canada
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21
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Saito K, Umena Y, Kawakami K, Shen JR, Kamiya N, Ishikita H. Deformation of Chlorin Rings in the Photosystem II Crystal Structure. Biochemistry 2012; 51:4290-9. [DOI: 10.1021/bi300428s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Keisuke Saito
- 202 Building E, Career-Path
Promotion Unit for Young Life Scientists, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto
606-8501, Japan
| | - Yasufumi Umena
- The OCU
Advanced Research Institute
for Natural Science and Technology (OCARINA)/Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic
Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012,
Japan
| | - Keisuke Kawakami
- The OCU
Advanced Research Institute
for Natural Science and Technology (OCARINA)/Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
| | - Jian-Ren Shen
- Division of Bioscience,
Graduate
School of Natural Science and Technology/Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Nobuo Kamiya
- The OCU
Advanced Research Institute
for Natural Science and Technology (OCARINA)/Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
- Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
| | - Hiroshi Ishikita
- 202 Building E, Career-Path
Promotion Unit for Young Life Scientists, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto
606-8501, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic
Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012,
Japan
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22
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Abstract
An overview of the use of classical mechanical molecular simulations of porphyrins, hydroporphyrins and heme proteins is given. The topics cover molecular mechanics calculations of structures and conformer energies of porphyrins, energies of barriers for interconversion between stable conformers, molecular dynamics of porphyrins and heme proteins, and normal-coordinate structural analysis of experimental and calculated porphyrin structures. Molecular mechanics and dynamics are currently a fertile area of research on porphyrins. In the future, other computational methods such as Monte Carlo simulations, which have yet to be applied to porphyrins, will come into use and open new avenues of research into molecular simulations of porphyrins.
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Affiliation(s)
- JOHN A. SHELNUTT
- Biomolecular Materials and Interfaces Department, Sandia National Laboratories, Albuquerque, NM 87185-1349, USA
- Department of Chemistry, The University of New Mexico, Albuquerque, NM 87131, USA
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23
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Haddad R, Lu Y, Quirke JME, Berget P, Sun L, Fettinger JC, Leung K, Qiu Y, Schore NE, van Swol F, Medforth CJ, Shelnutt JA. Steric bulkiness of pyrrole substituents and the out-of-plane deformations of porphyrins: nickel(II) octaisopropylporphyrin and its meso-nitro derivative. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424611003707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sterically bulky substituents at the β-carbons of the pyrrole rings of porphyrins are sufficient to cause large out-of-plane porphyrin distortions even in the absence of substituent groups at the meso carbons. It is well established that substituents at the meso-positions only or at both the β-pyrrole and the meso-positions are sufficiently bulky to result in large non-planar distortions of the macrocycle. However, no systematic studies of the effects of bulky β-pyrrole substituents alone have been reported. Herein, molecular simulations and X-ray crystallography of nickel(II) 2,3,7,8,12,13,17,18-octa(isopropyl)porphyrin reveal that large out-of-plane distortions (>1.5 Å) are induced by the steric repulsion of the β-isopropyl groups but fail to lead to a single strongly energetically favored conformer. The molecular simulations indicate that multiple conformers differing in the orientation of the isopropyl groups and the macrocycle conformation coexist in solution and this is confirmed by resonance Raman spectroscopy. Large downshifts in the structure-sensitive lines result from the non-planar distortion, and line broadenings result from structural heterogeneity. The heterogeneity originates from tradeoffs between energy contributions from steric repulsion and macrocycle distortion. Simulations for 5-nitro-2,3,7,8,12,13,17,18-octa(isopropyl)porphyrin suggest two possible orientations of the nitro group with respect to the macrocycle mean plane — one nearly vertical (as in the crystal structure) and another that is nearly parallel. INDO/S semiempirical calculations indicate an orbital of the NO2 group resides between the porphyrin frontier orbitals with significant mixing of the nitro and porphyrin orbitals.KEYWORDS: porphyrin, non-planar, resonance Raman, X-ray crystallography, crystal structure, isopropyl, nitro, conformer, molecular mechanics, molecular simulations, density functional theory, steric crowding, conformational heterogeneity.
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Affiliation(s)
- Raid Haddad
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185-1349, USA
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - Yi Lu
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - J. Martin E. Quirke
- Department of Chemistry, Florida International University, Miami, FL 33199, USA
| | - Patrick Berget
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Lisong Sun
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | | | - Kevin Leung
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185-1349, USA
| | - Yan Qiu
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - Neil E. Schore
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Frank van Swol
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185-1349, USA
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - Craig J. Medforth
- Departments of Chemistry & Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, USA
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - John A. Shelnutt
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185-1349, USA
- Department of Chemistry, University of Georgia, Athens, GA 30607, USA
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24
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Schweitzer-Stenner R. Using spectroscopic tools to probe porphyrin deformation and porphyrin-protein interactions. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424611003343] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The reactivity and functionality of heme proteins are to a significant extent determined by the conformation of their functional heme groups and by the interaction of axial ligands with their protein environment. This review focuses on experimental methods and theoretical concepts for elucidating symmetry lowering perturbations of the heme induced by the protein environment of the heme pocket. First, we discuss a variety of methods which can be used to probe the electric field at the heme, including spectral hole burning as well as low temperature absorption and room temperature circular dichroism spectroscopy. Second, we show how heme deformations can be described as superposition of deformations along normal coordinates, thereby using the irreducible representations of the D4h point group as a classification tool. Finally, resonance Raman spectroscopy is introduced as a tool to probe the deformations of metalloprophyrins in solution and in protein matrices by measuring and comparing intensities and depolarization properties rather than wavenumber positions.
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25
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Karunakaran V, Benabbas A, Youn H, Champion PM. Vibrational coherence spectroscopy of the heme domain in the CO-sensing transcriptional activator CooA. J Am Chem Soc 2011; 133:18816-27. [PMID: 21961804 DOI: 10.1021/ja206152m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Femtosecond vibrational coherence spectroscopy was used to investigate the low-frequency vibrational dynamics of the heme in the carbon monoxide oxidation activator protein (CooA) from the thermophilic anaerobic bacterium Carboxydothermus hydrogenoformans (Ch-CooA). Low frequency vibrational modes are important because they are excited by the ambient thermal bath (k(B)T = 200 cm(-1)) and participate in thermally activated barrier crossing events. However, such modes are nearly impossible to detect in the aqueous phase using traditional spectroscopic methods. Here, we present the low frequency coherence spectra of the ferric, ferrous, and CO-bound forms of Ch-CooA in order to compare the protein-induced heme distortions in its active and inactive states. Distortions take place predominantly along the coordinates of low-frequency modes because of their weak force constants, and such distortions are reflected in the intensity of the vibrational coherence signals. A strong mode near ~90 cm(-1) in the ferrous form of Ch-CooA is suggested to contain a large component of heme ruffling, consistent with the imidazole-bound ferrous heme crystal structure, which shows a significant protein-induced heme distortion along this coordinate. A mode observed at ~228 cm(-1) in the six-coordinate ferrous state is proposed to be the ν(Fe-His) stretching vibration. The observation of the Fe-His mode indicates that photolysis of the N-terminal α-amino axial ligand takes place. This is followed by a rapid (~8.5 ps) transient absorption recovery, analogous to methionine rebinding in photolyzed ferrous cytochrome c. We have also studied CO photolysis in CooA, which revealed very strong photoproduct state coherent oscillations. The observation of heme-CO photoproduct oscillations is unusual because most other heme systems have CO rebinding kinetics that are too slow to make the measurement possible. The low frequency coherence spectrum of the CO-bound form of Ch-CooA shows a strong vibration at ~230 cm(-1) that is broadened and up-shifted compared to the ν(Fe-His) of Rr-CooA (216 cm(-1)). We propose that the stronger Fe-His bond is related to the enhanced thermal stability of Ch-CooA and that there is a smaller (time dependent) tilt of the histidine ring with respect to the heme plane in Ch-CooA. The appearance of strong modes at ~48 cm(-1) in both the ferrous and CO-bound forms of Ch-CooA is consistent with coupling of the heme doming distortion to the photolysis reaction in both samples. Upon CO binding and protein activation, a heme mode near 112 ± 5 cm(-1) disappears, probably indicating a decreased heme saddling distortion. This reflects changes in the heme environment and geometry that must be associated with the conformational transition activating the DNA-binding domain. Protein-specific DNA binding to the CO-bound form of Ch-CooA was also investigated, and although the CO rebinding kinetics are significantly perturbed, there are negligible changes in the low-frequency vibrational spectrum of the heme.
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Affiliation(s)
- Venugopal Karunakaran
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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26
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Pacholska-Dudziak E, Gaworek A, Latos-Grażyński L. Iron(II) Vacataporphyrins: A Variable Annulene Conformation inside a Regular Porphyrin Frame. Inorg Chem 2011; 50:10956-65. [DOI: 10.1021/ic2015176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ewa Pacholska-Dudziak
- Department of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Aneta Gaworek
- Department of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
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27
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Battistuzzi G, Stampler J, Bellei M, Vlasits J, Soudi M, Furtmüller PG, Obinger C. Influence of the Covalent Heme–Protein Bonds on the Redox Thermodynamics of Human Myeloperoxidase. Biochemistry 2011; 50:7987-94. [DOI: 10.1021/bi2008432] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Gianantonio Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, via Campi 183,
41100 Modena, Italy
| | - Johanna Stampler
- Vienna
Institute of BioTechnology,
Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18,
A-1190 Vienna, Austria
| | - Marzia Bellei
- Department of Chemistry, University of Modena and Reggio Emilia, via Campi 183,
41100 Modena, Italy
| | - Jutta Vlasits
- Vienna
Institute of BioTechnology,
Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18,
A-1190 Vienna, Austria
| | - Monika Soudi
- Vienna
Institute of BioTechnology,
Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18,
A-1190 Vienna, Austria
| | - Paul G. Furtmüller
- Vienna
Institute of BioTechnology,
Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18,
A-1190 Vienna, Austria
| | - Christian Obinger
- Vienna
Institute of BioTechnology,
Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18,
A-1190 Vienna, Austria
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28
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Electronic properties of the highly ruffled heme bound to the heme degrading enzyme IsdI. Proc Natl Acad Sci U S A 2011; 108:13071-6. [PMID: 21788475 DOI: 10.1073/pnas.1101459108] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
IsdI, a heme-degrading protein from Staphylococcus aureus, binds heme in a manner that distorts the normally planar heme prosthetic group to an extent greater than that observed so far for any other heme-binding protein. To understand better the relationship between this distinct structural characteristic and the functional properties of IsdI, spectroscopic, electrochemical, and crystallographic results are reported that provide evidence that this heme ruffling is essential to the catalytic activity of the protein and eliminates the need for the water cluster in the distal heme pocket that is essential for the activity of classical heme oxygenases. The lack of heme orientational disorder in (1)H-NMR spectra of the protein argues that the catalytic formation of β- and δ-biliverdin in nearly equal yield results from the ability of the protein to attack opposite sides of the heme ring rather than from binding of the heme substrate in two alternative orientations.
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Karunakaran V, Denisov I, Sligar SG, Champion PM. Investigation of the low frequency dynamics of heme proteins: native and mutant cytochrome P450(cam) and redox partner complexes. J Phys Chem B 2011; 115:5665-77. [PMID: 21391540 DOI: 10.1021/jp112298y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Vibrational coherence spectroscopy (VCS) is used to investigate the low-frequency dynamics of camphor-free and camphor-bound cytochrome P450(cam) (CYP 101) and its L358P mutant. The low-frequency heme vibrations are found to be perturbed upon binding to the electron transfer partner putidaredoxin (Pdx). A strong correlation between the "detuned" vibrational coherence spectrum, which monitors frequencies between 100 and 400 cm(-1), and the lower frequency part of the Raman spectrum is also demonstrated. The very low frequency region ≤200 cm(-1), uniquely accessed by open-band VCS measurements, reveals a mode near 103 cm(-1) in P450(cam) when camphor is not present in the distal pocket. This reflects the presence of a specific heme distortion, such as saddling or ruffling, in the substrate-free state where water is coordinated to the low-spin iron atom. Such distortions are likely to retard the rate of electron transfer to the substrate-free protein. The presence of strong mode near ∼33 cm(-1) in the camphor-bound form suggests a significant heme-doming distortion, which is supported by analysis using normal coordinate structural decomposition. Pdx also displays a strong coherent vibration near 30 cm(-1) that in principle could be involved in vibrational resonance with its electron transfer target. A splitting of the 33 cm(-1) feature and intensification of a mode near 78 cm(-1) appear when the P450(cam)/Pdx complex is formed. These observations are consistent with vibrational mixing and heme geometric distortions upon Pdx binding that are coincident with the increased thiolate electron donation to the heme. The appearance of a mode near 65 cm(-1) in the coherence spectra of the L358P mutant is comparable to the mode at 78 cm(-1) seen in the P450(cam)/Pdx complex and is consistent with the view that the heme and its environment in the L358P mutant are similar to the Pdx-bound native protein. Resonance Raman spectra are presented for both P450(cam) and the L358P mutant and the changes are correlated with an increased amount of thiolate electron donation to the heme in the mutant sample.
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Affiliation(s)
- Venugopal Karunakaran
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
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Einsle O. Structure and Function of Formate-Dependent Cytochrome c Nitrite Reductase, NrfA. Methods Enzymol 2011; 496:399-422. [DOI: 10.1016/b978-0-12-386489-5.00016-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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31
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Liptak MD, Wen X, Bren KL. NMR and DFT investigation of heme ruffling: functional implications for cytochrome c. J Am Chem Soc 2010; 132:9753-63. [PMID: 20572664 DOI: 10.1021/ja102098p] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Out-of-plane (OOP) deformations of the heme cofactor are found in numerous heme-containing proteins and the type of deformation tends to be conserved within functionally related classes of heme proteins. We demonstrate correlations between the heme ruffling OOP deformation and the (13)C and (1)H nuclear magnetic resonance (NMR) hyperfine shifts of heme aided by density functional theory (DFT) calculations. The degree of ruffling in the heme cofactor of Hydrogenobacter thermophilus cytochrome c(552) has been modified by a single amino acid mutation in the second coordination sphere of the cofactor. The (13)C and (1)H resonances of the cofactor have been assigned using one- and two-dimensional NMR spectroscopy aided by selective (13)C-enrichment of the heme. DFT has been used to predict the NMR hyperfine shifts and electron paramagnetic resonance (EPR) g-tensor at several points along the ruffling deformation coordinate. The DFT-predicted NMR and EPR parameters agree with the experimental observations, confirming that an accurate theoretical model of the electronic structure and its response to ruffling has been established. As the degree of ruffling increases, the heme methyl (1)H resonances move upfield while the heme methyl and meso (13)C resonances move downfield. These changes are a consequence of altered overlap of the Fe 3d and porphyrin pi orbitals, which destabilizes all three occupied Fe 3d-based molecular orbitals and decreases the positive and negative spin density on the beta-pyrrole and meso carbons, respectively. Consequently, the heme ruffling deformation decreases the electronic coupling of the cofactor with external redox partners and lowers the reduction potential of heme.
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Affiliation(s)
- Matthew D Liptak
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
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32
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Ibrahim M, Derbyshire ER, Soldatova AV, Marletta MA, Spiro TG. Soluble guanylate cyclase is activated differently by excess NO and by YC-1: resonance Raman spectroscopic evidence. Biochemistry 2010; 49:4864-71. [PMID: 20459051 DOI: 10.1021/bi100506j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Modulation of soluble guanylate cyclase (sGC) activity by nitric oxide (NO) involves two distinct steps. Low-level activation of sGC is achieved by the stoichiometric binding of NO (1-NO) to the heme cofactor, while much higher activation is achieved by the binding of additional NO (xsNO) at a non-heme site. Addition of the allosteric activator YC-1 to the 1-NO form leads to activity comparable to that of the xsNO state. In this study, the mechanisms of sGC activation were investigated using electronic absorption and resonance Raman (RR) spectroscopic methods. RR spectroscopy confirmed that the 1-NO form contains five-coordinate NO-heme and showed that the addition of NO to the 1-NO form has no significant effect on the spectrum. In contrast, addition of YC-1 to either the 1-NO or xsNO forms alters the RR spectrum significantly, indicating a protein-induced change in the heme geometry. This change in the heme geometry was also observed when BAY 41-2272 was added to the xsNO form. Bands assigned to bending and stretching motions of the vinyl and propionate substituents undergo changes in intensity in a pattern suggesting altered tilting of the pyrrole rings to which they are attached. In addition, the N-O stretching frequency increases, with no change in the Fe-NO stretching frequency, an effect modeled via DFT calculations as resulting from a small opening of the Fe-N-O angle. These spectral differences demonstrate different mechanisms of activation by synthetic activators, such as YC-1 and BAY 41-2272, and excess NO.
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Affiliation(s)
- Mohammed Ibrahim
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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33
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Törő I, Petrutz C, Pacello F, D’Orazio M, Battistoni A, Djinović-Carugo K. Structural Basis of Heme Binding in the Cu,Zn Superoxide Dismutase from Haemophilus ducreyi. J Mol Biol 2009; 386:406-18. [DOI: 10.1016/j.jmb.2008.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2008] [Revised: 11/28/2008] [Accepted: 12/02/2008] [Indexed: 12/01/2022]
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Olea C, Boon EM, Pellicena P, Kuriyan J, Marletta MA. Probing the function of heme distortion in the H-NOX family. ACS Chem Biol 2008; 3:703-10. [PMID: 19032091 DOI: 10.1021/cb800185h] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hemoproteins carry out diverse functions utilizing a wide range of chemical reactivity while employing the same heme prosthetic group. It is clear from high-resolution crystal structures and biochemical studies that protein-bound hemes are not planar and adopt diverse conformations. The crystal structure of an H-NOX domain from Thermoanaerobacter tengcongensis (Tt H-NOX) contains the most distorted heme reported to date. In this study, Tt H-NOX was engineered to adopt a flatter heme by mutating proline 115, a conserved residue in the H-NOX family, to alanine. Decreasing heme distortion in Tt H-NOX increases affinity for oxygen and decreases the reduction potential of the heme iron. Additionally, flattening the heme is associated with significant shifts in the N-terminus of the protein. These results show a clear link between the heme conformation and Tt H-NOX structure and demonstrate that heme distortion is an important determinant for maintaining biochemical properties in H-NOX proteins.
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Affiliation(s)
| | - Elizabeth M. Boon
- Department of Chemistry, California Institute for Quantitative Biosciences
| | | | - John Kuriyan
- Department of Molecular and Cell Biology
- Department of Chemistry, California Institute for Quantitative Biosciences
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720
- Division of Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Michael A. Marletta
- Department of Molecular and Cell Biology
- Department of Chemistry, California Institute for Quantitative Biosciences
- Division of Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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Bis-histidine-coordinated hemes in four-helix bundles: how the geometry of the bundle controls the axial imidazole plane orientations in transmembrane cytochromes of mitochondrial complexes II and III and related proteins. J Biol Inorg Chem 2008; 13:481-98. [PMID: 18418633 DOI: 10.1007/s00775-008-0372-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2008] [Accepted: 03/27/2008] [Indexed: 10/22/2022]
Abstract
Early investigation of the electron paramagnetic resonance spectra of bis-histidine-coordinated membrane-bound ferriheme proteins led to the description of a spectral signal that had only one resolved feature. These became known as "highly anisotropic low-spin" or "large g(max)" ferriheme centers. Extensive work with small-molecule model heme complexes showed that this spectroscopic signature occurs in bis-imidazole ferrihemes in which the planes of the imidazole ligands are nearly perpendicular, deltaphi = 57-90 degrees. In the last decade protein crystallographic studies have revealed the atomic structures of a number of examples of bis-histidine heme proteins. A frequent characteristic of these large g(max) ferrihemes in membrane-bound proteins is the occurrence of the heme within a four-helix bundle with a left-handed twist. The histidine ligands occur at the same level on two diametrically opposed helices of the bundle. These ligands have the same side-chain conformation and ligate heme iron on the bundle axis, resulting in a quasi-twofold symmetric structure. The two non-ligand-bearing helices also obey this symmetry, and have a conserved small residue, usually glycine, where the edge of the heme ring makes contact with the helix backbones. In many cases this small residue is preceded by a threonine or serine residue whose side-chain hydroxyl oxygen acts as a hydrogen-bond acceptor from the N(delta1) atom of the heme-ligating histidine. The deltaphi angle is thus determined by the common histidine side-chain conformation and the crossing angle of the ligand-bearing helices, in some cases constrained by hydrogen bonds to the serine/threonine residues on the non-ligand-bearing helices.
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37
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Bowman SEJ, Bren KL. The chemistry and biochemistry of heme c: functional bases for covalent attachment. Nat Prod Rep 2008; 25:1118-30. [PMID: 19030605 DOI: 10.1039/b717196j] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A discussion of the literature concerning the synthesis, function, and activity of heme c-containing proteins is presented. Comparison of the properties of heme c, which is covalently bound to protein, is made to heme b, which is bound noncovalently. A question of interest is why nature uses biochemically expensive heme c in many proteins when its properties are expected to be similar to heme b. Considering the effects of covalent heme attachment on heme conformation and on the proximal histidine interaction with iron, it is proposed that heme attachment influences both heme reduction potential and ligand-iron interactions.
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Affiliation(s)
- Sarah E J Bowman
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
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38
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Lee WC, Reniere ML, Skaar EP, Murphy MEP. Ruffling of metalloporphyrins bound to IsdG and IsdI, two heme-degrading enzymes in Staphylococcus aureus. J Biol Chem 2008; 283:30957-63. [PMID: 18713745 DOI: 10.1074/jbc.m709486200] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
IsdG and IsdI are paralogous proteins that are intracellular components of a complex heme uptake system in Staphylococcus aureus. IsdG and IsdI were shown previously to reductively degrade hemin. Crystal structures of the apoproteins show that these proteins belong to a newly identified heme degradation family distinct from canonical eukaryotic and prokaryotic heme oxygenases. Here we report the crystal structures of an inactive N7A variant of IsdG in complex with Fe(3+)-protoporphyrin IX (IsdG-hemin) and of IsdI in complex with cobalt protoporphyrin IX (IsdI-CoPPIX) to 1.8 A or better resolution. These structures show that the metalloporphyrins are buried into similar deep clefts such that the propionic acids form salt bridges to two Arg residues. His(77) (IsdG) or His(76) (IsdI), a critical residue required for activity, is coordinated to the Fe(3+) or Co(3+) atoms, respectively. The bound porphyrin rings form extensive steric interactions in the binding cleft such that the rings are highly distorted from the plane. This distortion is best described as ruffled and places the beta- and delta-meso carbons proximal to the distal oxygen-binding site. In the IsdG-hemin structure, Fe(3+) is pentacoordinate, and the distal side is occluded by the side chain of Ile(55). However, in the structure of IsdI-CoPPIX, the distal side of the CoPPIX accommodates a chloride ion in a cavity formed through a conformational change in Ile(55). The chloride ion participates in a hydrogen bond to the side chain amide of Asn(6). Together the structures suggest a reaction mechanism in which a reactive peroxide intermediate proceeds with nucleophilic oxidation at the beta- or delta-meso carbon of the hemin.
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Affiliation(s)
- Woo Cheol Lee
- Department of Microbiology and Immunology, Life Sciences Institute, the University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Pauleta SR, Lu Y, Goodhew CF, Moura I, Pettigrew GW, Shelnutt JA. Calcium-Dependent Heme Structure in the Reduced Forms of the Bacterial Cytochrome c Peroxidase from Paracoccus pantotrophus. Biochemistry 2008; 47:5841-50. [DOI: 10.1021/bi702486d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sofia R. Pauleta
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Nanomaterials Sciences Department, Sandia National Laboratories, Albuquerque, New Mexico 87185-1349, Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556, and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, U.K
| | - Yi Lu
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Nanomaterials Sciences Department, Sandia National Laboratories, Albuquerque, New Mexico 87185-1349, Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556, and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, U.K
| | - Celia F. Goodhew
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Nanomaterials Sciences Department, Sandia National Laboratories, Albuquerque, New Mexico 87185-1349, Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556, and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, U.K
| | - Isabel Moura
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Nanomaterials Sciences Department, Sandia National Laboratories, Albuquerque, New Mexico 87185-1349, Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556, and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, U.K
| | - Graham W. Pettigrew
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Nanomaterials Sciences Department, Sandia National Laboratories, Albuquerque, New Mexico 87185-1349, Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556, and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, U.K
| | - John A. Shelnutt
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Nanomaterials Sciences Department, Sandia National Laboratories, Albuquerque, New Mexico 87185-1349, Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556, and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, U.K
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Matsumura H, Wakatabi M, Omi S, Ohtaki A, Nakamura N, Yohda M, Ohno H. Modulation of redox potential and alteration in reactivity via the peroxide shunt pathway by mutation of cytochrome P450 around the proximal heme ligand. Biochemistry 2008; 47:4834-42. [PMID: 18363338 DOI: 10.1021/bi800142v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the thermophilic cytochrome P450 from the thermoacidophilic crenarchaeon Sulfolobus tokodaii strain 7 (P450st), a phenylalanine residue at position 310 and an alanine residue at position 320 are located close to the heme thiolate ligand, Cys317. Single site-directed mutants F310A and A320Q and double mutant F310A/A320Q have been constructed. All mutant enzymes as well as wild-type (WT) P450st were expressed at high levels. The substitution of F310 with Ala and of A320 with Gln induced shifts in redox potential and blue shifts in Soret absorption of ferrous-CO forms, while spectral characterization showed that in the resting state, the mutants almost retained the structural integrity of the active site. The redox potential of the heme varied as follows: -481 mV (WT), -477 mV (A320Q), -453 mV (F310A), and -450 mV (F310A/A320Q). The trend in the Soret band of the ferrous-CO form was as follows: 450 nm (WT) < 449 nm (A320Q) < 446 nm (F310A) < 444 nm (F310A/A320Q). These results established that the reduction potential and electron density on the heme iron are modulated by the Phe310 and Ala320 residues in P450st. The electron density on the heme decreases in the following order: WT > A320Q > F310A > F310A/A320Q. The electron density on the heme iron infers an essential role in P450 activity. The decrease in electron density interferes with the formation of a high-valent oxo-ferryl species called Compound I. However, steady-state turnover rates of styrene epoxidation with H2O2 show the following trend: WT approximately equal to A320Q < F310A approximately equal to F310A/A320Q. The shunt pathway which can provide the two electrons and oxygen required for a P450 reaction instead of NAD(P)H and dioxygen can rule out the first and second heme reduction in the catalytic process. Because the electron density on the heme iron might be deeply involved in the k cat values in this system, the intermediate Compound 0 which is the precursor species of Compound I mainly appears to participate dominantly in epoxidation with H2O2.
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Affiliation(s)
- Hirotoshi Matsumura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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41
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Gruia F, Kubo M, Ye X, Ionascu D, Lu C, Poole RK, Yeh SR, Champion PM. Coherence spectroscopy investigations of the low-frequency vibrations of heme: effects of protein-specific perturbations. J Am Chem Soc 2008; 130:5231-44. [PMID: 18355013 DOI: 10.1021/ja7104027] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Femtosecond coherence spectroscopy is used to probe the low-frequency (20-200 cm(-1)) vibrational modes of heme proteins in solution. Horseradish peroxidase (HRP), myoglobin (Mb), and Campylobacter jejuni globin (Cgb) are compared and significant differences in the coherence spectra are revealed. It is concluded that hydrogen bonding and ligand charge do not strongly affect the low-frequency coherence spectra and that protein-specific deformations of the heme group lower its symmetry and control the relative spectral intensities. Such deformations potentially provide a means for proteins to tune heme reaction coordinates, so that they can perform a broad array of specific functions. Native HRP displays complex spectral behavior above approximately 50 cm(-1) and very weak activity below approximately 50 cm(-1). Binding of the substrate analog, benzhydroxamic acid, leads to distinct changes in the coherence and Raman spectra of HRP that are consistent with the stabilization of a heme water ligand. The CN derivatives of the three proteins are studied to make comparisons under conditions of uniform heme coordination and spin-state. MbCN is dominated by a doming mode near 40 cm(-1), while HRPCN displays a strong oscillation at higher frequency (96 cm(-1)) that can be correlated with the saddling distortion observed in the X-ray structure. In contrast, CgbCN displays low-frequency coherence spectra that contain strong modes near 30 and 80 cm(-1), probably associated with a combination of heme doming and ruffling. HRPNO displays a strong doming mode near 40 cm(-1) that is activated by photolysis. The damping of the coherent motions is significantly reduced when the heme is shielded from solvent fluctuations by the protein material and reduced still further when T approximately < 50 K, as pure dephasing processes due to the protein-solvent phonon bath are frozen out.
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Affiliation(s)
- Flaviu Gruia
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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42
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Michel LV, Ye T, Bowman SEJ, Levin BD, Hahn MA, Russell BS, Elliott SJ, Bren KL. Heme attachment motif mobility tunes cytochrome c redox potential. Biochemistry 2007; 46:11753-60. [PMID: 17900177 PMCID: PMC2606054 DOI: 10.1021/bi701177j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrogen exchange (HX) rates and midpoint potentials (Em) of variants of cytochrome c from Pseudomonas aeruginosa (Pa cyt c551) and Hydrogenobacter thermophilus (Ht cyt c552) have been characterized in an effort to develop an understanding of the impact of properties of the Cys-X-X-Cys-His pentapeptide c-heme attachment (CXXCH) motif on heme redox potential. Despite structural conservation of the CXXCH motif, Ht cyt c552 exhibits a low level of protection from HX for amide protons within this motif relative to Pa cyt c551. Site-directed mutants have been prepared to determine the structural basis for and functional implications of these variations on HX behavior. The double mutant Ht-M13V/K22M displays suppressed HX within the CXXCH motif as well as a decreased Em (by 81 mV), whereas the corresponding double mutant of Pa cyt c551 (V13M/M22K) exhibits enhanced HX within the CXXCH pentapeptide and a modest increase in Em (by 30 mV). The changes in Em correlate with changes in axial His chemical shifts in the ferric proteins reflecting the extent of histidinate character. Thus, the mobility of the CXXCH pentapeptide is found to impact the His-Fe(III) interaction and therefore the heme redox potential.
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Affiliation(s)
| | | | | | | | | | | | | | - Kara L. Bren
- To whom correspondence should be addressed: Department of Chemistry, University of Rochester, Rochester, NY 14627-0216. Telephone: (585) 275-4335. Fax: (585) 276-0205. e-mail:
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Di Paolo RE, Pereira PM, Gomes I, Valente FMA, Pereira IAC, Franco R. Resonance Raman fingerprinting of multiheme cytochromes from the cytochrome c 3 family. J Biol Inorg Chem 2005; 11:217-24. [PMID: 16341896 DOI: 10.1007/s00775-005-0067-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Accepted: 11/22/2005] [Indexed: 10/25/2022]
Abstract
Resonance Raman (RR) spectroscopy was used to investigate conformational characteristics of the hemes of several ferricytochromes of the cytochrome c3 family, electron transfer proteins isolated from the periplasm and membranes of sulfate-reducing bacteria. Our analysis concentrated on the low-frequency region of the RR spectra, a fingerprint region that includes vibrations for heme-protein C-S bonds [nu(C(a)S)]. It has been proposed that these bonds are directly involved in the electron transfer process. The three groups of tetraheme cytochrome c3 analyzed, namely Type I cytochrome c (3) (TpIc (3)s), Type II cytochrome c (3) (TpIIc (3)s) and Desulfomicrobium cytochromes c3, display different frequency separations for the two nu(C(a)S) lines that are similar among members of each group. These spectral differences correlate with differences in protein structure observed among the three groups of cytochromes c3. Two larger cytochromes of the cytochrome c3 family display RR spectral characteristics for the nu(C(a)S) lines that are closer to TpIIc3 than to TpIc3. Two other multiheme cytochromes from Desulfovibrio that do not belong to the cytochrome c3 family display nu(C(a)S) lines with reverse relative areas in comparison with the latter family. This RR study shows that the small differences in protein structure observed among these cytochrome c3 correlate to differences on the heme-protein bonds, which are likely to have an impact upon the protein function, making RR spectroscopy a sensitive and useful tool for characterizing these cytochromes.
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Affiliation(s)
- Roberto E Di Paolo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, Av. da República, 2781-901 Oeiras, Portugal
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45
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Silvernail NJ, Roth A, Schulz CE, Noll BC, Scheidt WR. Heme carbonyls: environmental effects on nu(C-O) and Fe-C/C-O bond length correlations. J Am Chem Soc 2005; 127:14422-33. [PMID: 16218637 PMCID: PMC1866288 DOI: 10.1021/ja053148x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis and characterization of four low-spin (carbonyl)iron(II) tetraphenylporphyrinates, [Fe(TPP)(CO)(L)], where L = 1-methylimidazole, 2-methylimidazole, 1,2-dimethylimidazole (unsolvated), and 1,2-dimethylimidazole (toluene solvate) are reported. The complexes show nearly the same value of nu(C-O) in toluene solution (1969-72 cm(-1)) but a large range of CO stretching frequencies in the solid-state (1926-1968 cm(-1)). The large solid-state variation results from CO interactions in the solid state, as shown by an examination of the crystal structures of the four complexes. The high precision of the four structures obtained allows us to make a number of structural and spectroscopic correlations that describe the Fe-C-O and N(Im)-Fe-CO units. The values of nu(C-O) and the Fe-C and C-O bond distances are strongly correlated and provide a structural, as well as a spectroscopic, correlation of the pi back-bonding model. The interactions of CO described are closely related to the large range of CO stretching frequencies observed in heme proteins and specific interactions observed in carbonylmyoglobin (MbCO).
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Affiliation(s)
- Nathan J Silvernail
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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Saitoh T, Tachibana Y, Higuchi Y, Hori H, Akutsu H. Correlation between thegTensors and the Nonplanarity of Porphyrin Rings inDesulfovibrio vulgarisMiyazaki F Cytochromec3, Studied by Single Crystal EPR. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2004. [DOI: 10.1246/bcsj.77.357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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47
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Walker FA. Models of the Bis-Histidine-Ligated Electron-Transferring Cytochromes. Comparative Geometric and Electronic Structure of Low-Spin Ferro- and Ferrihemes. Chem Rev 2004; 104:589-615. [PMID: 14871136 DOI: 10.1021/cr020634j] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F Ann Walker
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA.
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48
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Le Moigne C, Picaud T, Boussac A, Loock B, Momenteau M, Desbois A. Absorption and resonance Raman investigations of ligand rotation and nonplanar heme distortion in bis-base low-spin iron(II)-tetrakis(o-pivalamidophenyl)porphyrin complexes. Inorg Chem 2003; 42:6081-8. [PMID: 12971780 DOI: 10.1021/ic034449f] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The absorption and resonance Raman (RR) spectra of the bis-N-methylimidazole, bis-1,5-dicyclohexylimidazole, and bis-pyridine complexes of the meso-alphaalphabetabeta and meso-alphabetaalphabeta atropisomers of Fe(II)-tetrakis(o-pivalamidophenyl)porphyrins (Fe(II)TpivPP) were obtained in methylene chloride. The different spatial arrangements of the o-pivalamide pickets in these two Fe(II)TpivPP compounds are expected to control the absolute and relative positions of the axial ligand rings with respect to the Fe-N(pyrrole) bonds. In particular, the spectroscopic data obtained for the bis-N-methylimidazole and bis-dicyclohexylimidazole complexes of the Fe(II)[alphabetaalphabeta-TpivPP] derivative showed the most important differences. Redshifts of the B and Q absorption bands (+ 4-5 nm) as well as an upshift of the low frequency nu(8) RR mode (+ 5 cm(-)(1)) were observed. No shift of the skeletal high frequency modes was detected. These spectral effects were associated with a change in relative position of the axial imidazole rings from nearly parallel in the bis-N-methylimidazole complex to nearly perpendicular in the bis-dicyclohexylimidazole complex. On the basis of stereochemical considerations as well as previous spectroscopic investigations, the data were interpreted in terms of change in porphyrin structure from planar to saddled. Complementing to a parallel study on bis-base Fe(II) "basket handle" porphyrin complexes, this spectroscopic investigation provides an additional means to distinguish planar, ruffled, and saddled conformations for ferrous hemes included in proteins.
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Affiliation(s)
- Carole Le Moigne
- Département de Biologie Joliot-Curie, CEA et URA 2096, CEA/Saclay, F-91191 Gif-sur-Yvette Cedex, France
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49
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Huang Q, Szigeti K, Fidy J, Schweitzer-Stenner R. Structural Disorder of Native Horseradish Peroxidase C Probed by Resonance Raman and Low-Temperature Optical Absorption Spectroscopy. J Phys Chem B 2003. [DOI: 10.1021/jp026935e] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qing Huang
- Department of Chemistry, University of Puerto Rico, Rio Píedras Campus, San Juan, PR 00931, and Institute of Biophysics and Radiation Biology, Semmelweis University, Puskin u. 9, Hungary H-1088
| | - Krisztian Szigeti
- Department of Chemistry, University of Puerto Rico, Rio Píedras Campus, San Juan, PR 00931, and Institute of Biophysics and Radiation Biology, Semmelweis University, Puskin u. 9, Hungary H-1088
| | - Judit Fidy
- Department of Chemistry, University of Puerto Rico, Rio Píedras Campus, San Juan, PR 00931, and Institute of Biophysics and Radiation Biology, Semmelweis University, Puskin u. 9, Hungary H-1088
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, University of Puerto Rico, Rio Píedras Campus, San Juan, PR 00931, and Institute of Biophysics and Radiation Biology, Semmelweis University, Puskin u. 9, Hungary H-1088
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Haddad RE, Gazeau S, Pécaut J, Marchon JC, Medforth CJ, Shelnutt JA. Origin of the red shifts in the optical absorption bands of nonplanar tetraalkylporphyrins. J Am Chem Soc 2003; 125:1253-68. [PMID: 12553827 DOI: 10.1021/ja0280933] [Citation(s) in RCA: 231] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The view that the large red shifts seen in the UV-visible absorption bands of peripherally crowded nonplanar porphyrins are the result of nonplanar deformations of the macrocycle has recently been challenged by the suggestion that the red shifts arise from substituent-induced changes in the macrocycle bond lengths and bond angles, termed in-plane nuclear reorganization (IPNR). We have analyzed the contributions to the UV-visible band shifts in a series of nickel or zinc meso-tetraalkylporphyrins to establish the origins of the red shifts in these ruffled porphyrins. Structures were obtained using a molecular mechanics force field optimized for porphyrins, and the nonplanar deformations were quantified by using normal-coordinate structural decomposition (NSD). Transition energies were calculated by the INDO/S semiempirical method. These computational studies demonstrate conclusively that the large Soret band red shifts ( approximately 40 nm) seen for very nonplanar meso-tetra(tert-butyl)porphyrin compared to meso-tetra(methyl)porphyrin are primarily the result of nonplanar deformations and not IPNR. Strikingly, nonplanar deformations along the high-frequency 2B(1u) and 3B(1u) normal coordinates of the macrocycle are shown to contribute significantly to the observed red shifts, even though these deformations are an order of magnitude smaller than the observed ruffling (1B(1u)) deformation. Other structural and electronic influences on the UV-visible band shifts are discussed and problems with the recent studies are examined (e.g., the systematic underestimation of the 2B(1u) and 3B(1u) modes in artificially constrained porphyrin structures that leads to a mistaken attribution of the red shift to IPNR). The effect of nonplanar deformations on the UV-visible absorption bands is then probed experimentally with a series of novel bridled nickel chiroporphyrins. In these compounds, the substituent effect is essentially invariant and the amount of nonplanar deformation decreases as the length of the straps connecting adjacent meso-cyclopropyl substituents decreases (the opposite of the effect observed for conventional strapped porphyrins). Several spectroscopic markers for nonplanarity (UV-visible bands, resonance Raman lines, and (1)H NMR resonances) are found to correlate with time-averaged deformations obtained from an NSD analysis of molecular dynamics snapshot structures. These results suggest that UV-visible band shifts of tetrapyrroles in proteins are potentially useful indicators of changes in nonplanarity provided other structural and electronic factors can be eliminated.
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Affiliation(s)
- Raid E Haddad
- Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico 87131, USA
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