1
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Auerbach H, Faus I, Rackwitz S, Wolny JA, Chumakov AI, Knipp M, Walker FA, Schünemann V. Heme protonation affects iron-NO binding in the NO transport protein nitrophorin. J Inorg Biochem 2023; 246:112281. [PMID: 37352657 DOI: 10.1016/j.jinorgbio.2023.112281] [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: 01/31/2023] [Revised: 04/26/2023] [Accepted: 05/30/2023] [Indexed: 06/25/2023]
Abstract
The nitrophorins (NPs) comprise an unusual group of heme proteins with stable ferric heme iron nitric oxide (Fe-NO) complexes. They are found in the salivary glands of the blood-sucking kissing bug Rhodnius prolixus, which uses the NPs to transport the highly reactive signaling molecule NO. Nuclear resonance vibrational spectroscopy (NRVS) of both isoform NP2 and a mutant NP2(Leu132Val) show, after addition of NO, a strong structured vibrational band at around 600 cm-1, which is due to modes with significant Fe-NO bending and stretching contribution. Based on a hybrid calculation method, which uses density functional theory and molecular mechanics, it is demonstrated that protonation of the heme carboxyl groups does influence both the vibrational properties of the Fe-NO entity and its electronic ground state. Moreover, heme protonation causes a significant increase of the gap between the highest occupied and lowest unoccupied molecular orbital by almost one order of magnitude leading to a stabilization of the Fe-NO bond.
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Affiliation(s)
- Hendrik Auerbach
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Isabelle Faus
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Sergej Rackwitz
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Juliusz A Wolny
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | | | - Markus Knipp
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany; Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - F Ann Walker
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721-0041, United States
| | - Volker Schünemann
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany.
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2
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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3
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Scheidt WR, Li J, Sage JT. What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes. Chem Rev 2017; 117:12532-12563. [PMID: 28921972 PMCID: PMC5639469 DOI: 10.1021/acs.chemrev.7b00295] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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Nuclear resonance
vibrational spectroscopy (NRVS; also known as
nuclear inelastic scattering, NIS) is a synchrotron-based method that
reveals the full spectrum of vibrational dynamics for Mössbauer
nuclei. Another major advantage, in addition to its completeness (no
arbitrary optical selection rules), is the unique selectivity of NRVS.
The basics of this recently developed technique are first introduced
with descriptions of the experimental requirements and data analysis
including the details of mode assignments. We discuss the use of NRVS
to probe 57Fe at the center of heme and heme protein derivatives
yielding the vibrational density of states for the iron. The application
to derivatives with diatomic ligands (O2, NO, CO, CN–) shows the strong capabilities of identifying mode
character. The availability of the complete vibrational spectrum of
iron allows the identification of modes not available by other techniques.
This permits the correlation of frequency with other physical properties.
A significant example is the correlation we find between the Fe–Im
stretch in six-coordinate Fe(XO) hemes and the trans Fe–N(Im)
bond distance, not possible previously. NRVS also provides uniquely
quantitative insight into the dynamics of the iron. For example, it
provides a model-independent means of characterizing the strength
of iron coordination. Prediction of the temperature-dependent mean-squared
displacement from NRVS measurements yields a vibrational “baseline”
for Fe dynamics that can be compared with results from techniques
that probe longer time scales to yield quantitative insights into
additional dynamical processes.
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Affiliation(s)
- W Robert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556 United States
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences , YanQi Lake, HuaiRou District, Beijing 101408, China
| | - J Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , 120 Forsyth Street, Boston, Massachusetts 02115, United States
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4
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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] [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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5
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Loullis A, Pinakoulaki E. Probing the nitrite and nitric oxide reductase activity of cbb3 oxidase: resonance Raman detection of a six-coordinate ferrous heme-nitrosyl species in the binuclear b3/CuB center. Chem Commun (Camb) 2015; 51:17398-401. [PMID: 26465875 DOI: 10.1039/c5cc06802a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this work we report the first spectroscopic evidence demonstrating that cbb3 oxidase catalyzes the reduction of nitrite to nitrous oxide under reducing anaerobic conditions. The reaction proceeds through the formation of a ferrous six-coordinate heme b3-nitrosyl species that has been characterized by resonance Raman spectroscopy.
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Affiliation(s)
- Andreas Loullis
- University of Cyprus, Department of Chemistry, PO Box 20537, 1678 Nicosia, Cyprus.
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6
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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] [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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7
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Hunt AP, Lehnert N. Heme-nitrosyls: electronic structure implications for function in biology. Acc Chem Res 2015; 48:2117-25. [PMID: 26114618 DOI: 10.1021/acs.accounts.5b00167] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The question of why mammalian systems use nitric oxide (NO), a potentially hazardous and toxic diatomic, as a signaling molecule to mediate important functions such as vasodilation (blood pressure control) and nerve signal transduction initially perplexed researchers when this discovery was made in the 1980s. Through extensive research over the past two decades, it is now well rationalized why NO is used in vivo for these signaling functions, and that heme proteins play a dominant role in NO signaling in mammals. Key insight into the properties of heme-nitrosyl complexes that make heme proteins so well poised to take full advantage of the unique properties of NO has come from in-depth structural, spectroscopic, and theoretical studies on ferrous and ferric heme-nitrosyls. This Account highlights recent findings that have led to greater understanding of the electronic structures of heme-nitrosyls, and the contributions that model complex studies have made to elucidate Fe-NO bonding are highlighted. These results are then discussed in the context of the biological functions of heme-nitrosyls, in particular in soluble guanylate cyclase (sGC; NO signaling), nitrophorins (NO transport), and NO-producing enzymes. Central to this Account is the thermodynamic σ-trans effect of NO, and how this relates to the activation of the universal mammalian NO sensor sGC, which uses a ferrous heme as the high affinity "NO detection unit". It is shown via detailed spectroscopic and computational studies that the strong and very covalent Fe(II)-NO σ-bond is at the heart of the strong thermodynamic σ-trans effect of NO, which greatly weakens the proximal Fe-NHis (or Fe-SCys) bond in six-coordinate ferrous heme-nitrosyls. In sGC, this causes the dissociation of the proximally bound histidine ligand upon NO binding to the ferrous heme, inducing a significant conformational change that activates the sGC catalytic domain for the production of cGMP. This, in turn, leads to vasodilation and nerve signal transduction. Studies on ferrous heme-nitrosyl model complexes have allowed for a quantification of this thermodynamic σ-trans effect of NO, through the use of high-resolution crystal structures, binding constant studies, single-crystal vibrational spectroscopy and density functional theory (DFT) calculations. These studies have further identified the singly occupied molecular orbital (SOMO) of the NO complexes as the key MO that mediates the thermodynamic σ-trans effect of NO. In comparison to ferrous heme-nitrosyls, ferric heme-nitrosyls display thermodynamically much weaker Fe-NO bonds (from NO binding constants), but at the same time much stronger Fe-NO bonds in their ground states (from vibrational spectroscopy). Using spectroscopic investigations coupled to DFT calculations, this apparent contradiction has been rationalized with the involvement of at least three different electronic states in the binding/dissociation of NO to/from ferric hemes. This is of key significance for the release of NO from NO-producing enzymes like NOS, and further forms the basis for ferric hemes to serve as NO transporters in biological systems.
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Affiliation(s)
- Andrew P. Hunt
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicolai Lehnert
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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8
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Smith AT, Pazicni S, Marvin KA, Stevens DJ, Paulsen KM, Burstyn JN. Functional divergence of heme-thiolate proteins: a classification based on spectroscopic attributes. Chem Rev 2015; 115:2532-58. [PMID: 25763468 DOI: 10.1021/cr500056m] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aaron T Smith
- †Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208, United States
| | - Samuel Pazicni
- ‡Department of Chemistry, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Katherine A Marvin
- §Department of Chemistry, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032, United States
| | - Daniel J Stevens
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Katherine M Paulsen
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Judith N Burstyn
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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9
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Hough MA, Andrew CR. Cytochromes c': Structure, Reactivity and Relevance to Haem-Based Gas Sensing. Adv Microb Physiol 2015; 67:1-84. [PMID: 26616515 DOI: 10.1016/bs.ampbs.2015.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cytochromes c' are a group of class IIa cytochromes with pentacoordinate haem centres and are found in photosynthetic, denitrifying and methanotrophic bacteria. Their function remains unclear, although roles in nitric oxide (NO) trafficking during denitrification or in cellular defence against nitrosoative stress have been proposed. Cytochromes c' are typically dimeric with each c-type haem-containing monomer folding as a four-α-helix bundle. Their hydrophobic and crowded distal sites impose severe restrictions on the binding of distal ligands, including diatomic gases. By contrast, NO binds to the proximal haem face in a similar manner to that of the eukaryotic NO sensor, soluble guanylate cyclase and bacterial analogues. In this review, we focus on how structural features of cytochromes c' influence haem spectroscopy and reactivity with NO, CO and O2. We also discuss the relevance of cytochrome c' to understanding the mechanisms of gas binding to haem-based sensor proteins.
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10
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Li J, Peng Q, Oliver A, Alp EE, Hu MY, Zhao J, Sage JT, Scheidt WR. Comprehensive Fe-ligand vibration identification in {FeNO}6 hemes. J Am Chem Soc 2014; 136:18100-10. [PMID: 25490350 PMCID: PMC4295236 DOI: 10.1021/ja5105766] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Indexed: 01/06/2023]
Abstract
Oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS) has been used to obtain all iron vibrations in two {FeNO}(6) porphyrinate complexes, five-coordinate [Fe(OEP)(NO)]ClO4 and six-coordinate [Fe(OEP)(2-MeHIm)(NO)]ClO4. A new crystal structure was required for measurements of [Fe(OEP)(2-MeHIm)(NO)]ClO4, and the new structure is reported herein. Single crystals of both complexes were oriented to be either parallel or perpendicular to the porphyrin plane and/or axial imidazole ligand plane. Thus, the FeNO bending and stretching modes can now be unambiguously assigned; the pattern of shifts in frequency as a function of coordination number can also be determined. The pattern is quite distinct from those found for CO or {FeNO}(7) heme species. This is the result of unchanging Fe-N(NO) bonding interactions in the {FeNO}(6) species, in distinct contrast to the other diatomic ligand species. DFT calculations were also used to obtain detailed predictions of vibrational modes. Predictions were consistent with the intensity and character found in the experimental spectra. The NRVS data allow the assignment and observation of the challenging to obtain Fe-Im stretch in six-coordinate heme derivatives. NRVS data for this and related six-coordinate hemes with the diatomic ligands CO, NO, and O2 reveal a strong correlation between the Fe-Im stretch and Fe-N(Im) bond distance that is detailed for the first time.
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Affiliation(s)
- Jianfeng Li
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, YanQi Lake, HuaiRou District, Beijing 101408, China
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Qian Peng
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Allen
G. Oliver
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - E. Ercan Alp
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, 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
| | - J. Timothy Sage
- Department
of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 120 Forsyth Street, Boston, Massachusetts 02115, United States
| | - W. Robert Scheidt
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
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11
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Linder D, Silvernail NJ, Barabanschikov A, Zhao J, Alp EE, Sturhahn W, Sage JT, Scheidt WR, Rodgers KR. The diagnostic vibrational signature of pentacoordination in heme carbonyls. J Am Chem Soc 2014; 136:9818-21. [PMID: 24950373 PMCID: PMC4120987 DOI: 10.1021/ja503191z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Indexed: 11/28/2022]
Abstract
Heme-carbonyl complexes are widely exploited for the insight they provide into the structural basis of function in heme-based proteins, by revealing the nature of their bonded and nonbonded interactions with the protein. This report presents two novel results which clearly establish a FeCO vibrational signature for crystallographically verified pentacoordination. First, anisotropy in the NRVS density of states for ν(Fe-C) and δ(FeCO) in oriented single crystals of [Fe(OEP)(CO)] clearly reveals that the Fe-C stretch occurs at higher frequency than the FeCO bend and considerably higher than any previously reported heme carbonyl. Second, DFT calculations on a series of heme carbonyls reveal that the frequency crossover occurs near the weak trans O atom donor, furan. As ν(Fe-C) occurs at lower frequencies than δ(FeCO) in all heme protein carbonyls reported to date, the results reported herein suggest that they are all hexacoordinate.
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Affiliation(s)
- Douglas
P. Linder
- Department
of Chemistry and Biochemistry, North Dakota
State University, Fargo, North Dakota 58105, United States
| | - Nathan J. Silvernail
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, 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
| | - Wolfgang Sturhahn
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - J. Timothy Sage
- Department
of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - W. Robert Scheidt
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kenton R. Rodgers
- Department
of Chemistry and Biochemistry, North Dakota
State University, Fargo, North Dakota 58105, United States
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12
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Park K, Solomon EI. Modeling nuclear resonance vibrational spectroscopic data of binuclear non-heme iron enzymes using density functional theory. CAN J CHEM 2014; 92:975-978. [PMID: 28943644 DOI: 10.1139/cjc-2014-0067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nuclear resonance vibrational spectroscopy (NRVS) is a powerful technique that can provide geometric structural information on key reaction intermediates of Fe-containing systems when utilized in combination with density functional theory (DFT). However, in the case of binuclear non-heme iron enzymes, DFT-predicted NRVS spectra have been found to be sensitive to truncation method used to model the active sites of the enzymes. Therefore, in this study various-level truncation schemes have been tested to predict the NRVS spectrum of a binuclear non-heme iron enzyme, and a reasonably sized DFT model that is suitable for employing the NRVS/DFT combined methodology to characterize binuclear non-heme iron enzymes has been developed.
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Affiliation(s)
- Kiyoung Park
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305, USA
| | - Edward I Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305, USA
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13
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Pavlik J, Peng Q, Silvernail N, Alp EE, Hu MY, Zhao J, Sage JT, Scheidt WR. Anisotropic iron motion in nitrosyl iron porphyrinates: natural and synthetic hemes. Inorg Chem 2014; 53:2582-90. [PMID: 24528178 PMCID: PMC3993889 DOI: 10.1021/ic4028964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Indexed: 02/05/2023]
Abstract
The vibrational spectra of two five-coordinate nitrosyl iron porphyrinates, [Fe(OEP)(NO)] (OEP = dianion of 2,3,7,8,12,13,17,18-octaethylporphyrin) and [Fe(DPIX)(NO)] (DPIX = deuteroporphyrin IX), have been studied by oriented single-crystal nuclear resonance vibrational spectroscopy. Single crystals (both are in the triclinic crystal system) were oriented to give vibrational spectra perpendicular to the porphyrin plane. Additionally, two orthogonal in-plane measurements that were also either perpendicular or parallel to the projection of the FeNO plane onto the porphyrin plane yield the complete set of vibrations with iron motion. In addition to cleanly enabling the assignment of the FeNO bending and stretching modes, the measurements reveal that the two in-plane spectra from the parallel and perpendicular in-plane directions for both compounds have substantial differences. The assignment of these in-plane vibrations were aided by density functional theory predictions. The differences in the two in-plane directions result from the strongly bonded axial NO ligand. The direction of the in-plane iron motion is thus found to be largely parallel and perpendicular to the projection of the FeNO plane on the porphyrin plane. These axial ligand effects on the in-plane iron motion are related to the strength of the axial ligand-to-iron bond.
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Affiliation(s)
- Jeffrey
W. Pavlik
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Qian Peng
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nathan
J. Silvernail
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - E. Ercan Alp
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, 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
| | - J. Timothy Sage
- Department
of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 120 Forsyth Street, Boston, Massachusetts 02115, United States
| | - W. Robert Scheidt
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
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14
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Lehnert N, Scheidt WR, Wolf MW. Structure and Bonding in Heme–Nitrosyl Complexes and Implications for Biology. NITROSYL COMPLEXES IN INORGANIC CHEMISTRY, BIOCHEMISTRY AND MEDICINE II 2013. [DOI: 10.1007/430_2013_92] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Ohta T, Liu JG, Saito M, Kobayashi Y, Yoda Y, Seto M, Naruta Y. Axial Ligand Effects on Vibrational Dynamics of Iron in Heme Carbonyl Studied by Nuclear Resonance Vibrational Spectroscopy. J Phys Chem B 2012; 116:13831-8. [DOI: 10.1021/jp304398g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takehiro Ohta
- Institute
for Materials Chemistry
and Engineering and International Institute for Carbon-Neutral Energy
Research (WPI-I2CNER), Kyushu University, Fukuoka 812-8581, Japan
- JST, ACT-C, Saitama 332-0012,
Japan
| | - Jin-Gang Liu
- Institute
for Materials Chemistry
and Engineering and International Institute for Carbon-Neutral Energy
Research (WPI-I2CNER), Kyushu University, Fukuoka 812-8581, Japan
- Department of Chemistry, East China University of Science and Technology, 130
Meilong Rd, 200237, Shanghai, P. R. China
| | - Makina Saito
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
| | - Yasuhiro Kobayashi
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Makoto Seto
- Research Reactor Institute, Kyoto University, Osaka 590-0494, Japan
- Japan Atomic Energy Agency, Hyogo 679-5148, Japan
- CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Yoshinori Naruta
- Institute
for Materials Chemistry
and Engineering and International Institute for Carbon-Neutral Energy
Research (WPI-I2CNER), Kyushu University, Fukuoka 812-8581, Japan
- JST, ACT-C, Saitama 332-0012,
Japan
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16
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Guo Y, Brecht E, Aznavour K, Nix JC, Xiao Y, Wang H, George SJ, Bau R, Keable S, Peters JW, Adams MWW, Jenney F, Sturhahn W, Alp EE, Zhao J, Yoda Y, Cramer SP. Nuclear resonance vibrational spectroscopy (NRVS) of rubredoxin and MoFe protein crystals. ACTA ACUST UNITED AC 2012; 222:77-90. [PMID: 26052177 DOI: 10.1007/s10751-012-0643-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have applied 57Fe nuclear resonance vibrational spectroscopy (NRVS) for the first time to study the dynamics of Fe centers in Fe-S protein crystals, including oxidized wild type rubredoxin crystals from Pyrococcus furiosus, and the MoFe protein of nitrogenase from Azotobacter vinelandii. Thanks to the NRVS selection rule, selectively probed vibrational modes have been observed in both oriented rubredoxin and MoFe protein crystals. The NRVS work was complemented by extended X-ray absorption fine structure spectroscopy (EXAFS) measurements on oxidized wild type rubredoxin crystals from Pyrococcus furiosus. The EXAFS spectra revealed the Fe-S bond length difference in oxidized Pf Rd protein, which is qualitatively consistent with the X-ray crystal structure.
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Affiliation(s)
- Yisong Guo
- Department of Applied Science, University of California, Davis, CA 95616
| | - Eric Brecht
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Kristen Aznavour
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033
| | - Jay C Nix
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Yuming Xiao
- Department of Applied Science, University of California, Davis, CA 95616
| | - Hongxin Wang
- Department of Applied Science, University of California, Davis, CA 95616 ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Simon J George
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert Bau
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033
| | - Stephen Keable
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | | | - Francis Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA 30024
| | - Wolfgang Sturhahn
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Ercan E Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Yoshitaka Yoda
- JASRI, SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Stephen P Cramer
- Department of Applied Science, University of California, Davis, CA 95616 ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 ; Department of Chemistry, University of California, Davis, CA 95616
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17
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Spiro TG, Soldatova AV. Ambidentate H-bonding of NO and O2 in heme proteins. J Inorg Biochem 2012; 115:204-10. [PMID: 22824153 DOI: 10.1016/j.jinorgbio.2012.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 05/08/2012] [Accepted: 05/10/2012] [Indexed: 01/26/2023]
Abstract
The affinity and reactivity of the gaseous molecules CO, NO and O(2) (XO) in heme protein adducts are controlled by secondary interactions, especially by H-bonds donated from distal protein residues. Vibrational spectroscopy, supported by DFT (Density Functional Theory) modeling, has revealed that for NO and O(2), but not for CO, a critical issue is whether the H-bond is donated to the outer or inner atom of the bound diatomic ligand. DFT modeling shows that bound NO and O(2) are ambidentate, both atoms separately acting as H-bond acceptors. This is not the case for CO, whose π* orbital acts as a delocalized H-bond acceptor. Vibrational spectra of heme-XO adducts reveal a general pattern of backbonding variations, marked by families of negative correlations between frequencies associated with FeX and XO bond stretches. For heme-CO adducts, H-bonding increases backbonding, the νFeX/νXO points moving up the backbonding correlation established with model compounds. For NO and O(2) adducts, however, increased backbonding is only observed when the outer atom is the H-bond acceptor. H-bonding to the inner (X) atom instead produces a positive νFeX/νXO correlation. This effect can be reproduced by DFT modeling. Its mechanism is polarization of the sp(2) orbital on the X atom, on the back side of the bent FeXO unit, drawing electrons from both the FeX and XO bonds and weakening them together. Thus, the positioning of H-bond donors in the protein differentially affects bonding and reactivity in heme adducts of NO and O(2).
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Affiliation(s)
- Thomas G Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195, USA.
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18
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Moeser B, Janoschka A, Wolny JA, Paulsen H, Filippov I, Berry RE, Zhang H, Chumakov AI, Walker FA, Schünemann V. Nuclear inelastic scattering and Mössbauer spectroscopy as local probes for ligand binding modes and electronic properties in proteins: vibrational behavior of a ferriheme center inside a β-barrel protein. J Am Chem Soc 2012; 134:4216-28. [PMID: 22295945 DOI: 10.1021/ja210067t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this work, we present a study of the influence of the protein matrix on its ability to tune the binding of small ligands such as NO, cyanide (CN(-)), and histamine to the ferric heme iron center in the NO-storage and -transport protein Nitrophorin 2 (NP2) from the salivary glands of the blood-sucking insect Rhodnius prolixus. Conventional Mössbauer spectroscopy shows a diamagnetic ground state of the NP2-NO complex and Type I and II electronic ground states of the NP2-CN(-) and NP2-histamine complex, respectively. The change in the vibrational signature of the protein upon ligand binding has been monitored by Nuclear Inelastic Scattering (NIS), also called Nuclear Resonant Vibrational Spectroscopy (NRVS). The NIS data thus obtained have also been calculated by quantum mechanical (QM) density functional theory (DFT) coupled with molecular mechanics (MM) methods. The calculations presented here show that the heme ruffling in NP2 is a consequence of the interaction with the protein matrix. Structure optimizations of the heme and its ligands with DFT retain the characteristic saddling and ruffling only if the protein matrix is taken into account. Furthermore, simulations of the NIS data by QM/MM calculations suggest that the pH dependence of the binding of NO, but not of CN(-) and histamine, might be a consequence of the protonation state of the heme carboxyls.
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Affiliation(s)
- Beate Moeser
- Technische Universität Kaiserslautern, Fachbereich Physik, Erwin-Schrödinger-Str. 56, D-67663 Kaiserslautern, Germany
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19
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Paulsen H, Trautwein AX, Wegner P, Schmidt C, Chumakov AI, Schünemann V. Interpretation of Nuclear Resonant Vibrational Spectra of Rubredoxin Using a Combined Quantum Mechanics and Molecular Mechanics Approach. Chemphyschem 2011; 12:3434-41. [DOI: 10.1002/cphc.201100595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Indexed: 11/06/2022]
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20
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Li J, Peng Q, Barabanschikov A, Pavlik JW, Alp EE, Sturhahn W, Zhao J, Schulz CE, Sage JT, Scheidt WR. New perspectives on iron-ligand vibrations of oxyheme complexes. Chemistry 2011; 17:11178-85. [PMID: 21922552 PMCID: PMC3234299 DOI: 10.1002/chem.201101352] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Indexed: 11/12/2022]
Abstract
We report our studies of the vibrational dynamics of iron for three imidazole-ligated oxyheme derivatives that mimic the active sites of histidine-ligated heme proteins complexed with dioxygen. The experimental vibrational data are obtained from nuclear resonance vibrational spectroscopy (NRVS) measurements conducted on both powder samples and oriented single crystals, and which includes several in-plane (ip) and out-of-plane (oop) measurements. Vibrational spectral assignments have been made through a combination of the oriented sample spectra and predictions based on density functional theory (DFT) calculations. The two Fe-O(2) modes that have been previously observed by resonance Raman spectroscopy in heme proteins are clearly shown to be very strongly mixed and are not simply either a bending or stretching mode. In addition, a third Fe-O(2) mode, not previously reported, has been identified. The long-sought Fe-Im stretch, not observed in resonance Raman spectra, has been identified and compared with the frequencies observed for the analogous CO and NO species. The studies also suggest that the in-plane iron motion is anisotropic and is controlled by the orientation of the Fe-O(2) group and not sensitive to the in-plane Fe-N(p) bonds and/or imidazole orientations.
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Affiliation(s)
- Jianfeng Li
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA), Fax (574) 631-6652
| | - Qian Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA), Fax (574) 631-6652
| | - Alexander Barabanschikov
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115 (USA)
| | - Jeffrey W. Pavlik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA), Fax (574) 631-6652
| | - E. Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (USA)
| | - Wolfgang Sturhahn
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (USA)
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (USA)
| | - Charles E. Schulz
- Department of Physics, Knox College, Galesburg, Illinois 61401 (USA)
| | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115 (USA)
| | - W. Robert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA), Fax (574) 631-6652
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21
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Barabanschikov A, Demidov A, Kubo M, Champion PM, Sage JT, Zhao J, Sturhahn W, Alp EE. Spectroscopic identification of reactive porphyrin motions. J Chem Phys 2011; 135:015101. [PMID: 21744919 PMCID: PMC3144962 DOI: 10.1063/1.3598473] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Accepted: 05/18/2011] [Indexed: 11/14/2022] Open
Abstract
Nuclear resonance vibrational spectroscopy (NRVS) reveals the vibrational dynamics of a Mössbauer probe nucleus. Here, (57)Fe NRVS measurements yield the complete spectrum of Fe vibrations in halide complexes of iron porphyrins. Iron porphine serves as a useful symmetric model for the more complex spectrum of asymmetric heme molecules that contribute to numerous essential biological processes. Quantitative comparison with the vibrational density of states (VDOS) predicted for the Fe atom by density functional theory calculations unambiguously identifies the correct sextet ground state in each case. These experimentally authenticated calculations then provide detailed normal mode descriptions for each observed vibration. All Fe-ligand vibrations are clearly identified despite the high symmetry of the Fe environment. Low frequency molecular distortions and acoustic lattice modes also contribute to the experimental signal. Correlation matrices compare vibrations between different molecules and yield a detailed picture of how heme vibrations evolve in response to (a) halide binding and (b) asymmetric placement of porphyrin side chains. The side chains strongly influence the energetics of heme doming motions that control Fe reactivity, which are easily observed in the experimental signal.
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Affiliation(s)
- Alexander Barabanschikov
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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22
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NMR studies of nitrophorin distal pocket side chain effects on the heme orientation and seating of NP2 as compared to NP1. J Inorg Biochem 2011; 105:1238-57. [PMID: 21767470 DOI: 10.1016/j.jinorgbio.2011.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 06/03/2011] [Accepted: 06/08/2011] [Indexed: 11/23/2022]
Abstract
The nitrophorins (NP) of the adult blood-sucking insect Rhodnius prolixus fall into two pairs based on sequence identity (NP1,4 (90%) and NP2,3 (79%)), which differ significantly in the size of side chains of residues which contact the heme. These residues include those in the distal pocket of NP2 (I120) and NP1 (T121) and the "belt" that surrounds the heme of NP2 (S40, F42), and NP1(A42, L44). To determine the importance of these residues and others conserved or very similar for the two pairs, including L122(123), L132(133), appropriate mutants of NP2 and NP1 have been prepared and studied by (1)H NMR spectroscopy. Wild-type NP2 has heme orientation ratio (A:B) of 1:8 at equilibrium, while wild-type NP1 has A:B ~1:1 at equilibrium. Another difference between NP2 and NP1 is in the heme seating with regard to His57(59). It is found that among the distal pocket residues investigated, the residue most responsible for heme orientation and seating is I120(T121). F42(L44) and L106(F107) may also be important, but must be investigated in greater detail.
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23
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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] [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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24
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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] [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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25
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van Thor JJ. Photoconversion of the Green Fluorescent Protein and Related Proteins. SPRINGER SERIES ON FLUORESCENCE 2011. [DOI: 10.1007/4243_2011_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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26
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Pavlik JW, Barabanschikov A, Oliver AG, Alp EE, Sturhahn W, Zhao J, Sage JT, Scheidt WR. Probing vibrational anisotropy with nuclear resonance vibrational spectroscopy. Angew Chem Int Ed Engl 2010; 49:4400-4. [PMID: 20422668 DOI: 10.1002/anie.201000928] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeffrey W Pavlik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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27
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Lehnert N, Sage JT, Silvernail N, Scheidt WR, Alp EE, Sturhahn W, Zhao J. Oriented single-crystal nuclear resonance vibrational spectroscopy of [Fe(TPP)(MI)(NO)]: quantitative assessment of the trans effect of NO. Inorg Chem 2010; 49:7197-215. [PMID: 20586416 PMCID: PMC2917100 DOI: 10.1021/ic1010677] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper presents oriented single-crystal Nuclear Resonance Vibrational Spectroscopy (NRVS) data for the six-coordinate (6C) ferrous heme-nitrosyl model complex [(57)Fe(TPP)(MI)(NO)] (1; TPP(2-) = tetraphenylporphyrin dianion; MI = 1-methylimidazole). The availability of these data enables for the first time the detailed simulation of the complete NRVS data, including the porphyrin-based vibrations, of a 6C ferrous heme-nitrosyl, using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Importantly, the Fe-NO stretch is split by interaction with a porphyrin-based vibration into two features, observed at 437 and 472 cm(-1). The 437 cm(-1) feature is strongly out-of-plane (oop) polarized and shows a (15)N(18)O isotope shift of 8 cm(-1) and is therefore assigned to nu(Fe-NO). The admixture of Fe-N-O bending character is small. Main contributions to the Fe-N-O bend are observed in the 520-580 cm(-1) region, distributed over a number of in-plane (ip) polarized porphyrin-based vibrations. The main component, assigned to delta(ip)(Fe-N-O), is identified with the feature at 563 cm(-1). The Fe-N-O bend also shows strong mixing with the Fe-NO stretching internal coordinate, as evidenced by the oop NRVS intensity in the 520-580 cm(-1) region. Very accurate normal mode descriptions of nu(Fe-NO) and delta(ip)(Fe-N-O) have been obtained in this study. These results contradict previous interpretations of the vibrational spectra of 6C ferrous heme-nitrosyls where the higher energy feature at approximately 550 cm(-1) had usually been associated with nu(Fe-NO). Furthermore, these results provide key insight into NO binding to ferrous heme active sites in globins and other heme proteins, in particular with respect to (a) the effect of hydrogen bonding to the coordinated NO and (b) changes in heme dynamics upon NO coordination. [Fe(TPP)(MI)(NO)] constitutes an excellent model system for ferrous NO adducts of myoglobin (Mb) mutants where the distal histidine (His64) has been removed. Comparison to the reported vibrational data for wild-type (wt) Mb-NO then shows that the effect of H bonding to the coordinated NO is weak and mostly leads to a polarization of the pi/pi* orbitals of bound NO. In addition, the observation that delta(ip)(Fe-N-O) does not correlate well with nu(N-O) can be traced back to the very mixed nature of this mode. The Fe-N(imidazole) stretching frequency is observed at 149 cm(-1) in [Fe(TPP)(MI)(NO)], and spectral changes upon NO binding to five-coordinate ferrous heme active sites are discussed. The obtained high-quality force constants for the Fe-NO and N-O bonds of 2.57 and 11.55 mdyn/A can further be compared to those of corresponding 5C species, which allows for a quantitative analysis of the sigma trans interaction between the proximal imidazole (His) ligand and NO. This is key for the activation of the NO sensor soluble guanylate cyclase. Finally, DFT methods are calibrated against the experimentally determined vibrational properties of the Fe-N-O subunit in 1. DFT is in fact incapable of reproducing the vibrational energies and normal mode descriptions of the Fe-N-O unit well, and thus, DFT-based predictions of changes in vibrational properties upon heme modification or other perturbations of these 6C complexes have to be treated with caution.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115, USA
| | - Nathan Silvernail
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - W. Robert Scheidt
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - E. Ercan Alp
- Argonne National Laboratory, APS/XFD, 431/D003, Argonne, IL 60439, USA
| | - Wolfgang Sturhahn
- Argonne National Laboratory, APS/XFD, 431/D003, Argonne, IL 60439, USA
| | - Jiyong Zhao
- Argonne National Laboratory, APS/XFD, 431/D003, Argonne, IL 60439, USA
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28
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Scheidt WR, Barabanschikov A, Pavlik JW, Silvernail NJ, Sage JT. Electronic structure and dynamics of nitrosyl porphyrins. Inorg Chem 2010; 49:6240-52. [PMID: 20666384 PMCID: PMC2919577 DOI: 10.1021/ic100261b] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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Lehnert N, Galinato MGI, Paulat F, Richter-Addo GB, Sturhahn W, Xu N, Zhao J. Nuclear resonance vibrational spectroscopy applied to [Fe(OEP)(NO)]: the vibrational assignments of five-coordinate ferrous heme-nitrosyls and implications for electronic structure. Inorg Chem 2010; 49:4133-48. [PMID: 20345089 DOI: 10.1021/ic902181e] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This study presents Nuclear Resonance Vibrational Spectroscopy (NRVS) data on the five-coordinate (5C) ferrous heme-nitrosyl complex [Fe(OEP)(NO)] (1, OEP(2-) = octaethylporphyrinato dianion) and the corresponding (15)N(18)O labeled complex. The obtained spectra identify two isotope sensitive features at 522 and 388 cm(-1), which shift to 508 and 381 cm(-1), respectively, upon isotope labeling. These features are assigned to the Fe-NO stretch nu(Fe-NO) and the in-plane Fe-N-O bending mode delta(ip)(Fe-N-O), the latter has been unambiguously assigned for the first time for 1. The obtained NRVS data were simulated using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Since complex 1 can potentially exist in 12 different conformations involving the FeNO and peripheral ethyl orientations, extended density functional theory (DFT) calculations and QCC-NCA simulations were performed to determine how these conformations affect the NRVS properties of [Fe(OEP)NO]. These results show that the properties and force constants of the FeNO unit are hardly affected by the conformational changes involving the ethyl substituents. On the other hand, the NRVS-active porphyrin-based vibrations around 340-360, 300-320, and 250-270 cm(-1) are sensitive to the conformational changes. The spectroscopic changes observed in these regions are due to selective mechanical couplings of one component of E(u)-type (in ideal D(4h) symmetry) porphyrin-based vibrations with the in-plane Fe-N-O bending mode. This leads to the observed variations in Fe(OEP) core mode energies and NRVS intensities without affecting the properties of the FeNO unit. The QCC-NCA simulated NRVS spectra of 1 show excellent agreement with experiment, and indicate that conformer F is likely present in the samples of this complex investigated here. The observed porphyrin-based vibrations in the NRVS spectra of 1 are also assigned based on the QCC-NCA results. The obtained force constants of the Fe-NO and N-O bonds are 2.83-2.94 (based on the DFT functional applied) and about 12.15 mdyn/A, respectively. The electronic structures of 5C ferrous heme-nitrosyls in different model complexes are then analyzed, and variations in their properties based on different porphyrin substituents are explained. Finally, the shortcomings of different DFT functionals in describing the axial FeNO subunit in heme-nitrosyls are elucidated.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
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30
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Goodrich LE, Paulat F, Praneeth VKK, Lehnert N. Electronic Structure of Heme-Nitrosyls and Its Significance for Nitric Oxide Reactivity, Sensing, Transport, and Toxicity in Biological Systems. Inorg Chem 2010; 49:6293-316. [DOI: 10.1021/ic902304a] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Lauren E. Goodrich
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Florian Paulat
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - V. K. K. Praneeth
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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31
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Pavlik J, Barabanschikov A, Oliver A, Alp E, Sturhahn W, Zhao J, Sage J, Scheidt W. Probing Vibrational Anisotropy with Nuclear Resonance Vibrational Spectroscopy. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Leu BM, Ching TH, Zhao J, Sturhahn W, Alp EE, Sage JT. Vibrational dynamics of iron in cytochrome C. J Phys Chem B 2009; 113:2193-200. [PMID: 19173569 DOI: 10.1021/jp806574t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nuclear resonance vibrational spectroscopy (NRVS) and Raman spectroscopy on (54)Fe- and (57)Fe-enriched cytochrome c (cyt c) identify multiple bands involving vibrations of the heme Fe. Comparison with predictions from Fe isotope shifts reveals that 70% of the NRVS signal in the 300-450 cm(-1) frequency range corresponds to vibrations resolved in Soret-enhanced Raman spectra. This frequency range dominates the "stiffness", an effective force constant determined by the Fe vibrational density of states (VDOS), which measures the strength of nearest-neighbor interactions with Fe. The stiffness of the low-spin Fe environment in both oxidation states of cyt c significantly exceeds that for the high-spin Fe in deoxymyoglobin, where the 200-300 cm(-1) frequency range dominates the VDOS. This situation is reflected in the shorter Fe-ligand bond lengths in the former with respect to the latter. The longer Fe-S(Met80) in oxidized cyt c with respect to reduced cyt c leads to a decrease in the stiffness of the iron environment upon oxidation. Comparison with NRVS measurements allows us to assess assignments for vibrational modes resolved in this region of the heme Raman spectrum. We consider the possibility that the 372 cm(-1) band in reduced cyt c involves the Fe-S(Met80) bond.
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Affiliation(s)
- Bogdan M Leu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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33
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Paulat F, Berto TC, DeBeer George S, Goodrich L, Praneeth VKK, Sulok CD, Lehnert N. Vibrational Assignments of Six-Coordinate Ferrous Heme Nitrosyls: New Insight from Nuclear Resonance Vibrational Spectroscopy. Inorg Chem 2008; 47:11449-51. [DOI: 10.1021/ic801626w] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florian Paulat
- Department of Chemistry, The University of Michigan, 930 N. University, Ann Arbor, Michigan 48109-1055, and Stanford Synchrotron Radiation Laboratory (SSRL), SLAC, Stanford University, Stanford, California 94309
| | - Timothy C. Berto
- Department of Chemistry, The University of Michigan, 930 N. University, Ann Arbor, Michigan 48109-1055, and Stanford Synchrotron Radiation Laboratory (SSRL), SLAC, Stanford University, Stanford, California 94309
| | - Serena DeBeer George
- Department of Chemistry, The University of Michigan, 930 N. University, Ann Arbor, Michigan 48109-1055, and Stanford Synchrotron Radiation Laboratory (SSRL), SLAC, Stanford University, Stanford, California 94309
| | - Lauren Goodrich
- Department of Chemistry, The University of Michigan, 930 N. University, Ann Arbor, Michigan 48109-1055, and Stanford Synchrotron Radiation Laboratory (SSRL), SLAC, Stanford University, Stanford, California 94309
| | - V. K. K. Praneeth
- Department of Chemistry, The University of Michigan, 930 N. University, Ann Arbor, Michigan 48109-1055, and Stanford Synchrotron Radiation Laboratory (SSRL), SLAC, Stanford University, Stanford, California 94309
| | - Corinne D. Sulok
- Department of Chemistry, The University of Michigan, 930 N. University, Ann Arbor, Michigan 48109-1055, and Stanford Synchrotron Radiation Laboratory (SSRL), SLAC, Stanford University, Stanford, California 94309
| | - Nicolai Lehnert
- Department of Chemistry, The University of Michigan, 930 N. University, Ann Arbor, Michigan 48109-1055, and Stanford Synchrotron Radiation Laboratory (SSRL), SLAC, Stanford University, Stanford, California 94309
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Praneeth VKK, Paulat F, Berto TC, George SD, Näther C, Sulok CD, Lehnert N. Electronic Structure of Six-Coordinate Iron(III)−Porphyrin NO Adducts: The Elusive Iron(III)−NO(radical) State and Its Influence on the Properties of These Complexes. J Am Chem Soc 2008; 130:15288-303. [PMID: 18942830 DOI: 10.1021/ja801860u] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- V. K. K. Praneeth
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Florian Paulat
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Timothy C. Berto
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Serena DeBeer George
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Christian Näther
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Corinne D. Sulok
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
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35
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Ambidentate H-bonding by heme-bound NO: structural and spectral effects of -O versus -N H-bonding. J Biol Inorg Chem 2008; 13:613-21. [PMID: 18274790 DOI: 10.1007/s00775-008-0349-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2007] [Accepted: 01/31/2008] [Indexed: 10/22/2022]
Abstract
Resonance Raman studies have uncovered puzzling complexities in the structures of NO adducts of heme proteins. Although CO adducts of heme proteins obey well-behaved anti-correlations between Fe-C and C-O stretching frequencies, which reflect changes in backbonding induced by distal H-bonding residues, the corresponding NO data are scattered. This scatter can be traced to distal influences, since protein-free NO-hemes do show well-behaved anti-correlations. Why do distal effects produce irregularities in vFeN/ vNO plots but not in vFeC/vCO plots? We show via density functional theory (DFT) computations on model systems that the response to distal H-bonding differs markedly when the NO acceptor atom is N versus O. Backbonding is augmented by H-bonding to O, but the effect of H-bonding to N is to weaken both N-O and N-Fe bonds. The resulting downward deviation from the vFeN/vNO backbonding line increases with increasing H-bond strength. This effect explains the deviations observed for a series of myoglobin variants, in which the strength of distal H-bonding is modulated by distal pocket residue substitutions. Most of the data follow a positive vFeN/vNO correlation with the same slope as that calculated for H-bonding to N. Such deviations are not observed for CO adducts, because the CO pi* orbital is unoccupied, and serves as a delocalized acceptor of H-bonds. H-bonding to N primes NO-heme for reduction to the HNO adduct, a putative intermediate in NO-reducing enzymes.
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36
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Scheidt WR. Explorations in metalloporphyrin stereochemistry, physical properties and beyond. J PORPHYR PHTHALOCYA 2008; 12:979-992. [PMID: 20198111 PMCID: PMC2829777 DOI: 10.1142/s1088424608000364] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A review of selected portions of our work in the area of porphyrin structure and physical characterization is presented. Topics covered include early work on periodic trends in first row transtion metalloporphyrins, a survey of electronic structure of iron derivatives including spin-state trends, ligand orientation effects and the elucidtion of unusual low-spin states for iron(II). A discussion of the different tlypes of high-spin iron(II) complexes and the effects of hydrogen bonding is given. A survey of nitric oxide (NO) derivatives is presented as well as a brief introduction into the use of nuclear resonance vibrational spectroscopy for the study of iron porphyrins and heme proteins.
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Affiliation(s)
- W Robert Scheidt
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, USA
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37
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Petrenko T, DeBeer George S, Aliaga-Alcalde N, Bill E, Mienert B, Xiao Y, Guo Y, Sturhahn W, Cramer SP, Wieghardt K, Neese F. Characterization of a Genuine Iron(V)−Nitrido Species by Nuclear Resonant Vibrational Spectroscopy Coupled to Density Functional Calculations. J Am Chem Soc 2007; 129:11053-60. [PMID: 17711275 DOI: 10.1021/ja070792y] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The characterization of high-valent iron species is of interest due to their relevance to biological reaction mechanisms. Recently, we have synthesized and characterized an [Fe(V)-nitrido-cyclam-acetato]+ complex, which has been characterized by Mössbauer, magnetic susceptibility data, and XAS spectroscopies combined with DFT calculations (Aliaga-Alcade, N.; DeBeer George, S.; Bill, E.; Wieghardt, K.; Neese, F. Angew. Chem., Int. Ed. 2005, 44, 2908-2912). The results of this study indicated that the [Fe(V)-nitrido-cyclam-acetato]+ complex is an unusual d3 system with a nearly orbitally degenerate S=1/2 ground state. Although the calculations predicted fairly different Fe-N stretching frequencies for the S=1/2 and the competing S=3/2 ground states, a direct experimental determination of this important fingerprint quantity was missing. Here we apply synchrotron-based nuclear resonance vibrational scattering (NRVS) to characterize the Fe-N stretching frequency of an Fe(V)-nitrido complex and its Fe(III)-azide precursor. The NRVS data show a new isolated band at 864 cm(-1) in the Fe(V)-nitrido complex that is absent in the precursor. The NRVS spectra are fit and simulated using a DFT approach, and the new feature is unambiguously assigned to a Fe(V)-N stretch. The calculated Fe-N stretching frequency is too high by approximately 75 cm(-1). Anharmonic contributions to the Fe-N stretching frequency have been evaluated and have been found to be small (-5.5 cm(-1)). The NRVS data provided a unique opportunity to obtain this vibrational information, which had eluded characterization by more traditional vibrational spectroscopies.
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Affiliation(s)
- Taras Petrenko
- Institut für Physikalische und Theoretische Chemie, Wegelerstr. 12, D-53115 Bonn, Germany
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Leu BM, Silvernail NJ, Zgierski MZ, Wyllie GRA, Ellison MK, Scheidt WR, Zhao J, Sturhahn W, Alp EE, Sage JT. Quantitative vibrational dynamics of iron in carbonyl porphyrins. Biophys J 2007; 92:3764-83. [PMID: 17350996 PMCID: PMC1868970 DOI: 10.1529/biophysj.106.093773] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We use nuclear resonance vibrational spectroscopy and computational predictions based on density functional theory (DFT) to explore the vibrational dynamics of (57)Fe in porphyrins that mimic the active sites of histidine-ligated heme proteins complexed with carbon monoxide. Nuclear resonance vibrational spectroscopy yields the complete vibrational spectrum of a Mössbauer isotope, and provides a valuable probe that is not only selective for protein active sites but quantifies the mean-squared amplitude and direction of the motion of the probe nucleus, in addition to vibrational frequencies. Quantitative comparison of the experimental results with DFT calculations provides a detailed, rigorous test of the vibrational predictions, which in turn provide a reliable description of the observed vibrational features. In addition to the well-studied stretching vibration of the Fe-CO bond, vibrations involving the Fe-imidazole bond, and the Fe-N(pyr) bonds to the pyrrole nitrogens of the porphyrin contribute prominently to the observed experimental signal. All of these frequencies show structural sensitivity to the corresponding bond lengths, but previous studies have failed to identify the latter vibrations, presumably because the coupling to the electronic excitation is too small in resonance Raman measurements. We also observe the FeCO bending vibrations, which are not Raman active for these unhindered model compounds. The observed Fe amplitude is strongly inconsistent with three-body oscillator descriptions of the FeCO fragment, but agrees quantitatively with DFT predictions. Over the past decade, quantum chemical calculations have suggested revised estimates of the importance of steric distortion of the bound CO in preventing poisoning of heme proteins by carbon monoxide. Quantitative agreement with the predicted frequency, amplitude, and direction of Fe motion for the FeCO bending vibrations provides direct experimental support for the quantum chemical description of the energetics of the FeCO unit.
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Affiliation(s)
- Bogdan M Leu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts, USA
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Ibrahim M, Xu C, Spiro TG. Differential sensing of protein influences by NO and CO vibrations in heme adducts. J Am Chem Soc 2006; 128:16834-45. [PMID: 17177434 PMCID: PMC2530899 DOI: 10.1021/ja064859d] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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