1
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Yoo BK, Lambry JC, Negrerie M. Controlling the trans effect induced by nitric oxide and carbon monoxide: H93C myoglobin versus H-NOX sensors and soluble guanylate cyclase. Protein Sci 2024; 33:e5231. [PMID: 39576123 PMCID: PMC11583245 DOI: 10.1002/pro.5231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 10/22/2024] [Accepted: 11/06/2024] [Indexed: 11/25/2024]
Abstract
Myoglobin (Mb) has been engineered to replace the proximal histidine (His93) with a cysteine in order to investigate the trans effect induced by diatomic ligands using time-resolved electronic absorption spectroscopy. This single mutation induces a change of heme coordination state and bonding character which change carbon monoxide (CO) and nitric oxide (NO) dynamics. In H93C Mb the increased Fe2+-S distance weakens this bond which is replaced with a distal Fe2+-His64 ligation. We measured dynamics very different from wild type Mb but similar with those measured in soluble guanylate cyclase (sGC). Whereas NO induces a direct negative trans effect, the strain on His64 ligation is sufficient to counteract the positive trans effect due to CO. After photodissociation, geminate recombination of NO to the transient 4-coordinate heme of H93C occurred with a fast time constant (6.9 ps) identical to that in sGC. Remarkably, we also observed picosecond geminate rebinding of CO to H93C Mb, similarly with sGC in the simultaneous presence of CO and an allosteric stimulator. This CO rebinding dynamics to the 4c-heme in H93C Mb was never measured in other Mb mutants and demonstrates the existence of 5-coordinate heme with CO, explaining the synergistic activation of sGC in presence of CO and a stimulator.
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Affiliation(s)
- Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences, INSERM U-1182, CNRS UMR 7645, Ecole Polytechnique, Palaiseau, France
| | - Jean-Christophe Lambry
- Laboratoire d'Optique et Biosciences, INSERM U-1182, CNRS UMR 7645, Ecole Polytechnique, Palaiseau, France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences, INSERM U-1182, CNRS UMR 7645, Ecole Polytechnique, Palaiseau, France
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2
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Adams HR, Svistunenko DA, Wilson MT, Fujii S, Strange RW, Hardy ZA, Vazquez PA, Dabritz T, Streblow GJ, Andrew CR, Hough MA. A Heme Pocket Aromatic Quadrupole Modulates Gas Binding to Cytochrome c'-β: Implications for NO Sensors. J Biol Chem 2023:104742. [PMID: 37100286 DOI: 10.1016/j.jbc.2023.104742] [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: 01/24/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023] Open
Abstract
The structural basis by which gas-binding heme proteins control their interactions with NO, CO, and O2, is fundamental to enzymology, biotechnology and human health. Cytochromes c´ (cyts c´) are a group of putative NO-binding heme proteins that fall into two families: the well characterised four alpha helix bundle fold (cyts c´-α) and an unrelated family with a largely beta sheet fold (cyts c´-β) resembling that of cytochromes P460. A recent structure of cyt c´-β from Methylococcus capsulatus Bath (McCP-β) revealed two heme pocket phenylalanine residues (Phe 32 and Phe 61) positioned near the distal gas binding site. This feature, dubbed the "Phe cap", is highly conserved within the sequences of other cyts c´-β, but is absent in their close homologues, the hydroxylamine oxidizing cytochromes P460, although some do contain a single Phe residue. Here we report an integrated structural, spectroscopic, and kinetic characterization of McCP-β complexes with diatomic gases, focusing on the interaction of the Phe cap with NO and CO. Significantly, crystallographic and resonance Raman data show that orientation of the electron rich aromatic ring face of Phe 32 towards distally-bound NO or CO is associated with weakened backbonding and higher off rates. Moreover, we propose that an aromatic quadrupole also contributes to the unusually weak backbonding reported for some heme-based gas sensors, including the mammalian NO-sensor, soluble guanylate cyclase (sGC). Collectively, this study sheds light on the influence of highly conserved distal Phe residues on heme-gas complexes of cytochrome c'-β, including the potential for aromatic quadrupoles to modulate NO and CO binding in other heme proteins.
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Affiliation(s)
- Hannah R Adams
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Sotaro Fujii
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima, Hiroshima, 739-8528, Japan; Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Richard W Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Zoe A Hardy
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Priscilla A Vazquez
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Tyler Dabritz
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Gabriel J Streblow
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Colin R Andrew
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA.
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK; Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
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3
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Ultrafast dynamics of heme distortion in the O 2-sensor of a thermophilic anaerobe bacterium. Commun Chem 2021; 4:31. [PMID: 36697566 PMCID: PMC9814294 DOI: 10.1038/s42004-021-00471-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/05/2021] [Indexed: 01/28/2023] Open
Abstract
Heme-Nitric oxide and Oxygen binding protein domains (H-NOX) are found in signaling pathways of both prokaryotes and eukaryotes and share sequence homology with soluble guanylate cyclase, the mammalian NO receptor. In bacteria, H-NOX is associated with kinase or methyl accepting chemotaxis domains. In the O2-sensor of the strict anaerobe Caldanaerobacter tengcongensis (Ct H-NOX) the heme appears highly distorted after O2 binding, but the role of heme distortion in allosteric transitions was not yet evidenced. Here, we measure the dynamics of the heme distortion triggered by the dissociation of diatomics from Ct H-NOX using transient electronic absorption spectroscopy in the picosecond to millisecond time range. We obtained a spectroscopic signature of the heme flattening upon O2 dissociation. The heme distortion is immediately (<1 ps) released after O2 dissociation to produce a relaxed state. This heme conformational change occurs with different proportions depending on diatomics as follows: CO < NO < O2. Our time-resolved data demonstrate that the primary structural event of allostery is the heme distortion in the Ct H-NOX sensor, contrastingly with hemoglobin and the human NO receptor, in which the primary structural events are respectively the motion of the proximal histidine and the rupture of the iron-histidine bond.
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4
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Brown BN, Robinson KJ, Durfee QC, Kekilli D, Hough MA, Andrew CR. Hydroxylamine Complexes of Cytochrome c': Influence of Heme Iron Redox State on Kinetic and Spectroscopic Properties. Inorg Chem 2020; 59:14162-14170. [PMID: 32970420 DOI: 10.1021/acs.inorgchem.0c01925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxylamine (NH2OH or HA) is a redox-active nitrogen oxide that occurs as a toxic intermediate in the oxidation of ammonium by nitrifying and methanotrophic bacteria. Within ammonium containing environments, HA is generated by ammonia monooxygenase (nitrifiers) or methane monooxygenase (methanotrophs). Subsequent oxidation of HA is catalyzed by heme proteins, including cytochromes P460 and multiheme hydroxylamine oxidoreductases, the former contributing to emissions of N2O, an ozone-depleting greenhouse gas. A heme-HA complex is also a proposed intermediate in the reduction of nitrite to ammonia by cytochrome c nitrite reductase. Despite the importance of heme-HA complexes within the biogeochemical nitrogen cycle, fundamental aspects of their coordination chemistry remain unknown, including the effect of the Fe redox state on heme-HA affinity, kinetics, and spectroscopy. Using stopped-flow UV-vis and resonance Raman spectroscopy, we investigated HA complexes of the L16G distal pocket variant of Alcaligenes xylosoxidans cytochrome c'-α (L16G AxCP-α), a pentacoordinate c-type cytochrome that we show binds HA in its Fe(III) (Kd ∼ 2.5 mM) and Fe(II) (Kd = 0.0345 mM) states. The ∼70-fold higher HA affinity of the Fe(II) state is due mostly to its lower koff value (0.0994 s-1 vs 11 s-1), whereas kon values for Fe(II) (2880 M-1 s-1) and Fe(III) (4300 M-1 s-1) redox states are relatively similar. A comparison of the HA and imidazole affinities of L16G AxCP-α was also used to predict the influence of Fe redox state on HA binding to other proteins. Although HA complexes of L16G AxCP-α decompose via redox reactions, the lifetime of the Fe(II)HA complex was prolonged in the presence of excess reductant. Spectroscopic parameters determined for the Fe(II)HA complex include the N-O stretching vibration of the NH2OH ligand, ν(N-O) = 906 cm-1. Overall, the kinetic trends and spectroscopic benchmarks from this study provide a foundation for future investigations of heme-HA reaction mechanisms.
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Affiliation(s)
- Brianna N Brown
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Kelsey J Robinson
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Quentin C Durfee
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Demet Kekilli
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Colin R Andrew
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
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5
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Négrerie M. Iron transitions during activation of allosteric heme proteins in cell signaling. Metallomics 2020; 11:868-893. [PMID: 30957812 DOI: 10.1039/c8mt00337h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.
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Affiliation(s)
- Michel Négrerie
- Laboratoire d'Optique et Biosciences, INSERM, CNRS, Ecole Polytechnique, 91120 Palaiseau, France.
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6
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Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer. Proc Natl Acad Sci U S A 2020; 117:1788-1798. [PMID: 31911476 PMCID: PMC6983364 DOI: 10.1073/pnas.1906823117] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The lipid dependence of the nicotinic acetylcholine receptor from the Torpedo electric organ has long been recognized, and one of the most consistent experimental observations is that, when reconstituted in membranes formed by zwitterionic phospholipids alone, exposure to agonist fails to elicit ion-flux activity. More recently, it has been suggested that the bacterial homolog ELIC (Erwinia chrysanthemi ligand-gated ion channel) has a similar lipid sensitivity. As a first step toward the elucidation of the structural basis of this phenomenon, we solved the structures of ELIC embedded in palmitoyl-oleoyl-phosphatidylcholine- (POPC-) only nanodiscs in both the unliganded (4.1-Å resolution) and agonist-bound (3.3 Å) states using single-particle cryoelectron microscopy. Comparison of the two structural models revealed that the largest differences occur at the level of loop C-at the agonist-binding sites-and the loops at the interface between the extracellular and transmembrane domains (ECD and TMD, respectively). On the other hand, the transmembrane pore is occluded in a remarkably similar manner in both structures. A straightforward interpretation of these findings is that POPC-only membranes frustrate the ECD-TMD coupling in such a way that the "conformational wave" of liganded-receptor gating takes place in the ECD and the interfacial M2-M3 linker but fails to penetrate the membrane and propagate into the TMD. Furthermore, analysis of the structural models and molecular simulations suggested that the higher affinity for agonists characteristic of the open- and desensitized-channel conformations results, at least in part, from the tighter confinement of the ligand to its binding site; this limits the ligand's fluctuations, and thus delays its escape into bulk solvent.
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7
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Norisada J, Fujimura K, Amaya F, Kohno H, Hirata Y, Oh-hashi K. Application of NanoBiT for Monitoring Dimerization of the Null Hong Kong Variant of α-1-Antitrypsin, NHK, in Living Cells. Mol Biotechnol 2018; 60:539-549. [DOI: 10.1007/s12033-018-0092-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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8
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Lábas A, Menyhárd DK, Harvey JN, Oláh J. First Principles Calculation of the Reaction Rates for Ligand Binding to Myoglobin: The Cases of NO and CO. Chemistry 2018; 24:5350-5358. [PMID: 29285802 DOI: 10.1002/chem.201704867] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Indexed: 12/12/2022]
Abstract
Ligand binding by proteins is among the most fundamental processes in nature. Among these processes the binding of small gas molecules, such as O2 , CO and NO to heme proteins has traditionally received vivid interest, which was further boosted by their recently recognized significant role in gas sensing in the body. At the heart of the binding of these ligands to the heme group is the spinforbidden reaction between high-spin iron(II) and the ligand yielding a low-spin adduct. We use computational means to address the complete mechanism of CO and NO binding by myoglobin. Considering that it involves several steps occurring on different time scales, molecular dynamics simulations were performed to address the diffusion of the ligand through the enzyme, and DFT calculations in combination with statistical rate calculation to investigate the spin-forbidden reaction. The calculations yielded rate constants in qualitative agreement with experiments and revealed that the bottleneck of NO and CO binding is different; for NO, diffusion was found to be rate-limiting, whereas for CO, the spin-forbidden step is the slowest.
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Affiliation(s)
- Anikó Lábas
- Department of Inorganic Chemistry, Budapest University of Technology and Economics, H-1111, Budapest, Szent Gellért tér 4., Hungary
| | - Dóra K Menyhárd
- MTA-ELTE Protein Modelling Research Group, H-1117, Budapest, Pázmány Péter st. 1/A, Hungary
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, B-3001, Leuven Celestijnenlaan 200F- box 2404, Belgium
| | - Julianna Oláh
- Department of Inorganic Chemistry, Budapest University of Technology and Economics, H-1111, Budapest, Szent Gellért tér 4., Hungary
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9
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Nye DB, Preimesberger MR, Majumdar A, Lecomte JTJ. Histidine-Lysine Axial Ligand Switching in a Hemoglobin: A Role for Heme Propionates. Biochemistry 2018; 57:631-644. [PMID: 29271191 DOI: 10.1021/acs.biochem.7b01155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The hemoglobin of Synechococcus sp. PCC 7002, GlbN, is a monomeric group I truncated protein (TrHb1) that coordinates the heme iron with two histidine ligands at neutral pH. One of these is the distal histidine (His46), a residue that can be displaced by dioxygen and other small molecules. Here, we show with mutagenesis, electronic absorption spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy that at high pH and exclusively in the ferrous state, Lys42 competes with His46 for the iron coordination site. When b heme is originally present, the population of the lysine-bound species remains too small for detailed characterization; however, the population can be increased significantly by using dimethyl-esterified heme. Electronic absorption and NMR spectroscopies showed that the reversible ligand switching process occurs with an apparent pKa of 9.3 and a Lys-ligated population of ∼60% at the basic pH limit in the modified holoprotein. The switching rate, which is slow on the chemical shift time scale, was estimated to be 20-30 s-1 by NMR exchange spectroscopy. Lys42-His46 competition and attendant conformational rearrangement appeared to be related to weakened bis-histidine ligation and enhanced backbone dynamics in the ferrous protein. The pH- and redox-dependent ligand exchange process observed in GlbN illustrates the structural plasticity allowed by the TrHb1 fold and demonstrates the importance of electrostatic interactions at the heme periphery for achieving axial ligand selection. An analogy is drawn to the alkaline transition of cytochrome c, in which Lys-Met competition is detected at alkaline pH, but, in contrast to GlbN, in the ferric state only.
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Affiliation(s)
- Dillon B Nye
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Matthew R Preimesberger
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
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10
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Nilsson ZN, Mandella BL, Sen K, Kekilli D, Hough MA, Moenne-Loccoz P, Strange RW, Andrew CR. Distinguishing Nitro vs Nitrito Coordination in Cytochrome c' Using Vibrational Spectroscopy and Density Functional Theory. Inorg Chem 2017; 56:13205-13213. [PMID: 29053273 PMCID: PMC5677563 DOI: 10.1021/acs.inorgchem.7b01945] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitrite coordination to heme cofactors is a key step in the anaerobic production of the signaling molecule nitric oxide (NO). An ambidentate ligand, nitrite has the potential to coordinate via the N- (nitro) or O- (nitrito) atoms in a manner that can direct its reactivity. Distinguishing nitro vs nitrito coordination, along with the influence of the surrounding protein, is therefore of particular interest. In this study, we probed Fe(III) heme-nitrite coordination in Alcaligenes xylosoxidans cytochrome c' (AXCP), an NO carrier that excludes anions in its native state but that readily binds nitrite (Kd ∼ 0.5 mM) following a distal Leu16 → Gly mutation to remove distal steric constraints. Room-temperature resonance Raman spectra (407 nm excitation) identify ν(Fe-NO2), δ(ONO), and νs(NO2) nitrite ligand vibrations in solution. Illumination with 351 nm UV light results in photoconversion to {FeNO}6 and {FeNO}7 states, enabling FTIR measurements to distinguish νs(NO2) and νas(NO2) vibrations from differential spectra. Density functional theory calculations highlight the connections between heme environment, nitrite coordination mode, and vibrational properties and confirm that nitrite binds to L16G AXCP exclusively through the N atom. Efforts to obtain the nitrite complex crystal structure were hampered by photochemistry in the X-ray beam. Although low dose crystal structures could be modeled with a mixed nitrite (nitro)/H2O distal population, their photosensitivity and partial occupancy underscores the value of the vibrational approach. Overall, this study sheds light on steric determinants of heme-nitrite binding and provides vibrational benchmarks for future studies of heme protein nitrite reactions.
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Affiliation(s)
- Zach N. Nilsson
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Brian L. Mandella
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Kakali Sen
- School of Biological Sciences, University of Essex, Colchester Essex, CO4 3SQ, United Kingdom
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, United Kingdom
| | - Demet Kekilli
- School of Biological Sciences, University of Essex, Colchester Essex, CO4 3SQ, United Kingdom
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Colchester Essex, CO4 3SQ, United Kingdom
| | - Pierre Moenne-Loccoz
- Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, Oregon 97239, United States
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Colchester Essex, CO4 3SQ, United Kingdom
| | - Colin R. Andrew
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
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11
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Choosing the optimal spectroscopic toolkit to understand protein function. Biosci Rep 2017; 37:BSR20160378. [PMID: 28522552 PMCID: PMC5463260 DOI: 10.1042/bsr20160378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 12/02/2022] Open
Abstract
Spectroscopy was one of the earliest methods used to study the properties and reactions of proteins, and remains one of the most powerful and widely used approaches to this day. A sometimes bewildering range of spectroscopies is now available, applicable to different sample states, timescales and indeed biological questions. This editorial describes some of the most relevant spectroscopic methods together with a selection of illustrative examples.
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12
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Kekilli D, Petersen CA, Pixton DA, Ghafoor DD, Abdullah GH, Dworkowski FSN, Wilson MT, Heyes DJ, Hardman SJO, Murphy LM, Strange RW, Scrutton NS, Andrew CR, Hough MA. Engineering proximal vs. distal heme-NO coordination via dinitrosyl dynamics: implications for NO sensor design. Chem Sci 2017; 8:1986-1994. [PMID: 28451315 PMCID: PMC5390784 DOI: 10.1039/c6sc04190f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/08/2016] [Indexed: 01/18/2023] Open
Abstract
Proximal vs. distal heme-NO coordination is a novel strategy for selective gas response in heme-based NO-sensors. In the case of Alcaligenes xylosoxidans cytochrome c' (AXCP), formation of a transient distal 6cNO complex is followed by scission of the trans Fe-His bond and conversion to a proximal 5cNO product via a putative dinitrosyl species. Here we show that replacement of the AXCP distal Leu16 residue with smaller or similar sized residues (Ala, Val or Ile) traps the distal 6cNO complex, whereas Leu or Phe residues lead to a proximal 5cNO product with a transient or non-detectable distal 6cNO precursor. Crystallographic, spectroscopic, and kinetic measurements of 6cNO AXCP complexes show that increased distal steric hindrance leads to distortion of the Fe-N-O angle and flipping of the heme 7-propionate. However, it is the kinetic parameters of the distal NO ligand that determine whether 6cNO or proximal 5cNO end products are formed. Our data support a 'balance of affinities' mechanism in which proximal 5cNO coordination depends on relatively rapid release of the distal NO from the dinitrosyl precursor. This mechanism, which is applicable to other proteins that form transient dinitrosyls, represents a novel strategy for 5cNO formation that does not rely on an inherently weak Fe-His bond. Our data suggest a general means of engineering selective gas response into biologically-derived gas sensors in synthetic biology.
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Affiliation(s)
- Demet Kekilli
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Christine A Petersen
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - David A Pixton
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Dlzar D Ghafoor
- Faculty of Science and Education Science , University of Sulaimani , Sulaymaniyah , Iraq
| | | | | | - Michael T Wilson
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Derren J Heyes
- Manchester Institute of Biotechnology , 131 Princess Street , Manchester M1 7DN , UK
| | - Samantha J O Hardman
- Manchester Institute of Biotechnology , 131 Princess Street , Manchester M1 7DN , UK
| | - Loretta M Murphy
- School of Chemistry , Bangor University , Bangor , Gwynedd , Wales LL57 2UW , UK
| | - Richard W Strange
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
- Molecular Biophysics Group , Institute of Integrative Biology , Faculty of Health and Life Sciences , University of Liverpool , Liverpool , L69 7ZB , UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology , 131 Princess Street , Manchester M1 7DN , UK
| | - Colin R Andrew
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Michael A Hough
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
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13
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Kruglik SG, Yoo BK, Lambry JC, Martin JL, Negrerie M. Structural changes and picosecond to second dynamics of cytochrome c in interaction with nitric oxide in ferrous and ferric redox states. Phys Chem Chem Phys 2017; 19:21317-21334. [DOI: 10.1039/c7cp02634j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
After dissociation NO rebinds to Cyt c in 10 ps whereas Met80 rebinds in 5 μs after NO release from Cyt c. A complete view of heme – NO dynamics within 12 orders of magnitude of time in Cyt c is presented.
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Affiliation(s)
- Sergei G. Kruglik
- Laboratoire Jean Perrin
- Sorbonne Universités
- UPMC Univ. Paris 06
- CNRS
- 75005 Paris
| | - Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
| | | | - Jean-Louis Martin
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
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