1
|
Schweitzer-Stenner R. Probing the versatility of cytochrome c by spectroscopic means: A Laudatio on resonance Raman spectroscopy. J Inorg Biochem 2024; 259:112641. [PMID: 38901065 DOI: 10.1016/j.jinorgbio.2024.112641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Over the last 50 years resonance Raman spectroscopy has become an invaluable tool for the exploration of chromophores in biological macromolecules. Among them, heme proteins and metal complexes have attracted considerable attention. This interest results from the fact that resonance Raman spectroscopy probes the vibrational dynamics of these chromophores without direct interference from the surrounding. However, the indirect influence via through-bond and through-space chromophore-protein interactions can be conveniently probed and analyzed. This review article illustrates this point by focusing on class 1 cytochrome c, a comparatively simple heme protein generally known as electron carrier in mitochondria. The article demonstrates how through selective excitation of resonance Raman active modes information about the ligation, the redox state and the spin state of the heme iron can be obtained from band positions in the Raman spectra. The investigation of intensities and depolarization ratios emerged as tools for the analysis of in-plane and out-of-plane deformations of the heme macrocycle. The article further shows how resonance Raman spectroscopy was used to characterize partially unfolded states of oxidized cytochrome c. Finally, it describes its use for exploring structural changes due to the protein's binding to anionic surfaces like cardiolipin containing membranes.
Collapse
|
2
|
Schweitzer-Stenner R. Heme-Protein Interactions and Functional Relevant Heme Deformations: The Cytochrome c Case. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248751. [PMID: 36557884 PMCID: PMC9781506 DOI: 10.3390/molecules27248751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Heme proteins are known to perform a plethora of biologically important functions. This article reviews work that has been conducted on various class I cytochrome c proteins over a period of nearly 50 years. The article focuses on the relevance of symmetry-lowering heme-protein interactions that affect the function of the electron transfer protein cytochrome c. The article provides an overview of various, mostly spectroscopic studies that explored the electronic structure of the heme group in these proteins and how it is affected by symmetry-lowering deformations. In addition to discussing a large variety of spectroscopic studies, the article provides a theoretical framework that should enable a comprehensive understanding of the physical chemistry that underlies the function not only of cytochrome c but of all heme proteins.
Collapse
|
3
|
Khan FST, Samanta D, Chandel D, Shah SJ, Rath SP. Heme-Heme Interactions in Diheme Cytochromes: Effect of Mixed-Axial Ligation on the Electronic Structure and Electrochemical Properties. Inorg Chem 2021; 60:12870-12882. [PMID: 34370470 DOI: 10.1021/acs.inorgchem.1c01215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diheme cytochromes, the simplest members in the multiheme family, play substantial biochemical roles in enzymatic catalysis as well as in electron transfer. A series of diiron(III) porphyrin dimers have been synthesized as active site analogues of diheme cytochromes. The complexes contain six-coordinated iron(III) having thiophenol and imidazole at the fifth and sixth coordination sites, respectively. The iron centers in the complexes have been found to be in a low-spin state, as confirmed through solid-state Mössbauer and electron paramagnetic resonance (EPR) spectroscopic investigations. Mössbauer quadrupole splitting of complexes having mixed ligands is substantially larger than that observed when both axial ligands are the same. Rhombic types of EPR spectra with narrow separation between gx, gy, and gz clearly distinguish heme thiolate coordination compared to bis(imidazole)-ligated low-spin heme centers. The redox potential in diheme cytochromes has been found to be tuned by interheme interactions along with the nature of axial ligands. The effect of mixed-axial ligation within the diiron(III) porphyrin dimers is demonstrated by a positive shift in the Fe(III)/Fe(II) redox couple upon thiophenolate coordination compared to their bis(imidazole) analogues. The pKa of the imidazole also decides the extent of the shift for the Fe(III)/Fe(II) couple, while the potential of the mixed-ligated diiron(III) porphyrin dimer is more positive compared to their monomeric analogue. A variation of around 1.1 V for the Fe(III)/Fe(II) redox potential in the diiron(III) porphyrin dimer can be achieved with the combined effect of axial ligation and a metal spin state, while such a large variation in the redox potential, compared to their monomeric analogues, is attributed to the heme-heme interactions observed in dihemes. Moreover, theoretical calculations also support the experimental shifts in the redox potential values.
Collapse
Affiliation(s)
| | - Deepannita Samanta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Dolly Chandel
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Syed Jehanger Shah
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| |
Collapse
|
4
|
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.
Collapse
|
5
|
Ponomarenko N, Niklas J, Pokkuluri PR, Poluektov O, Tiede DM. Electron Paramagnetic Resonance Characterization of the Triheme Cytochrome from Geobacter sulfurreducens. Biochemistry 2018; 57:1722-1732. [DOI: 10.1021/acs.biochem.7b00917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
6
|
Engineered holocytochrome c synthases that biosynthesize new cytochromes c. Proc Natl Acad Sci U S A 2017; 114:2235-2240. [PMID: 28196881 DOI: 10.1073/pnas.1615929114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome c (cyt c), required for electron transport in mitochondria, possesses a covalently attached heme cofactor. Attachment is catalyzed by holocytochrome c synthase (HCCS), leading to two thioether bonds between heme and a conserved CXXCH motif of cyt c In cyt c, histidine (His19) of CXXCH acts as an axial ligand to heme iron and upon release of holocytochrome c from HCCS, folding leads to formation of a second axial interaction with methionine (Met81). We previously discovered mutations in human HCCS that facilitate increased biosynthesis of cyt c in recombinant Escherichia coli Focusing on HCCS E159A, novel cyt c variants in quantities that are sufficient for biophysical analysis are biosynthesized. Cyt c H19M, the first bis-Met liganded cyt c, is compared with other axial ligand variants (M81A, M81H) and single thioether cyt c variants. For variants with axial ligand substitutions, electronic absorption, near-UV circular dichroism, and electron paramagnetic resonance spectroscopy provide evidence that axial ligands are changed and the heme environment is altered. Circular dichroism spectra in far UV and thermal denaturation analyses demonstrate that axial ligand changes do not affect secondary structures and stability. Redox potentials span a 400-mV range (+349 mV vs. standard hydrogen electrode, H19M; +252 mV, WT; -19 mV, M81A; -69 mV, M81H). We discuss the results in the context of a four-step mechanism for HCCS, whereby HCCS mutants such as E159A are enhanced in release (step 4) of cyt c from the HCCS active site; thus, we term these "release mutants."
Collapse
|
7
|
Liu Q, Tang M, Zeng W, Zhang X, Wang J, Zhou Z. Optimal Size Matching and Minimal Distortion Energy: Implications for Natural Selection by the Macrocycle of the Iron Species in Heme. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Qiuhua Liu
- College of Chemistry and Chemical EngineeringCentral South University410083ChangshaChina
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules of the Ministry of EducationSchool of Chemistry and Chemical EngineeringHunan University of Science and Technology411201XiangtanChina
| | - Min Tang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules of the Ministry of EducationSchool of Chemistry and Chemical EngineeringHunan University of Science and Technology411201XiangtanChina
| | - Wennan Zeng
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules of the Ministry of EducationSchool of Chemistry and Chemical EngineeringHunan University of Science and Technology411201XiangtanChina
| | - Xi Zhang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules of the Ministry of EducationSchool of Chemistry and Chemical EngineeringHunan University of Science and Technology411201XiangtanChina
| | - Jianxiu Wang
- College of Chemistry and Chemical EngineeringCentral South University410083ChangshaChina
| | - Zaichun Zhou
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules of the Ministry of EducationSchool of Chemistry and Chemical EngineeringHunan University of Science and Technology411201XiangtanChina
| |
Collapse
|
8
|
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
| |
Collapse
|
9
|
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.
Collapse
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 . ;
| |
Collapse
|
10
|
Abstract
![]()
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.
Collapse
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
| |
Collapse
|
11
|
Liu Q, Zhang X, Zeng W, Wang J, Zhou Z. Fine-Tuning of Electronic Structure of Cobalt(II) Ion in Nonplanar Porphyrins and Tracking of a Cross-Hybrid Stage: Implications for the Distortion of Natural Tetrapyrrole Macrocycles. J Phys Chem B 2015; 119:14102-10. [DOI: 10.1021/acs.jpcb.5b08431] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qiuhua Liu
- College
of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
- Key
Laboratory of Theoretical Organic Chemistry and Functional Molecule
of the Ministry of Education; School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Xi Zhang
- Key
Laboratory of Theoretical Organic Chemistry and Functional Molecule
of the Ministry of Education; School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Wennan Zeng
- Key
Laboratory of Theoretical Organic Chemistry and Functional Molecule
of the Ministry of Education; School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Jianxiu Wang
- College
of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Zaichun Zhou
- Key
Laboratory of Theoretical Organic Chemistry and Functional Molecule
of the Ministry of Education; School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| |
Collapse
|
12
|
Cytochrome c: A Multifunctional Protein Combining Conformational Rigidity with Flexibility. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/484538] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cytochrome has served as a model system for studying redox reactions, protein folding, and more recently peroxidase activity induced by partial unfolding on membranes. This review illuminates some important aspects of the research on this biomolecule. The first part summarizes the results of structural analyses of its active site. Owing to heme-protein interactions the heme group is subject to both in-plane and out-of-plane deformations. The unfolding of the protein as discussed in detail in the second part of this review can be induced by changes of pH and temperature and most prominently by the addition of denaturing agents. Both the kinetic and thermodynamic folding and unfolding involve intermediate states with regard to all unfolding conditions. If allowed to sit at alkaline pH (11.5) for a week, the protein does not return to its folding state when the solvent is switched back to neutral pH. It rather adopts a misfolded state that is prone to aggregation via domain swapping. On the surface of cardiolipin containing liposomes, the protein can adopt a variety of partially unfolded states. Apparently, ferricytochrome c can perform biological functions even if it is only partially folded.
Collapse
|
13
|
Karunakaran V, Sun Y, Benabbas A, Champion PM. Investigations of the low frequency modes of ferric cytochrome c using vibrational coherence spectroscopy. J Phys Chem B 2014; 118:6062-70. [PMID: 24823442 PMCID: PMC4059251 DOI: 10.1021/jp501298c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Femtosecond vibrational coherence
spectroscopy is used to investigate
the low frequency vibrational dynamics of the electron transfer heme
protein, cytochrome c (cyt c). The
vibrational coherence spectra of ferric cyt c have
been measured as a function of excitation wavelength within the Soret
band. Vibrational coherence spectra obtained with excitation between
412 and 421 nm display a strong mode at ∼44 cm–1 that has been assigned to have a significant contribution from heme
ruffling motion in the electronic ground state. This assignment is
based partially on the presence of a large heme ruffling distortion
in the normal coordinate structural decomposition (NSD) analysis of
the X-ray crystal structures. When the excitation wavelength is moved
into the ∼421–435 nm region, the transient absorption
increases along with the relative intensity of two modes near ∼55
and 30 cm–1. The intensity of the mode near 44 cm–1 appears to minimize in this region and then recover
(but with an opposite phase compared to the blue excitation) when
the laser is tuned to 443 nm. These observations are consistent with
the superposition of both ground and excited state coherence in the
421–435 nm region due to the excitation of a weak porphyrin-to-iron
charge transfer (CT) state, which has a lifetime long enough to observe
vibrational coherence. The mode near 55 cm–1 is
suggested to arise from ruffling in a transient CT state that has
a less ruffled heme due to its iron d6 configuration.
Collapse
Affiliation(s)
- Venugopal Karunakaran
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | | | | | | |
Collapse
|
14
|
The class Ib ribonucleotide reductase from Mycobacterium tuberculosis has two active R2F subunits. J Biol Inorg Chem 2014; 19:893-902. [PMID: 24585102 DOI: 10.1007/s00775-014-1121-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/13/2014] [Indexed: 10/25/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to their corresponding deoxyribonucleotides, playing a crucial role in DNA repair and replication in all living organisms. Class Ib RNRs require either a diiron-tyrosyl radical (Y·) or a dimanganese-Y· cofactor in their R2F subunit to initiate ribonucleotide reduction in the R1 subunit. Mycobacterium tuberculosis, the causative agent of tuberculosis, contains two genes, nrdF1 and nrdF2, encoding the small subunits R2F-1 and R2F-2, respectively, where the latter has been thought to serve as the only active small subunit in the M. tuberculosis class Ib RNR. Here, we present evidence for the presence of an active Fe 2 (III) -Y· cofactor in the M. tuberculosis RNR R2F-1 small subunit, supported and characterized by UV-vis, X-band electron paramagnetic resonance, and resonance Raman spectroscopy, showing features similar to those for the M. tuberculosis R2F-2-Fe 2 (III) -Y· cofactor. We also report enzymatic activity of Fe 2 (III) -R2F-1 when assayed with R1, and suggest that the active M. tuberculosis class Ib RNR can use two different small subunits, R2F-1 and R2F-2, with similar activity.
Collapse
|
15
|
Kleingardner JG, Bowman SEJ, Bren KL. The influence of heme ruffling on spin densities in ferricytochromes c probed by heme core 13C NMR. Inorg Chem 2013; 52:12933-46. [PMID: 24187968 DOI: 10.1021/ic401250d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The heme in cytochromes c undergoes a conserved out-of-plane distortion known as ruffling. For cytochromes c from the bacteria Hydrogenobacter thermophilus and Pseudomonas aeruginosa , NMR and EPR spectra have been shown to be sensitive to the extent of heme ruffling and to provide insights into the effect of ruffling on the electronic structure. Through the use of mutants of each of these cytochromes that differ in the amount of heme ruffling, NMR characterization of the low-spin (S = ½) ferric proteins has confirmed and refined the developing understanding of how ruffling influences the spin distribution on heme. The chemical shifts of the core heme carbons were obtained through site-specific labeling of the heme via biosynthetic incorporation of (13)C-labeled 5-aminolevulinic acid derivatives. Analysis of the contact shifts of these core heme carbons allowed Fermi contact spin densities to be estimated and changes upon ruffling to be evaluated. The results allow a deconvolution of the contributions to heme hyperfine shifts and a test of the influence of heme ruffling on the electronic structure and hyperfine shifts. The data indicate that as heme ruffling increases, the spin densities on the β-pyrrole carbons decrease while the spin densities on the α-pyrrole carbons and meso carbons increase. Furthermore, increased ruffling is associated with stronger bonding to the heme axial His ligand.
Collapse
Affiliation(s)
- Jesse G Kleingardner
- Department of Chemistry, University of Rochester , Rochester, New York 14627-0216, United States
| | | | | |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- Ravinder Kaur
- Center for Infectious Disease and Immunology, Research Institute, Rochester General Hospital , Rochester, New York 14621, United States
| | | |
Collapse
|
17
|
Can M, Krucinska J, Zoppellaro G, Andersen NH, Wedekind JE, Hersleth HP, Andersson KK, Bren KL. Structural characterization of nitrosomonas europaea cytochrome c-552 variants with marked differences in electronic structure. Chembiochem 2013; 14:1828-38. [PMID: 23908017 DOI: 10.1002/cbic.201300118] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Indexed: 11/09/2022]
Abstract
Nitrosomonas europaea cytochrome c-552 (Ne c-552) variants with the same His/Met axial ligand set but with different EPR spectra have been characterized structurally, to aid understanding of how molecular structure determines heme electronic structure. Visible light absorption, Raman, and resonance Raman spectroscopy of the protein crystals was performed along with structure determination. The structures solved are those of Ne c-552, which displays a "HALS" (or highly anisotropic low-spin) EPR spectrum, and of the deletion mutant Ne N64Δ, which has a rhombic EPR spectrum. Two X-ray crystal structures of wild-type Ne c-552 are reported; one is of the protein isolated from N. europaea cells (Ne c-552n, 2.35 Å resolution), and the other is of recombinant protein expressed in Escherichia coli (Ne c-552r, 1.63 Å resolution). Ne N64Δ crystallized in two different space groups, and two structures are reported [monoclinic (2.1 Å resolution) and hexagonal (2.3 Å resolution)]. Comparison of the structures of the wild-type and mutant proteins reveals that heme ruffling is increased in the mutant; increased ruffling is predicted to yield a more rhombic EPR spectrum. The 2.35 Å Ne c-552n structure shows 18 molecules in the asymmetric unit; analysis of the structure is consistent with population of more than one axial Met configuration, as seen previously by NMR. Finally, the mutation was shown to yield a more hydrophobic heme pocket and to expel water molecules from near the axial Met. These structures reveal that heme pocket residue 64 plays multiple roles in regulating the axial ligand orientation and the interaction of water with the heme. These results support the hypothesis that more ruffled hemes lead to more rhombic EPR signals in cytochromes c with His/Met axial ligation.
Collapse
Affiliation(s)
- Mehmet Can
- Department of Chemistry, University of Rochester, Rochester, NY 14627 (USA)
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Astashkin AV, Walker FA. Determination of the principal g-values of Type I or highly-anisotropic low spin (HALS) ferriheme centers in frozen solutions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 231:15-21. [PMID: 23562666 PMCID: PMC3660502 DOI: 10.1016/j.jmr.2013.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/07/2013] [Accepted: 03/08/2013] [Indexed: 06/02/2023]
Abstract
Continuous wave (CW) electron paramagnetic resonance (EPR) spectroscopy of highly-anisotropic low spin (HALS) ferric heme centers in frozen solutions is not a very informative approach because usually only one feature is reliably observed in the spectra, that at the maximal principal g-value of, typically, 3.3-3.79. The other two EPR turning points are severely broadened by g-strain and are not easily observed in the first-derivative CW EPR spectra. In this work, we have explored the potential of alternative EPR techniques, the electron spin echo (ESE) field sweep and electron spin transient nutation (TN), for obtaining information about the g-tensors of such systems, using as an example a typical HALS ferric heme center, [Fe(III)((15)N-coproporphyrin)(CN)2]. The analysis of the experimental g-tensor of [Fe(III)((15)N-coproporphyrin)(CN)2](-) has shown that the widths of the underlying energy distributions for this HALS center are comparable to those found for the rhombic bis-imidazole complex. The greater effect on the g-value distributions for HALS centers is determined by near degeneracy of two of the three lower-energy d-orbitals, d(yz) and d(xz), which contain the unpaired electron.
Collapse
Affiliation(s)
- Andrei V Astashkin
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721-0041, USA.
| | | |
Collapse
|
19
|
Tomter AB, Zoppellaro G, Andersen NH, Hersleth HP, Hammerstad M, Røhr ÅK, Sandvik GK, Strand KR, Nilsson GE, Bell CB, Barra AL, Blasco E, Le Pape L, Solomon EI, Andersson KK. Ribonucleotide reductase class I with different radical generating clusters. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
20
|
Patra R, Sahoo D, Dey S, Sil D, Rath SP. Switching Orientation of Two Axial Imidazole Ligands between Parallel and Perpendicular in Low-Spin Fe(III) and Fe(II) Nonplanar Porphyrinates. Inorg Chem 2012; 51:11294-305. [DOI: 10.1021/ic300229u] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ranjan Patra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
| | - Dipankar Sahoo
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
| | - Soumyajit Dey
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
| | - Debangsu Sil
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
| |
Collapse
|
21
|
He C, Ogata H, Knipp M. Insertion of an H-Bonding Residue into the Distal Pocket of the Ferriheme Protein Nitrophorin 4: Effect on NitriteIron Coordination and Nitrite Disproportionation. Chem Biodivers 2012; 9:1761-75. [DOI: 10.1002/cbdv.201100401] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
22
|
Spectroscopic studies of the iron and manganese reconstituted tyrosyl radical in Bacillus cereus ribonucleotide reductase R2 protein. PLoS One 2012; 7:e33436. [PMID: 22432022 PMCID: PMC3303829 DOI: 10.1371/journal.pone.0033436] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 02/08/2012] [Indexed: 11/24/2022] Open
Abstract
Ribonucleotide reductase (RNR) catalyzes the rate limiting step in DNA synthesis where ribonucleotides are reduced to the corresponding deoxyribonucleotides. Class Ib RNRs consist of two homodimeric subunits: R1E, which houses the active site; and R2F, which contains a metallo cofactor and a tyrosyl radical that initiates the ribonucleotide reduction reaction. We studied the R2F subunit of B. cereus reconstituted with iron or alternatively with manganese ions, then subsequently reacted with molecular oxygen to generate two tyrosyl-radicals. The two similar X-band EPR spectra did not change significantly over 4 to 50 K. From the 285 GHz EPR spectrum of the iron form, a g1-value of 2.0090 for the tyrosyl radical was extracted. This g1-value is similar to that observed in class Ia E. coli R2 and class Ib R2Fs with iron-oxygen cluster, suggesting the absence of hydrogen bond to the phenoxyl group. This was confirmed by resonance Raman spectroscopy, where the stretching vibration associated to the radical (C-O, ν7a = 1500 cm−1) was found to be insensitive to deuterium-oxide exchange. Additionally, the 18O-sensitive Fe-O-Fe symmetric stretching (483 cm−1) of the metallo-cofactor was also insensitive to deuterium-oxide exchange indicating no hydrogen bonding to the di-iron-oxygen cluster, and thus, different from mouse R2 with a hydrogen bonded cluster. The HF-EPR spectrum of the manganese reconstituted RNR R2F gave a g1-value of ∼2.0094. The tyrosyl radical microwave power saturation behavior of the iron-oxygen cluster form was as observed in class Ia R2, with diamagnetic di-ferric cluster ground state, while the properties of the manganese reconstituted form indicated a magnetic ground state of the manganese-cluster. The recent activity measurements (Crona et al., (2011) J Biol Chem 286: 33053–33060) indicates that both the manganese and iron reconstituted RNR R2F could be functional. The manganese form might be very important, as it has 8 times higher activity.
Collapse
|
23
|
Can M, Zoppellaro G, Andersson KK, Bren KL. Modulation of ligand-field parameters by heme ruffling in cytochromes c revealed by EPR spectroscopy. Inorg Chem 2011; 50:12018-24. [PMID: 22044358 DOI: 10.1021/ic201479q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electron paramagnetic resonance (EPR) spectra of variants of Hydrogenobacter thermophilus cytochrome c(552) (Ht c-552) and Pseudomonas aeruginosa cytochrome c(551) (Pa c-551) are analyzed to determine the effect of heme ruffling on ligand-field parameters. Mutations introduced at positions 13 and 22 in Ht c-552 were previously demonstrated to influence hydrogen bonding in the proximal heme pocket and to tune reduction potential (E(m)) over a range of 80 mV [Michel, L. V.; Ye, T.; Bowman, S. E. J.; Levin, B. D.; Hahn, M. A.; Russell, B. S.; Elliott, S. J.; Bren, K. L. Biochemistry 2007, 46, 11753-11760]. These mutations are shown here to also increase heme ruffling as E(m) decreases. The primary effect on electronic structure of increasing heme ruffling is found to be a decrease in the axial ligand-field term Δ/λ, which is proposed to arise from an increase in the energy of the d(xy) orbital. Mutations at position 7, previously demonstrated to influence heme ruffling in Pa c-551 and Ht c-552, are utilized to test this correlation between molecular and electronic structure. In conclusion, the structure of the proximal heme pocket of cytochromes c is shown to play a role in determining heme conformation and electronic structure.
Collapse
Affiliation(s)
- Mehmet Can
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
| | | | | | | |
Collapse
|
24
|
Harbitz E, Andersson KK. Cytochrome c-554 from Methylosinus trichosporium OB3b; a protein that belongs to the cytochrome c2 family and exhibits a HALS-Type EPR signal. PLoS One 2011; 6:e22014. [PMID: 21789203 PMCID: PMC3138771 DOI: 10.1371/journal.pone.0022014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 06/10/2011] [Indexed: 11/19/2022] Open
Abstract
A small soluble cytochrome c-554 purified from Methylosinus trichosporium OB3b has been purified and analyzed by amino acid sequencing, mass spectrometry, visible, CD and EPR spectroscopies. It is found to be a mono heme protein with a characteristic cytochrome c fold, thus fitting into the class of cytochrome c2, which is the bacterial homologue of mitochondrial cytochrome c. The heme iron has a Histidine/Methionine axial ligation and exhibits a highly anisotropic/axial low spin (HALS) EPR signal, with a gmax at 3.40, and ligand field parameters V/ξ = 0.99, Δ/ξ = 4.57. This gives the rhombicity V/Δ = 0.22. The structural basis for this HALS EPR signal in Histidine/Methionine ligated hemes is not resolved. The ligand field parameters observed for cytochrome c-554 fits the observed pattern for other cytochromes with similar ligation and EPR behaviour.
Collapse
Affiliation(s)
- Espen Harbitz
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | | |
Collapse
|
25
|
Rajapandian V, Subramanian V. Calculations on the Structure and Spectral Properties of Cytochrome c551 Using DFT and ONIOM Methods. J Phys Chem A 2011; 115:2866-76. [DOI: 10.1021/jp110983v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. Rajapandian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| |
Collapse
|
26
|
Liptak MD, Wen X, Bren KL. NMR and DFT investigation of heme ruffling: functional implications for cytochrome c. J Am Chem Soc 2010; 132:9753-63. [PMID: 20572664 DOI: 10.1021/ja102098p] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Out-of-plane (OOP) deformations of the heme cofactor are found in numerous heme-containing proteins and the type of deformation tends to be conserved within functionally related classes of heme proteins. We demonstrate correlations between the heme ruffling OOP deformation and the (13)C and (1)H nuclear magnetic resonance (NMR) hyperfine shifts of heme aided by density functional theory (DFT) calculations. The degree of ruffling in the heme cofactor of Hydrogenobacter thermophilus cytochrome c(552) has been modified by a single amino acid mutation in the second coordination sphere of the cofactor. The (13)C and (1)H resonances of the cofactor have been assigned using one- and two-dimensional NMR spectroscopy aided by selective (13)C-enrichment of the heme. DFT has been used to predict the NMR hyperfine shifts and electron paramagnetic resonance (EPR) g-tensor at several points along the ruffling deformation coordinate. The DFT-predicted NMR and EPR parameters agree with the experimental observations, confirming that an accurate theoretical model of the electronic structure and its response to ruffling has been established. As the degree of ruffling increases, the heme methyl (1)H resonances move upfield while the heme methyl and meso (13)C resonances move downfield. These changes are a consequence of altered overlap of the Fe 3d and porphyrin pi orbitals, which destabilizes all three occupied Fe 3d-based molecular orbitals and decreases the positive and negative spin density on the beta-pyrrole and meso carbons, respectively. Consequently, the heme ruffling deformation decreases the electronic coupling of the cofactor with external redox partners and lowers the reduction potential of heme.
Collapse
Affiliation(s)
- Matthew D Liptak
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
| | | | | |
Collapse
|
27
|
Zoppellaro G, Bren KL, Ensign AA, Harbitz E, Kaur R, Hersleth HP, Ryde U, Hederstedt L, Andersson KK. Review: studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with bis-histidine and histidine-methionine axial iron coordination. Biopolymers 2009; 91:1064-82. [PMID: 19536822 PMCID: PMC2852197 DOI: 10.1002/bip.21267] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Six-coordinated heme groups are involved in a large variety of electron transfer reactions because of their ability to exist in both the ferrous (Fe(2+)) and ferric (Fe(3+)) state without any large differences in structure. Our studies on hemes coordinated by two histidines (bis-His) and hemes coordinated by histidine and methionine (His-Met) will be reviewed. In both of these coordination environments, the heme core can exhibit ferric low spin (electron paramagnetic resonance EPR) signals with large g(max) values (also called Type I, highly anisotropic low spin, or highly axial low spin, HALS species) as well as rhombic EPR (Type II) signals. In bis-His coordinated hemes rhombic and HALS envelopes are related to the orientation of the His groups with respect to each other such that (i) parallel His planes results in a rhombic signal and (ii) perpendicular His planes results in a HALS signal. Correlation between the structure of the heme and its ligands for heme with His-Met axial ligation and ligand-field parameters, as derived from a large series of cytochrome c variants, show, however, that for such a combination of axial ligands there is no clear-cut difference between the large g(max) and the "small g-anisotropy" cases as a result of the relative Met-His arrangements. Nonetheless, a new linear correlation links the average shift delta of the heme methyl groups with the g(max) values.
Collapse
Affiliation(s)
- Giorgio Zoppellaro
- Department of Molecular Biosciences, University of Oslo, PO Box 1041 Blindern, Oslo NO–0316, Norway
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, New York 146270216, USA
| | - Amy A. Ensign
- Department of Chemistry, University of Rochester, Rochester, New York 146270216, USA
| | - Espen Harbitz
- Department of Molecular Biosciences, University of Oslo, PO Box 1041 Blindern, Oslo NO–0316, Norway
| | - Ravinder Kaur
- Department of Chemistry, University of Rochester, Rochester, New York 146270216, USA
| | - Hans-Petter Hersleth
- Department of Molecular Biosciences, University of Oslo, PO Box 1041 Blindern, Oslo NO–0316, Norway
| | - Ulf Ryde
- Department Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE–221 00 Lund, Sweden
| | - Lars Hederstedt
- Department of Cell & Organism Biology, Lund University, Sölvegatan 35, SE–22362 Lund, Sweden
| | - K. Kristoffer Andersson
- Department of Molecular Biosciences, University of Oslo, PO Box 1041 Blindern, Oslo NO–0316, Norway
| |
Collapse
|