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Foley EL, Hvitved AN, Eich RF, Olson JS. Mechanisms of nitric oxide reactions with Globins using mammalian myoglobin as a model system. J Inorg Biochem 2022; 233:111839. [DOI: 10.1016/j.jinorgbio.2022.111839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 12/15/2022]
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2
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Peng Q, Pavlik JW, Silvernail NJ, Alp EE, Hu MY, Zhao J, Sage JT, Scheidt WR. 3D Motions of Iron in Six-Coordinate {FeNO}(7) Hemes by Nuclear Resonance Vibration Spectroscopy. Chemistry 2016; 22:6323-6332. [PMID: 26999733 PMCID: PMC4999340 DOI: 10.1002/chem.201505155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Indexed: 11/08/2022]
Abstract
The vibrational spectrum of a six-coordinate nitrosyl iron porphyrinate, monoclinic [Fe(TpFPP)(1-MeIm)(NO)] (TpFPP=tetra-para-fluorophenylporphyrin; 1-MeIm=1-methylimidazole), has been studied by oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS). The crystal was oriented to give spectra perpendicular to the porphyrin plane and two in-plane spectra perpendicular or parallel to the projection of the FeNO plane. These enable assignment of the FeNO bending and stretching modes. The measurements reveal that the two in-plane spectra have substantial differences that result from the strongly bonded axial NO ligand. The direction of the in-plane iron motion is found to be largely parallel and perpendicular to the projection of the bent FeNO on the porphyrin plane. The out-of-plane Fe-N-O stretching and bending modes are strongly mixed with each other, as well as with porphyrin ligand modes. The stretch is mixed with v50 as was also observed for dioxygen complexes. The frequency of the assigned stretching mode of eight Fe-X-O (X=N, C, and O) complexes is correlated with the Fe-XO bond lengths. The nature of highest frequency band at ≈560 cm(-1) has also been examined in two additional new derivatives. Previously assigned as the Fe-NO stretch (by resonance Raman), it is better described as the bend, as the motion of the central nitrogen atom of the FeNO group is very large. There is significant mixing of this mode. The results emphasize the importance of mode mixing; the extent of mixing must be related to the peripheral phenyl substituents.
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Affiliation(s)
- Qian Peng
- Contribution from Department of Chemistry and Biochemistry, University of Notre Dame, University of Notre Dame, Notre Dame, Indiana 46556 USA
| | - Jeffrey W. Pavlik
- Contribution from Department of Chemistry and Biochemistry, University of Notre Dame, University of Notre Dame, Notre Dame, Indiana 46556 USA
| | - Nathan J. Silvernail
- Contribution from Department of Chemistry and Biochemistry, University of Notre Dame, University of Notre Dame, Notre Dame, Indiana 46556 USA
| | - E. Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Michael Y. Hu
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 120 Forsyth Street, Boston, MA 02115, USA
| | - W. Robert Scheidt
- Contribution from Department of Chemistry and Biochemistry, University of Notre Dame, University of Notre Dame, Notre Dame, Indiana 46556 USA
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Chakraborty S, Reed J, Sage JT, Branagan NC, Petrik ID, Miner KD, Hu MY, Zhao J, Alp EE, Lu Y. Recent advances in biosynthetic modeling of nitric oxide reductases and insights gained from nuclear resonance vibrational and other spectroscopic studies. Inorg Chem 2015; 54:9317-29. [PMID: 26274098 PMCID: PMC4677664 DOI: 10.1021/acs.inorgchem.5b01105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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This Forum Article focuses on recent
advances in structural and spectroscopic studies of biosynthetic models
of nitric oxide reductases (NORs). NORs are complex metalloenzymes
found in the denitrification pathway of Earth’s nitrogen cycle
where they catalyze the proton-dependent two-electron reduction of
nitric oxide (NO) to nitrous oxide (N2O). While much progress
has been made in biochemical and biophysical studies of native NORs
and their variants, a clear mechanistic understanding of this important
metalloenzyme related to its function is still elusive. We report
herein UV–vis and nuclear resonance vibrational spectroscopy
(NRVS) studies of mononitrosylated intermediates of the NOR reaction
of a biosynthetic model. The ability to selectively substitute metals
at either heme or nonheme metal sites allows the introduction of independent 57Fe probe atoms at either site, as well as allowing the preparation
of analogues of stable reaction intermediates by replacing either
metal with a redox inactive metal. Together with previous structural
and spectroscopic results, we summarize insights gained from studying
these biosynthetic models toward understanding structural features
responsible for the NOR activity and its mechanism. The outlook on
NOR modeling is also discussed, with an emphasis on the design of
models capable of catalytic turnovers designed based on close mimics
of the secondary coordination sphere of native NORs. New insights into nitric oxide reductases (NORs) are obtained. Using
nuclear resonance vibrational spectroscopy, we probe both iron atoms
in mononitrosylated intermediates of the NOR reaction in a biosynthetic
protein model that reveal new insights into the structural and electronic
features responsible for the NOR activity and its likely mechanism.
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Affiliation(s)
| | | | - J Timothy Sage
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - Nicole C Branagan
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | | | | | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - E Ercan Alp
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
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Matsumura H, Hayashi T, Chakraborty S, Lu Y, Moënne-Loccoz P. The production of nitrous oxide by the heme/nonheme diiron center of engineered myoglobins (Fe(B)Mbs) proceeds through a trans-iron-nitrosyl dimer. J Am Chem Soc 2014; 136:2420-31. [PMID: 24432820 PMCID: PMC4004238 DOI: 10.1021/ja410542z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Denitrifying NO reductases are transmembrane
protein complexes
that are evolutionarily related to heme/copper terminal oxidases.
They utilize a heme/nonheme diiron center to reduce two NO molecules
to N2O. Engineering a nonheme FeB site within
the heme distal pocket of sperm whale myoglobin has offered well-defined
diiron clusters for the investigation of the mechanism of NO reduction
in these unique active sites. In this study, we use FTIR spectroscopy
to monitor the production of N2O in solution and to show
that the presence of a distal FeBII is not sufficient
to produce the expected product. However, the addition of a glutamate
side chain peripheral to the diiron site allows for 50% of a productive
single-turnover reaction. Unproductive reactions are characterized
by resonance Raman spectroscopy as dinitrosyl complexes, where one
NO molecule is bound to the heme iron to form a five-coordinate low-spin
{FeNO}7 species with ν(FeNO)heme and ν(NO)heme at 522 and 1660 cm–1, and a second NO
molecule is bound to the nonheme FeB site with a ν(NO)FeB at 1755 cm–1. Stopped-flow UV–vis
absorption coupled with rapid-freeze-quench resonance Raman spectroscopy
provide a detailed map of the reaction coordinates leading to the
unproductive iron-nitrosyl dimer. Unexpectedly, NO binding to FeB is kinetically favored and occurs prior to the binding of
a second NO to the heme iron, leading to a (six-coordinate low-spin
heme-nitrosyl/FeB-nitrosyl) transient dinitrosyl complex
with characteristic ν(FeNO)heme at 570 ± 2 cm–1 and ν(NO)FeB at 1755 cm–1. Without the addition of a peripheral glutamate, the dinitrosyl
complex is converted to a dead-end product after the dissociation
of the proximal histidine of the heme iron, but the added peripheral
glutamate side chain in FeBMb2 lowers the rate of dissociation
of the promixal histidine which in turn allows the (six-coordinate
low-spin heme-nitrosyl/FeB-nitrosyl) transient dinitrosyl
complex to decay with production of N2O at a rate of 0.7
s–1 at 4 °C. Taken together, our results support
the proposed trans mechanism of NO reduction in NORs.
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Affiliation(s)
- Hirotoshi Matsumura
- Divison of Environmental & Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
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5
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Kim J, Park J, Lee T, Lim M. Dynamics of Geminate Rebinding of NO with Cytochrome c in Aqueous Solution Using Femtosecond Vibrational Spectroscopy. J Phys Chem B 2012; 116:13663-71. [PMID: 23113639 DOI: 10.1021/jp308468j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jooyoung Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735,
Korea
| | - Jaeheung Park
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735,
Korea
| | - Taegon Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735,
Korea
| | - Manho Lim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735,
Korea
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Dalosto SD, Vanderkooi JM, Sharp KA. Vibrational Stark Effects on Carbonyl, Nitrile, and Nitrosyl Compounds Including Heme Ligands, CO, CN, and NO, Studied with Density Functional Theory. J Phys Chem B 2012; 108:6450-7. [PMID: 18950134 DOI: 10.1021/jp0310697] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Changes in the matrix electric field in a protein, due for example to mutations or structural fluctuations, can be correlated with changes in the vibrational transition frequencies of suitable chromophores measured by IR spectroscopy through the Stark tuning rate. To make this correlation, the Stark tuning rate must be known from experiment or theory. In this paper, density functional theory at the B3LYP/TZV level of theory is used to compute the Stark tuning rate of adducts of heme porphyrin, namely, -CO, -CN, and -NO+ compounds. The results are compared with the corresponding vibrational frequencies-field dependencies from vibrational Stark spectroscopy of heme-proteins. The zero-field computed Stark tuning rate of 1.3 cm-1/MV/cm for heme-CO is in agreement with experiment, where typically the rate is 2.4/f cm-1/MV/cm for myoglobin, where f is a local field correction between 1.1 and 1.4. Several small nitrile, carbonyl, and dinitrile molecules were studied to rationalize the findings for the heme-adducted models. Here, the higher B3LYP/6-311++G(2d,2p) level of theory could be used so the agreement with recent experimental results is even better than for heme-adducted groups.
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Affiliation(s)
- Sergio D Dalosto
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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7
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Franzen S, Brown D, Gaff J, Delley B. A Resonance Raman Enhancement Mechanism for Axial Vibrational Modes in the Pyridine Adduct of Myoglobin Proximal Cavity Mutant (H93G). J Phys Chem B 2012; 116:10514-21. [DOI: 10.1021/jp302049p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Derek Brown
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - John Gaff
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - B. Delley
- Paul-Scherrer-Institut,
WHGA/123, CH-5232 Villigen, Switzerland
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8
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Iordache PZ, Lungu RM, Safta I. Encapsulation of highly toxic organic compounds: Novelly functionalized nanoparticles for the safe storage of pollutants and their by-products. RSC Adv 2012. [DOI: 10.1039/c2ra20959d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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9
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Bellota-antón C, Munnoch J, Robb K, Adamczyk K, Candelaresi M, Parker A, Dixon R, Hutchings M, Hunt N, Tucker N. Spectroscopic analysis of protein Fe–NO complexes. Biochem Soc Trans 2011; 39:1293-8. [DOI: 10.1042/bst0391293] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The toxic free radical NO (nitric oxide) has diverse biological roles in eukaryotes and bacteria, being involved in signalling, vasodilation, blood clotting and immunity, and as an intermediate in microbial denitrification. The predominant biological mechanism of detecting NO is through the formation of iron nitrosyl complexes, although this is a deleterious process for other iron-containing enzymes. We have previously applied techniques such as UV–visible and EPR spectroscopy to the analysis of protein Fe–NO complex formation in order to study how NO controls the activity of the bacterial transcriptional regulators NorR and NsrR. These studies have analysed NO-dependent biological activity both in vitro and in vivo using diverse biochemical, molecular and spectroscopic methods. Recently, we have applied ultrafast 2D-IR (two-dimensional IR) spectroscopy to the analysis of NO–protein interactions using Mb (myoglobin) and Cc (cytochrome c) as model haem proteins. The ultrafast fluctuations of Cc and Mb show marked differences, indicating altered flexibility of the haem pockets. We have extended this analysis to bacterial catalase enzymes that are known to play a role in the nitrosative stress response by detoxifying peroxynitrite. The first 2D-IR analysis of haem nitrosylation and perspectives for the future are discussed.
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10
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Hayashi T, Miner KD, Yeung N, Lin YW, Lu Y, Moënne-Loccoz P. Spectroscopic characterization of mononitrosyl complexes in heme--nonheme diiron centers within the myoglobin scaffold (Fe(B)Mbs): relevance to denitrifying NO reductase. Biochemistry 2011; 50:5939-47. [PMID: 21634416 DOI: 10.1021/bi200409a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Denitrifying NO reductases are evolutionarily related to the superfamily of heme--copper terminal oxidases. These transmembrane protein complexes utilize a heme-nonheme diiron center to reduce two NO molecules to N(2)O. To understand this reaction, the diiron site has been modeled using sperm whale myoglobin as a scaffold and mutating distal residues Leu-29 and Phe-43 to histidines and Val-68 to a glutamic acid to create a nonheme Fe(B) site. The impact of incorporation of metal ions at this engineered site on the reaction of the ferrous heme with one NO was examined by UV-vis absorption, EPR, resonance Raman, and FTIR spectroscopies. UV--vis absorption and resonance Raman spectra demonstrate that the first NO molecule binds to the ferrous heme, but while the apoproteins and Cu(I)- or Zn(II)-loaded proteins show characteristic EPR signatures of S = 1/2 six-coordinate heme {FeNO}(7) species that can be observed at liquid nitrogen temperature, the Fe(II)-loaded proteins are EPR silent at ≥30 K. Vibrational modes from the heme [Fe-N-O] unit are identified in the RR and FTIR spectra using (15)NO and (15)N(18)O. The apo and Cu(I)-bound proteins exhibit ν(FeNO) and ν(NO) that are only marginally distinct from those reported for native myoglobin. However, binding of Fe(II) at the Fe(B) site shifts the heme ν(FeNO) by 17 cm(-1) and the ν(NO) by -50 cm(-1) to 1549 cm(-1). This low ν(NO) is without precedent for a six-coordinate heme {FeNO}(7) species and suggests that the NO group adopts a strong nitroxyl character stabilized by electrostatic interaction with the nearby nonheme Fe(II). Detection of a similarly low ν(NO) in the Zn(II)-loaded protein supports this interpretation.
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Affiliation(s)
- Takahiro Hayashi
- Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Beaverton, Oregon 97006, United States
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11
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Lanucara F, Chiavarino B, Crestoni ME, Scuderi D, Sinha RK, Maı̂tre P, Fornarini S. Naked Five-Coordinate FeIII(NO) Porphyrin Complexes: Vibrational and Reactivity Features. Inorg Chem 2011; 50:4445-52. [DOI: 10.1021/ic200073v] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Francesco Lanucara
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Debora Scuderi
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Rajeev K. Sinha
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Philippe Maı̂tre
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
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12
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Abstract
Nitric oxide (NO) is a signaling molecule employed to regulate essential physiological processes. Thus, there is great interest in understanding the interaction of NO with heme, which is found at the active site of many proteins that recognize NO, as well as those involved in its creation and elimination. We summarize what we have learned from investigations of the structure, vibrational properties, and conformational dynamics of NO complexes with ferrous porphyrins, as well as computational investigations in support of these experimental studies. Multitemperature crystallographic data reveal variations in the orientational disorder of the nitrosyl ligand. In some cases, equilibria among NO orientations can be analyzed using the van't Hoff relationship and the free energy and enthalpy of the solid-state transitions evaluated experimentally. Density functional theory (DFT) calculations predict that intrinsic barriers to torsional rotation are smaller than thermal energies at physiological temperatures, and the coincidence of observed NO orientations with minima in molecular mechanics potentials indicates that nonbonded interactions with other chemical groups control the conformational freedom of the bound NO. In favorable cases, reduced disorder at low temperatures exposes subtle structural features including off-axis tilting of the Fe-NO bond and anisotropy of the equatorial Fe-N bonds. We also present the results of nuclear resonance vibrational spectroscopy measurements on oriented single crystals of [Fe(TPP)(NO)] and [Fe(TPP)(1-MeIm)(NO)]. These describe the anisotropic vibrational motion of iron in five- and six-coordinate heme-NO complexes and reveal vibrations of all Fe-ligand bonds as well as low-frequency molecular distortions associated with the doming of the heme upon ligand binding. A quantitative comparison with predicted frequencies, amplitudes, and directions facilitates identification of the vibrational modes but also suggests that commonly used DFT functionals are not fully successful at capturing the trans interaction between the axial NO and imidazole ligands. This supports previous conclusions that heme-NO complexes exhibit an unusual degree of variability with respect to the computational method, and we speculate that this variability hints at a genuine electronic instability that a protein can exploit to tune its reactivity. We anticipate that ongoing characterization of heme-NO complexes will deepen our understanding of their structure, dynamics, and reactivity.
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Affiliation(s)
- W. Robert Scheidt
- To whom correspondence should be addressed: WRS: , Fax (574) 631-6652; JTS , FAX (617)-373-2943
| | | | | | | | - J. Timothy Sage
- To whom correspondence should be addressed: WRS: , Fax (574) 631-6652; JTS , FAX (617)-373-2943
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13
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Garofalo F, Pellegrino D, Amelio D, Tota B. The Antarctic hemoglobinless icefish, fifty five years later: a unique cardiocirculatory interplay of disaptation and phenotypic plasticity. Comp Biochem Physiol A Mol Integr Physiol 2009; 154:10-28. [PMID: 19401238 DOI: 10.1016/j.cbpa.2009.04.621] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 04/17/2009] [Accepted: 04/18/2009] [Indexed: 11/18/2022]
Abstract
The teleostean Channichthyidae (icefish), endemic stenotherms of the Antarctic waters, perennially at or near freezing, represent a unique example of disaptation among adult vertebrates for their loss of functional traits, particularly hemoglobin (Hb) and, in some species, cardiac myoglobin (Mb), once considered to be essential-life oxygen-binding chromoproteins. Conceivably, this stably frigid, oxygen-rich habitat has permitted high tolerance of disaptation, followed by subsequent adaptive recovery based on gene expression reprogramming and compensatory responses, including an alternative cardio-circulatory design, Hb-free blood and Mb-free cardiac muscle. This review revisits the functional significance of the multilevel cardio-circulatory compensations (hypervolemia, near-zero hematocrit and low blood viscosity, large bore capillaries, increased vascularity with great capacitance, cardiomegaly with very large cardiac output, high blood flow with low systemic pressure and systemic resistance) that counteract the challenge of hypoxemic hypoxia by increasing peripheral oxygen transcellular movement for aerobic tissues, including the myocardium. Reconsidered in the context of recent knowledge on both polar cold adaptation and the new questions related to the advent of nitric oxide (NO) biology, these compensations can be interpreted either according to the "loss-without-penalty" alternative, or in the context of an excessive environmental oxygen supply at low cellular cost and oxygen requirement in the cold. Therefore, rather than reflecting oxygen limitation, several traits may indicate structural overcompensation of oxygen supply reductions at cell/tissue levels. At the multilevel cardio-circulatory adjustments, NO is revealing itself as a major integrator, compensating disaptation with functional phenotypic plasticity, as illustrated by the heart paradigm. Beside NOS-dependent NO generation, recent knowledge concerning Hb/Mb interplay with NO and nitrite has revealed unexpected functions in addition to the classical respiratory role of these proteins. In fact, nitrite, a major biologic reservoir of NO, generates it through deohyHb- and deoxyMb-dependent nitrite reduction, thereby regulating hypoxic vasodilation, cellular respiration and signalling. We suggest that both Hb and Mb are involved as nitrite reductases under hypoxic conditions in a number of cardiocirculatory processes. On the whole, this opens new horizons in environmental and evolutionary physiology.
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Affiliation(s)
- F Garofalo
- Ponte Pietro Bucci cubo 6c, Department of Cellular Biology, University of Calabria, 87030, Arcavacata di Rende, CS, Italy.
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14
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Abstract
Heme proteins bind the gaseous ligands XO (X = C, N, O) via backbonding from Fe d(pi) electrons. Backbonding is modulated by distal interactions of the bound ligand with the surrounding protein and by variations in the strength of the trans proximal ligand. Vibrational modes associated with FeX and XO bond stretching coordinates report on these interactions, but the interpretive framework developed for CO adducts, involving anticorrelations of nuFeC and nuCO, has seemed not to apply to NO adducts. We have now obtained an excellent anticorrelation of nuFeN and nuNO, via resonance Raman spectroscopy on (N-methylimidazole)Fe(II)TPP-Y(NO), where TPP-Y is tetraphenylporphine with electron-donating or -withdrawing substituents, Y, that modulate the backbonding; the problem of laser-induced dissociation of the axial base was circumvented by using frozen solutions. New data are also reported for CO adducts. The anticorrelations are supported by DFT calculations of structures and spectra. When protein data are examined, the NO adducts show large deviations from the modeled anticorrelation when there are distal H-bonds or positive charges. These deviations are proposed to result from closing of the FeNO angle due to a shift in the valence isomer equilibrium toward the Fe(III)(NO-) form, an effect that is absent in CO adducts. The differing vibrational patterns of CO and NO adducts provide complementary information with respect to protein interactions, which may help to elucidate the mechanisms of ligand discrimination and signaling in heme sensor proteins.
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Affiliation(s)
- Mohammed Ibrahim
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Changliang Xu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Thomas G. Spiro
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544
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15
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Negrerie M, Kruglik SG, Lambry JC, Vos MH, Martin JL, Franzen S. Role of Heme Iron Coordination and Protein Structure in the Dynamics and Geminate Rebinding of Nitric Oxide to the H93G Myoglobin Mutant. J Biol Chem 2006; 281:10389-98. [PMID: 16476730 DOI: 10.1074/jbc.m513375200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The influence of the heme iron coordination on nitric oxide binding dynamics was investigated for the myoglobin mutant H93G (H93G-Mb) by picosecond absorption and resonance Raman time-resolved spectroscopies. In the H93G-Mb, the glycine replacing the proximal histidine does not interact with the heme iron so that exogenous substituents like imidazole may coordinate to the iron at the proximal position. Nitrosylation of H93G-Mb leads to either 6- or 5-coordinate species depending on the imidazole concentration. At high concentrations, (imidazole)-(NO)-6-coordinate heme is formed, and the photoinduced rebinding kinetics reveal two exponential picosecond phases ( approximately 10 and approximately 100 ps) similar to those of wild type myoglobin. At low concentrations, imidazole is displaced by the trans effect leading to a (NO)-5-coordinate heme, becoming 4-coordinate immediately after photolysis as revealed from the transient Raman spectrum. In this case, NO rebinding kinetics remain bi-exponential with no change in time constant of the fast component whose amplitude increases with respect to the 6-coordinate species. Bi-exponential NO geminate rebinding in 5-coordinate H93G-Mb is in contrast with the single-exponential process reported for nitrosylated soluble guanylate cyclase (Negrerie, M., Bouzhir, L., Martin, J. L., and Liebl, U. (2001) J. Biol. Chem. 276, 46815-46821). Thus, our data show that the iron coordination state or the heme iron out-of-plane motion are not at the origin of the bi-exponential kinetics, which depends upon the protein structure, and that the 4-coordinate state favors the fast phase of NO geminate rebinding. Consequently, the heme coordination state together with the energy barriers provided by the protein structure control the dynamics and affinity for NO-binding enzymes.
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Affiliation(s)
- Michel Negrerie
- INSERM U696, Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Palaiseau F91120, 91128 Palaiseau Cedex, France.
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16
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Abstract
Soluble guanylate cyclase (sGC) is a heterodimeric, nitric oxide (NO)-sensing hemoprotein composed of two subunits, alpha1 and beta1. NO binds to the heme cofactor in the beta1 subunit, forming a five-coordinate NO complex that activates the enzyme several hundred-fold. In this paper, the heme domain has been localized to the N-terminal 194 residues of the beta1 subunit. This fragment represents the smallest construct of the beta1 subunit that retains the ligand-binding characteristics of the native enzyme, namely, tight affinity for NO and no observable binding of O(2). A functional heme domain from the rat beta2 subunit has been localized to the first 217 amino acids beta2(1-217). These proteins are approximately 40% identical to the rat beta1 heme domain and form five-coordinate, low-spin NO complexes and six-coordinate, low-spin CO complexes. Similar to sGC, these constructs have a weak Fe-His stretch [208 and 207 cm(-)(1) for beta1(1-194) and beta2(1-217), respectively]. beta2(1-217) forms a CO complex that is very similar to sGC and has a high nu(CO) stretching frequency at 1994 cm(-)(1). The autoxidation rate of beta1(1-194) was 0.073/min, while the beta2(1-217) was substantially more stable in the ferrous form with an autoxidation rate of 0.003/min at 37 degrees C. This paper has identified and characterized the minimum functional ligand-binding heme domain derived from sGC, providing key details toward a comprehensive characterization.
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Affiliation(s)
- David S Karow
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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Zeng W, Silvernail NJ, Wharton DC, Georgiev GY, Leu BM, Scheidt WR, Zhao J, Sturhahn W, Alp EE, Sage JT. Direct probe of iron vibrations elucidates NO activation of heme proteins. J Am Chem Soc 2005; 127:11200-1. [PMID: 16089422 PMCID: PMC1502376 DOI: 10.1021/ja051052x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use nuclear resonance vibrational spectroscopy (NRVS) to identify the Fe-NO stretching frequency in the NO adduct of myoglobin (MbNO) and in the related six-coordinate porphyrin Fe(TPP)(1-MeIm)(NO). Frequency shifts observed in MbNO Raman spectra upon isotopic substitution of Fe or the nitrosyl nitrogen confirm and extend the NRVS results. In contrast with previous assignments, the Fe-NO frequency of these six-coordinate complexes lies 70-100 cm-1 lower than in the analogous five-coordinate nitrosyl complexes, indicating a significant weakening of the Fe-NO bond in the presence of a trans imidazole ligand. This result supports proposed mechanisms for NO activation of heme proteins and underscores the value of NRVS as a direct probe of metal reactivity in complex biomolecules.
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Affiliation(s)
- Weiqiao Zeng
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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18
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Abstract
Ligands such as CO, O(2), or NO are involved in the biological function of myoglobin. Here we investigate the energetics and dynamics of NO interacting with the Fe(II) heme group in native myoglobin using ab initio and molecular dynamics simulations. At the global minimum of the ab initio potential energy surface (PES), the binding energy of 23.4 kcal/mol and the Fe-NO structure compare well with the experimental results. Interestingly, the PES is found to exhibit two minima: There exists a metastable, linear Fe-O-N minimum in addition to the known, bent Fe-N-O global minimum conformation. Moreover, the T-shaped configuration is found to be a saddle point, in contrast to the corresponding minimum for NO interacting with Fe(III). To use the ab initio results for finite temperature molecular dynamics simulations, an analytical function was fitted to represent the Fe-NO interaction. The simulations show that the secondary minimum is dynamically stable up to 250 K and has a lifetime of several hundred picoseconds at 300 K. The difference in the topology of the heme-NO PES from that assumed previously (one deep, single Fe-NO minimum) suggests that it is important to use the full PES for a quantitative understanding of this system. Why the metastable state has not been observed in the many spectroscopic studies of myoglobin interacting with NO is discussed, and possible approaches to finding it are outlined.
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Affiliation(s)
- David R Nutt
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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Zhang W, Olson JS, Phillips GN. Biophysical and kinetic characterization of HemAT, an aerotaxis receptor from Bacillus subtilis. Biophys J 2005; 88:2801-14. [PMID: 15653746 PMCID: PMC1305375 DOI: 10.1529/biophysj.104.047936] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2004] [Accepted: 11/24/2004] [Indexed: 11/18/2022] Open
Abstract
HemAT from Bacillus subtilis is a new type of heme protein responsible for sensing oxygen. The structural and functional properties of the full-length HemAT protein, the sensor domain (1-178), and Tyr-70 mutants have been characterized. Kinetic and equilibrium measurements reveal that both full-length HemAT and the sensor domain show two distinct O(2) binding components. The high-affinity component has a K(dissociation) approximately 1-2 microM and a normal O(2) dissociation rate constant, k(O2) = 50-80 s(-1). The low-affinity component has a K(dissociation) approximately 50-100 microM and a large O(2) dissociation rate constant equal to approximately 2000 s(-1). The low n-value and biphasic character of the equilibrium curve indicate that O(2) binding to HemAT involves either independent binding to high- and low-affinity subunits in the dimer or negative cooperativity. Replacement of Tyr-70(B10) with Phe, Leu, or Trp in the sensor domain causes dramatic increases in k(O2) for both the high- and low-affinity components. In contrast, the rates and affinity for CO binding are little affected by loss of the Tyr-70 hydroxyl group. These results suggest highly dynamic behavior for the Tyr-70 side chain and the fraction of the "up" versus "down" conformation is strongly influenced by the nature of the iron-ligand complex. As a result of having both high- and low-affinity components, HemAT can respond to oxygen concentration gradients under both hypoxic (0-10 microM) and aerobic (50-250 microM) conditions, a property which could, in principle, be important for a robust sensing system. The unusual ligand-binding properties of HemAT suggest that asymmetry and apparent negative cooperativity play an important role in the signal transduction pathway.
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Affiliation(s)
- Wei Zhang
- Department of Biochemistry and Cell Biology, W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA
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Linder DP, Rodgers KR, Banister J, Wyllie GRA, Ellison MK, Scheidt WR. Five-coordinate Fe(III)NO and Fe(II)CO porphyrinates: where are the electrons and why does it matter? J Am Chem Soc 2004; 126:14136-48. [PMID: 15506779 PMCID: PMC1525220 DOI: 10.1021/ja046942b] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent years have seen dramatic growth in our understanding of the biological roles of nitric oxide (NO). Yet, the fundamental underpinnings of its reactivities with transition metal centers in proteins and enzymes, the stabilities of their structures, and the relationships between structure and reactivity remains, to a significant extent, elusive. This is especially true for the so-called ferric heme nitrosyls ([FeNO](6) in the Enemark-Feltham scheme). The Fe-CO and C-O bond strengths in the isoelectronic ferrous carbonyl complexes are widely recognized to be inversely correlated and sensitive to structural, environmental, and electronic factors. On the other hand, the Fe-NO and N-O bonds in [FeNO](6) heme complexes exhibit seemingly inconsistent behavior in response to varying structure and environment. This report contains resonance Raman and density functional theory results that suggest a new model for FeNO bonding in five-coordinate [FeNO](6) complexes. On the basis of resonance Raman and FTIR data, a direct correlation between the nu(Fe)(-)(NO) and nu(N)(-)(O) frequencies of [Fe(OEP)NO](ClO(4)) and [Fe(OEP)NO](ClO(4)).CHCl(3) (two crystal forms of the same complex) has been established. Density functional theory calculations show that the relationship between Fe-NO and N-O bond strengths is responsive to FeNO electron density in three molecular orbitals. The highest energy orbital of the three is sigma-antibonding with respect to the entire FeNO unit. The other two comprise a lower-energy, degenerate, or nearly degenerate pair that is pi-bonding with respect to Fe-NO and pi-antibonding with respect to N-O. The relative sensitivities of the electron density distributions in these orbitals are shown to be consistent with all published indicators of Fe-N-O bond strengths and angles, including the examples reported here.
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Kim S, Jin G, Lim M. Dynamics of Geminate Recombination of NO with Myoglobin in Aqueous Solution Probed by Femtosecond Mid-IR Spectroscopy. J Phys Chem B 2004. [DOI: 10.1021/jp0489020] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seongheun Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Geunyeong Jin
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Manho Lim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
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22
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Abstract
Nitric oxide (NO) is extremely toxic to Clostridium botulinum, but its molecular targets are unknown. Here, we identify a heme protein sensor (SONO) that displays femtomolar affinity for NO. The crystal structure of the SONO heme domain reveals a previously undescribed fold and a strategically placed tyrosine residue that modulates heme-nitrosyl coordination. Furthermore, the domain architecture of a SONO ortholog cloned from Chlamydomonas reinhardtii indicates that NO signaling through cyclic guanosine monophosphate arose before the origin of multicellular eukaryotes. Our findings have broad implications for understanding bacterial responses to NO, as well as for the activation of mammalian NO-sensitive guanylyl cyclase.
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Affiliation(s)
- Pierre Nioche
- Structural Biology Research Center and Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, TX 77030, USA
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Leu BM, Zgierski MZ, Wyllie GRA, Scheidt WRE, Sturhahn W, Alp EE, Durbin SM, Sage JT. Quantitative vibrational dynamics of iron in nitrosyl porphyrins. J Am Chem Soc 2004; 126:4211-27. [PMID: 15053610 PMCID: PMC1570756 DOI: 10.1021/ja038526h] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We use quantitative experimental and theoretical approaches to characterize the vibrational dynamics of the Fe atom in porphyrins designed to model heme protein active sites. Nuclear resonance vibrational spectroscopy (NRVS) yields frequencies, amplitudes, and directions for 57Fe vibrations in a series of ferrous nitrosyl porphyrins, which provide a benchmark for evaluation of quantum chemical vibrational calculations. Detailed normal mode predictions result from DFT calculations on ferrous nitrosyl tetraphenylporphyrin Fe(TPP)(NO), its cation [Fe(TPP)(NO)]+, and ferrous nitrosyl porphine Fe(P)(NO). Differing functionals lead to significant variability in the predicted Fe-NO bond length and frequency for Fe(TPP)(NO). Otherwise, quantitative comparison of calculated and measured Fe dynamics on an absolute scale reveals good overall agreement, suggesting that DFT calculations provide a reliable guide to the character of observed Fe vibrational modes. These include a series of modes involving Fe motion in the plane of the porphyrin, which are rarely identified using infrared and Raman spectroscopies. The NO binding geometry breaks the four-fold symmetry of the Fe environment, and the resulting frequency splittings of the in-plane modes predicted for Fe(TPP)(NO) agree with observations. In contrast to expectations of a simple three-body model, mode energy remains localized on the FeNO fragment for only two modes, an N-O stretch and a mode with mixed Fe-NO stretch and FeNO bend character. Bending of the FeNO unit also contributes to several of the in-plane modes, but no primary FeNO bending mode is identified for Fe(TPP)(NO). Vibrations associated with hindered rotation of the NO and heme doming are predicted at low frequencies, where Fe motion perpendicular to the heme is identified experimentally at 73 and 128 cm-1. Identification of the latter two modes is a crucial first step toward quantifying the reactive energetics of Fe porphyrins and heme proteins.
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Affiliation(s)
- Bogdan M. Leu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115
| | - Marek Z. Zgierski
- Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Graeme R. A. Wyllie
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - W. Rob ert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Wolfgang Sturhahn
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - E. Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | | | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115
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Ilangovan G, Pal R, Zweier JL, Kuppusamy P. Electrochemical Preparation and EPR Studies of Lithium Phthalocyanine. 4. Effect of Nitric Oxide. J Phys Chem B 2002. [DOI: 10.1021/jp026360l] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Govindasamy Ilangovan
- Biomedical EPR Imaging Center, Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University, 420 West 12th Avenue, Columbus, Ohio 43210
| | - Ranjeeta Pal
- Biomedical EPR Imaging Center, Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University, 420 West 12th Avenue, Columbus, Ohio 43210
| | - Jay L. Zweier
- Biomedical EPR Imaging Center, Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University, 420 West 12th Avenue, Columbus, Ohio 43210
| | - Periannan Kuppusamy
- Biomedical EPR Imaging Center, Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University, 420 West 12th Avenue, Columbus, Ohio 43210
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25
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Park ES, Boxer SG. Origins of the Sensitivity of Molecular Vibrations to Electric Fields: Carbonyl and Nitrosyl Stretches in Model Compounds and Proteins. J Phys Chem B 2002. [DOI: 10.1021/jp0203043] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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