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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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2
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Influence of heme c attachment on heme conformation and potential. J Biol Inorg Chem 2018; 23:1073-1083. [PMID: 30143872 DOI: 10.1007/s00775-018-1603-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
Heme c is characterized by its covalent attachment to a polypeptide. The attachment is typically to a CXXCH motif in which the two Cys form thioether bonds with the heme, "X" can be any amino acid other than Cys, and the His serves as a heme axial ligand. Some cytochromes c, however, contain heme attachment motifs with three or four intervening residues in a CX3CH or CX4CH motif. Here, the impacts of these variations in the heme attachment motif on heme ruffling and electronic structure are investigated by spectroscopically characterizing CX3CH and CX4CH variants of Hydrogenobacter thermophilus cytochrome c552. In addition, a novel CXCH variant is studied. 1H and 13C NMR, EPR, and resonance Raman spectra of the protein variants are analyzed to deduce the extent of ruffling using previously reported relationships between these spectral data and heme ruffling. In addition, the reduction potentials of these protein variants are measured using protein film voltammetry. The CXCH and CX4CH variants are found to have enhanced heme ruffling and lower reduction potentials. Implications of these results for the use of these noncanonical motifs in nature, and for the engineering of novel heme peptide structures, are discussed.
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3
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Bren KL. Going with the Electron Flow: Heme Electronic Structure and Electron Transfer in Cytochrome
c. Isr J Chem 2016. [DOI: 10.1002/ijch.201600021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kara L. Bren
- Department of Chemistry University of Rochester Rochester NY 14627-0216 USA
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He C, Ogata H, Lubitz W. Elucidation of the heme active site electronic structure affecting the unprecedented nitrite dismutase activity of the ferriheme b proteins, the nitrophorins. Chem Sci 2016; 7:5332-5340. [PMID: 30155185 PMCID: PMC6020753 DOI: 10.1039/c6sc01019a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/23/2016] [Indexed: 12/14/2022] Open
Abstract
Nitrophorins (NPs) catalyze the nitrite dismutation reaction that is unprecedented in ferriheme proteins. Despite progress in studying the reaction mechanism, fundamental issues regarding the correlation of the structural features with the nitrite dismutase activity of NPs remain elusive. On the other hand, it has been shown that the nitrite complexes of NPs are unique among those of the ferriheme proteins since some of their electron paramagnetic resonance (EPR) spectra show significant highly anisotropic low spin (HALS) signals with large gmax values over 3.2. The origin of HALS signals in ferriheme proteins or models is not well understood, especially in cases where axial ligands other than histidine are present. In this study several mutations were introduced in NP4. The related nitrite coordination and dismutation reaction were investigated. As a result, the EPR spectra of the NP-nitrite complexes were found to be tightly correlated with the extent of heme ruffling and protonation state of the proximal His ligand-dictated by an extended H-bonding network at the heme active site. Furthermore, it is established that the two factors are essential in determining the nitrite dismutase activity of NPs. These results may provide a valuable guide for identifying or designing novel heme proteins with similar activity.
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Affiliation(s)
- Chunmao He
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
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Abstract
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Metal ions and metallocofactors play important
roles in a broad
range of biochemical reactions. Accordingly, it has been estimated
that as much as 25–50% of the proteome uses transition metal
ions to carry out a variety of essential functions. The metal ions
incorporated within metalloproteins fulfill functional roles based
on chemical properties, the diversity of which arises as transition
metals can adopt different redox states and geometries, dictated by
the identity of the metal and the protein environment. The coupling
of a metal ion with an organic framework in metallocofactors, such
as heme and cobalamin, further expands the chemical functionality
of metals in biology. The three-dimensional visualization of metal
ions and complex metallocofactors within a protein scaffold is often
a starting point for enzymology, highlighting the importance of structural
characterization of metalloproteins. Metalloprotein crystallography,
however, presents a number of implicit challenges including correctly
incorporating the relevant metal or metallocofactor, maintaining the
proper environment for the protein to be purified and crystallized
(including providing anaerobic, cold, or aphotic environments), and
being mindful of the possibility of X-ray induced damage to the proteins
or incorporated metal ions. Nevertheless, the incorporated metals
or metallocofactors also present unique advantages in metalloprotein
crystallography. The significant resonance that metals undergo with
X-ray photons at wavelengths used for protein crystallography and
the rich electronic properties of metals, which provide intense and
spectroscopically unique signatures, allow a metalloprotein crystallographer
to use anomalous dispersion to determine phases for structure solution
and to use simultaneous or parallel spectroscopic techniques on single
crystals. These properties, coupled with the improved brightness of
beamlines, the ability to tune the wavelength of the X-ray beam, the
availability of advanced detectors, and the incorporation of spectroscopic
equipment at a number of synchrotron beamlines, have yielded exciting
developments in metalloprotein structure determination. Here we will
present results on the advantageous uses of metals in metalloprotein
crystallography, including using metallocofactors to obtain phasing
information, using K-edge X-ray absorption spectroscopy to identify
metals coordinated in metalloprotein crystals, and using UV–vis
spectroscopy on crystals to probe the enzymatic activity of the crystallized
protein.
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Affiliation(s)
- Sarah E. J. Bowman
- Department
of Chemistry, ‡Department of Biology, and §Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jennifer Bridwell-Rabb
- Department
of Chemistry, ‡Department of Biology, and §Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Catherine L. Drennan
- Department
of Chemistry, ‡Department of Biology, and §Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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6
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Harvilla PB, Wolcott HN, Magyar JS. The structure of ferricytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H. Metallomics 2015; 6:1126-30. [PMID: 24727932 DOI: 10.1039/c4mt00045e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Approximately 40% of all proteins are metalloproteins, and approximately 80% of Earth's ecosystems are at temperatures ≤5 °C, including 90% of the global ocean. Thus, an essential aspect of marine metallobiochemistry is an understanding of the structure, dynamics, and mechanisms of cold adaptation of metalloproteins from marine microorganisms. Here, the molecular structure of the electron-transfer protein cytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H has been determined by X-ray crystallography (PDB: ). The structure is highly superimposable with that of the homologous cytochrome from the mesophile Marinobacter hydrocarbonoclasticus. Based on structural analysis and comparison of psychrophilic, psychrotolerant, and mesophilic sequences, a methionine-based ligand-substitution mechanism for psychrophilic protein stabilization is proposed.
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Affiliation(s)
- Paul B Harvilla
- Department of Chemistry, Barnard College, Columbia University, 3009 Broadway, New York NY 10027, USA.
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Jobichen C, Swaminathan K. Molecular replacement with a large number of molecules in the asymmetric unit. Acta Crystallogr F Struct Biol Commun 2014; 70:1296-302. [PMID: 25195913 PMCID: PMC4157440 DOI: 10.1107/s2053230x14014381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 06/18/2014] [Indexed: 11/11/2022] Open
Abstract
The exponential increase in protein structures deposited in the Protein Data Bank (PDB) has resulted in the elucidation of most, if not all, protein folds, thus making molecular replacement (MR) the most frequently used method for structure determination. A survey of the PDB shows that most of the structures determined by molecular replacement contain less than ten molecules in the asymmetric unit and that it is predominantly virus and ribosome structures that contain more than 20 molecules in the asymmetric unit. While the success of the MR method depends on several factors, such as the homology and the size of an input model, it is also a well known fact that this method can become significantly difficult in cases with a large number of molecules in the asymmetric unit, higher crystallographic symmetry and tight packing. In this paper, five representative structures containing 16-18 homomeric molecules in the asymmetric unit and the strategies that have been used to solve these structures are described. The difficulties faced and the lessons learned from these structure-determination efforts will be useful for selected and similar future situations with a large number of molecules in the asymmetric unit.
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Affiliation(s)
- Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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8
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Structure of a mitochondrial cytochrome c conformer competent for peroxidase activity. Proc Natl Acad Sci U S A 2014; 111:6648-53. [PMID: 24760830 DOI: 10.1073/pnas.1323828111] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
At the onset of apoptosis, the peroxidation of cardiolipin at the inner mitochondrial membrane by cytochrome c requires an open coordination site on the heme. We report a 1.45-Å resolution structure of yeast iso-1-cytochrome c with the Met80 heme ligand swung out of the heme crevice and replaced by a water molecule. This conformational change requires modest adjustments to the main chain of the heme crevice loop and is facilitated by a trimethyllysine 72-to-alanine mutation. This mutation also enhances the peroxidase activity of iso-1-cytochrome c. The structure shows a buried water channel capable of facilitating peroxide access to the active site and of moving protons produced during peroxidase activity to the protein surface. Alternate positions of the side chain of Arg38 appear to mediate opening and closing of the buried water channel. In addition, two buried water molecules can adopt alternate positions that change the network of hydrogen bonds in the buried water channel. Taken together, these observations suggest that low and high proton conductivity states may mediate peroxidase function. Comparison of yeast and mammalian cytochrome c sequences, in the context of the steric factors that permit opening of the heme crevice, suggests that higher organisms have evolved to inhibit peroxidase activity, providing a more stringent barrier to the onset of apoptosis.
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Kaur R, Bren KL. Redox state dependence of axial ligand dynamics in Nitrosomonas europaea cytochrome c552. J Phys Chem B 2013; 117:15720-8. [PMID: 23909651 DOI: 10.1021/jp4064577] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analysis of NMR spectra reveals that the heme axial Met ligand orientation and dynamics in Nitrosomonas europaea cytochrome c552 (Ne cyt c) are dependent on the heme redox state. In the oxidized state, the heme axial Met is fluxional, interconverting between two conformers related to each other by inversion through the Met δS atom. In the reduced state, there is no evidence of fluxionality, with the Met occupying one conformation similar to that seen in the homologous Pseudomonas aeruginosa cytochrome c551. Comparison of the observed and calculated pseudocontact shifts for oxidized Ne cyt c using the reduced protein structure as a reference structure reveals a redox-dependent change in the structure of the loop bearing the axial Met (loop 3). Analysis of nuclear Overhauser effects (NOEs) and existing structural data provides further support for the redox state dependence of the loop 3 structure. Implications for electron transfer function are discussed.
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Affiliation(s)
- Ravinder Kaur
- Center for Infectious Disease and Immunology, Research Institute, Rochester General Hospital , Rochester, New York 14621, United States
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