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Harper-Leatherman AS, Wallace JM, Long JW, Rhodes CP, Graffam ME, Abunar BH, Rolison DR. Redox Cycling within Nanoparticle-Nucleated Protein Superstructures: Electron Transfer between Nanoparticulate Gold, Molecular Reductant, and Cytochrome c. J Phys Chem B 2021; 125:1735-1745. [PMID: 33576630 DOI: 10.1021/acs.jpcb.0c09688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We previously described how thousands of the heme protein cytochrome c (cyt.c) self-organize into multilayered, roughly spherical superstructures as initiated by nucleation around one colloidal gold or silver nanoparticle. Within these superstructures, the protein is stabilized to unfolding in buffered media and survives superstructure encapsulation within silica gels and processing to form bioaerogels. We now report that Au∼cyt.c superstructures in buffered media are not simply static groupings of proteins, but that the Au core and protein corona exhibit dynamic electron-transfer reactions within the superstructure as verified by UV-visible and resonance Raman spectroscopy. Within the superstructure, hundreds to thousands of ferricytochrome c (FeIII-cyt.c) are reduced to ferrocytochrome c (FeII-cyt.c) following first-order kinetics with an average apparent forward rate constant of 1.9 ±0.4 × 10-5 s-1. The reducing power in the microheterogeneous medium is derived from two multielectron reductants: tannic acid used to stabilize the commercial gold sol and the Au nanoparticle at the center of the protein superstructure. Fluorescence monitoring of guanidinium chloride-induced unfolding reveals that superstructure-associated cyt.c is stabilized to unfolding before and after chemical reduction of FeIII-cyt.c to form FeII-cyt.c, indicating that the superstructures remain intact during microheterogeneous redox reactions. Smaller nucleating Au nanoparticles or lower ionic strength in the buffered medium yields a greater extent of cyt.c reduction. Partial oxidation of the cyt.c-associated nanoparticulate Au is verified by X-ray photoelectron spectroscopy. The Au nanoparticle at the heart of the superstructure functions as a direct electron donor to the heme with oxidized Au atoms being recycled back to Au(0) as long as residual tannic acid, derived from the Au sol mother liquor, is present in the aqueous microheterogeneous medium.
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Affiliation(s)
- Amanda S Harper-Leatherman
- Department of Chemistry and Biochemistry, Fairfield University, 1073 North Benson Road, Fairfield, Connecticut 06824, United States
| | - Jean Marie Wallace
- Nova Research, Inc., 1900 Elkin Street, Alexandria, Virginia 22308, United States
| | - Jeffrey W Long
- Surface Chemistry Branch, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Christopher P Rhodes
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
| | - Molly E Graffam
- Department of Chemistry and Biochemistry, Fairfield University, 1073 North Benson Road, Fairfield, Connecticut 06824, United States
| | - Bayan H Abunar
- Department of Chemistry and Biochemistry, Fairfield University, 1073 North Benson Road, Fairfield, Connecticut 06824, United States
| | - Debra R Rolison
- Surface Chemistry Branch, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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2
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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3
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Kubryk P, Kölschbach JS, Marozava S, Lueders T, Meckenstock RU, Niessner R, Ivleva NP. Exploring the Potential of Stable Isotope (Resonance) Raman Microspectroscopy and Surface-Enhanced Raman Scattering for the Analysis of Microorganisms at Single Cell Level. Anal Chem 2015; 87:6622-30. [DOI: 10.1021/acs.analchem.5b00673] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Patrick Kubryk
- Technische Universität München, Institute
of Hydrochemistry, Chair for Analytical Chemistry, Marchioninistr. 17, 81377 Munich, Germany
| | - Janina S. Kölschbach
- Helmholtz Zentrum München, Institute of Groundwater
Ecology, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
| | - Sviatlana Marozava
- Helmholtz Zentrum München, Institute of Groundwater
Ecology, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
| | - Tillmann Lueders
- Helmholtz Zentrum München, Institute of Groundwater
Ecology, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
| | - Rainer U. Meckenstock
- Helmholtz Zentrum München, Institute of Groundwater
Ecology, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
| | - Reinhard Niessner
- Technische Universität München, Institute
of Hydrochemistry, Chair for Analytical Chemistry, Marchioninistr. 17, 81377 Munich, Germany
| | - Natalia P. Ivleva
- Technische Universität München, Institute
of Hydrochemistry, Chair for Analytical Chemistry, Marchioninistr. 17, 81377 Munich, Germany
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4
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Luck M, Bruun S, Keidel A, Hegemann P, Hildebrandt P. Photochemical chromophore isomerization in histidine kinase rhodopsin HKR1. FEBS Lett 2015; 589:1067-71. [DOI: 10.1016/j.febslet.2015.03.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 03/20/2015] [Indexed: 11/26/2022]
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5
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Surface-enhanced resonance Raman scattering (SERRS) as a tool for the studies of electron transfer proteins attached to biomimetic surfaces: Case of cytochrome c. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2013.08.140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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6
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Heme-protein vibrational couplings in cytochrome c provide a dynamic link that connects the heme-iron and the protein surface. Proc Natl Acad Sci U S A 2012; 109:8896-900. [PMID: 22619327 DOI: 10.1073/pnas.1200345109] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The active site of cytochrome c (Cyt c) consists of a heme covalently linked to a pentapeptide segment (Cys-X-X-Cys-His), which provides a link between the heme and the protein surface, where the redox partners of Cyt c bind. To elucidate the vibrational properties of heme c, nuclear resonance vibrational spectroscopy (NRVS) measurements were performed on (57)Fe-labeled ferric Hydrogenobacter thermophilus cytochrome c(552), including (13)C(8)-heme-, (13)C(5)(15)N-Met-, and (13)C(15)N-polypeptide (pp)-labeled samples, revealing heme-based vibrational modes in the 200- to 450-cm(-1) spectral region. Simulations of the NRVS spectra of H. thermophilus cytochrome c(552) allowed for a complete assignment of the Fe vibrational spectrum of the protein-bound heme, as well as the quantitative determination of the amount of mixing between local heme vibrations and pp modes from the Cys-X-X-Cys-His motif. These results provide the basis to propose that heme-pp vibrational dynamic couplings play a role in electron transfer (ET) by coupling vibrations of the heme directly to vibrations of the pp at the protein-protein interface. This could allow for the direct transduction of the thermal (vibrational) energy from the protein surface to the heme that is released on protein/protein complex formation, or it could modulate the heme vibrations in the protein/protein complex to minimize reorganization energy. Both mechanisms lower energy barriers for ET. Notably, the conformation of the distal Met side chain is fine-tuned in the protein to localize heme-pp mixed vibrations within the 250- to 400-cm(-1) spectral region. These findings point to a particular orientation of the distal Met that maximizes ET.
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7
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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: 21] [Impact Index Per Article: 1.4] [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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8
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Pätzold R, Keuntje M, Theophile K, Müller J, Mielcarek E, Ngezahayo A, Anders-von Ahlften A. In situ mapping of nitrifiers and anammox bacteria in microbial aggregates by means of confocal resonance Raman microscopy. J Microbiol Methods 2008; 72:241-8. [DOI: 10.1016/j.mimet.2007.12.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Revised: 12/09/2007] [Accepted: 12/10/2007] [Indexed: 11/30/2022]
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9
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Tripathi A, Jabbour RE, Treado PJ, Neiss JH, Nelson MP, Jensen JL, Snyder AP. Waterborne pathogen detection using Raman spectroscopy. APPLIED SPECTROSCOPY 2008; 62:1-9. [PMID: 18230198 DOI: 10.1366/000370208783412546] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Raman spectroscopy is being evaluated as a candidate technology for waterborne pathogen detection. We have investigated the impact of key experimental and background interference parameters on the bacterial species level identification performance of Raman detection. These parameters include laser-induced photodamage threshold, composition of water matrix, and organism aging in water. The laser-induced photodamage may be minimized by operating a 532 nm continuous wave laser excitation at laser power densities below 2300 W/cm(2) for Grampositive Bacillus atrophaeus (formerly Bacillus globigii, BG) vegetative cells, 2800 W/cm(2) for BG spores, and 3500 W/cm(2) for Gram-negative E. coli (EC) organisms. In general, Bacillus spore microorganism preparations may be irradiated with higher laser power densities than the equivalent Bacillus vegetative preparations. In order to evaluate the impact of background interference and organism aging, we selected a biomaterials set comprising Gram-positive (anthrax simulants) organisms, Gram-negative (plague simulant) organisms, and proteins (toxin simulants) and constructed a Raman signature classifier that identifies at the species level. Subsequently, we evaluated the impact of tap water and storage time in water (aging) on the classifier performance when characterizing B. thuringiensis spores, BG spores, and EC cell preparations. In general, the measured Raman signatures of biological organisms exhibited minimal spectral variability with respect to the age of a resting suspension and water matrix composition. The observed signature variability did not substantially degrade discrimination performance at the genus and species levels. In addition, Raman chemical imaging spectroscopy was used to distinguish a mixture of BG spores and EC cells at the single cell level.
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Affiliation(s)
- Ashish Tripathi
- Science Applications International Corp., P.O. Box 68, Gunpowder Branch, Aberdeen Proving Ground, Maryland 21010-5424, USA
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de Vitry C, Desbois A, Redeker V, Zito F, Wollman FA. Biochemical and spectroscopic characterization of the covalent binding of heme to cytochrome b6. Biochemistry 2004; 43:3956-68. [PMID: 15049703 DOI: 10.1021/bi036093p] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The three-dimensional structure of the cytochrome b(6)f complex disclosed the unexpected presence of a new heme c(i) [Stroebel, D., Choquet, Y., Popot, J.-L., and Picot, D. (2003) Nature 426, 413-418; Kurisu, G., Zhang, H., Smith, J. L., and Cramer, W. A. (2003) Science 302, 1009-1014]. Here we present a biochemical, spectroscopic, and mutagenesis study of this unusual heme binding in Chlamydomonas reinhardtii. As predicted by the structure data, we identify a Cys(35)-containing proteolytic fragment (Tyr(25)-Lys(111)) from cytochrome b(6) as a peptide that covalently binds a heme. Resonance Raman spectra of cyt b(6)f complexes show particular frequencies in nu(2), nu(3), nu(4), and nu(8) regions that identify this extra heme as a ferrous c'-like heme under a five-coordinated high-spin state. The set of frequencies is consistent with a coordination by either a water molecule or a hydroxide ion. Other changes in resonance Raman bands, observed in the mid- and low-frequency regions, point to a modification in conformation and/or environment of at least one b heme methyl and/or propionate group. Site-directed mutagenesis of apocytochrome b(6), leading to a Cys(35)Val substitution, generates Chlamydomonas strains that are unable to assemble cytochrome b(6)f complexes. On the basis of the mutant phenotype, we discuss the participation, in the covalent binding of heme c(i), of the nuclear CCB factors that we identified previously as controlling the apo to holo conversion of cytochrome b(6) [Kuras, R., de Vitry, C., Choquet, Y., Girard-Bascou, J., Culler, D., Büschlen, S., Merchant, S., and Wollman, F.-A. (1997) J. Biol. Chem. 272, 32427-32435].
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Affiliation(s)
- Catherine de Vitry
- Physiologie Membranaire et Moléculaire du Chloroplaste CNRS UPR 1261, Institut de Biologie Physico-Chimique CNRS FRC 550, 13 Rue Pierre et Marie Curie, 75005 Paris, France.
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11
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Oellerich S, Wackerbarth H, Hildebrandt P. Conformational equilibria and dynamics of cytochrome c induced by binding of sodium dodecyl sulfate monomers and micelles. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2003; 32:599-613. [PMID: 12768249 DOI: 10.1007/s00249-003-0306-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2002] [Revised: 04/07/2003] [Accepted: 04/07/2003] [Indexed: 10/26/2022]
Abstract
Circular dichroism, nuclear magnetic resonance, electron paramagnetic resonance, UV-vis absorption, and resonance Raman (RR) spectroscopic techniques were employed to study protein and heme structural changes of cytochrome c (Cyt-c) induced by sodium dodecyl sulfate (SDS) monomers and micelles via hydrophobic and electrostatic interactions, respectively. Both modes of interactions cause the transition to the conformational state B2, which is implicated to be involved in the physiological processes of Cyt-c. At sub-micellar concentrations of SDS, specific binding of only ca. three SDS monomers, which is likely to occur at the hydrophobic peptide segment 81-85, is sufficient for a complete conversion to a B2 state in which Met80 is replaced by His33 (His26). These heme pocket structural changes are not linked to secondary structure changes of the protein brought about by nonspecific binding of SDS monomers in different regions of the protein. Upon binding of micelles, B2 high-spin species can also be stabilized by electrostatic interactions. In addition, the micelle interaction domain is located on the front surface of Cyt-c, which includes a ring-like arrangement of lysine residues appropriate for binding one micelle. According to freeze-quench RR and stopped-flow experiments, state B2 is formed on the long millisecond timescale and reveals a complex dependence on the SDS concentration that can be interpreted in terms of competitive binding of monomers and micelles.
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Affiliation(s)
- Silke Oellerich
- Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34-36, 45470 Mulheim, Germany
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12
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Lushington GH, Cowley AB, Silchenko S, Lukat-Rodgers GS, Rodgers KR, Benson DR. Comparison of Thioethers and Sulfoxides as Axial Ligands for N-Acetylmicroperoxidase-8: Implications for Oxidation of Methionine-80 in Cytochrome c. Inorg Chem 2003; 42:7550-9. [PMID: 14606851 DOI: 10.1021/ic034689v] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methionine-80 (Met-80) in mitochondrial cytochrome c (cyt c) can be oxidized to the corresponding sulfoxide by reactive oxygen species, a reaction of potential biological significance. As an approach to investigating how oxidation of Met-80 would influence its interactions with heme iron, we have examined binding of 2-(methylthio)ethanol (MTE) and dimethyl sulfoxide (DMSO), models for the side chains of Met and Met(SO), respectively, to ferrous and ferric N-acetylmicroperoxidase-8 (AcMP8). We find that DMSO coordinates 1.2 kcal/mol less strongly to Fe(III)-AcMP8 than does MTE, although both ligands form low-spin complexes. Comparison of spectroscopic data for the DMSO complex of Fe(III)-AcMP8 with published data for the Met(SO)-80 form of ferric cyt c allows us to conclude that Met(SO)-80 does not coordinate to iron in the latter. DMSO coordinates to Fe(II)-AcMP8 1.3 kcal/mol more strongly than does MTE, whereas Met-80 and Met(SO)-80 are reported to have approximately equal affinity for Fe(II) in cyt c. This result suggests that the steric environment near the heme iron in cyt c discriminates against coordination of Met(SO)-80. Vacuum quantum chemical density functional theory calculations confirm the greater affinity of the sulfoxide and show that coordination via oxygen is strongly favored. Resonance Raman spectroscopic data indicate that the preference for coordination via oxygen is maintained in solution. The computational data further indicate that the DMSO complex derives significant enthalpic stabilization from pi back-bonding but that iron to sulfur pi back-bonding does not make a significant contribution to bonding in the thioether complex.
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14
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Gao F, Qin H, Knaff DB, Zhang L, Yu L, Yu CA, Gray KA, Daldal F, Ondrias MR. Q-Band resonance Raman investigation of turnip cytochrome f and Rhodobacter capsulatus cytochrome c1. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1430:203-13. [PMID: 10082948 DOI: 10.1016/s0167-4838(98)00284-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The results of a comprehensive Q-band resonance Raman investigation of cytochrome c1 and cytochrome f subunits of bc1 and b6f complexes are presented. Q-band excitation provides a particularly effective probe of the local heme environments of these species. The effects of protein conformation (particularly axial ligation) on heme structure and function were further investigated by comparison of spectra obtained from native subunits to those of a site directed c1 mutant (M183L) and various pH-dependent species of horse heart cytochrome c. In general, all species examined displayed variability in their axial amino acid ligation that suggests a good deal of flexibility in their hemepocket conformations. Surprisingly, the large scale protein rearrangements that accompany axial ligand replacement have little or no effect on macrocycle geometry in these species. This indicates the identity and/or conformation of the peptide linkage between the two cysteines that are covalently linked to the heme periphery may determine heme geometry.
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Affiliation(s)
- F Gao
- Department of Chemistry, University of New Mexico, Albuquerque, NM 87131, USA
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15
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Keating CD, Kovaleski KM, Natan MJ. Protein:Colloid Conjugates for Surface Enhanced Raman Scattering: Stability and Control of Protein Orientation. J Phys Chem B 1998. [DOI: 10.1021/jp982723z] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Keating CD, Kovaleski KK, Natan MJ. Heightened Electromagnetic Fields between Metal Nanoparticles: Surface Enhanced Raman Scattering from Metal−Cytochromec-Metal Sandwiches. J Phys Chem B 1998. [DOI: 10.1021/jp982724r] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Döpner S, Hildebrandt P, Rosell FI, Mauk AG. Alkaline Conformational Transitions of Ferricytochrome c Studied by Resonance Raman Spectroscopy. J Am Chem Soc 1998. [DOI: 10.1021/ja9717572] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Susanne Döpner
- Contribution from the Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Federal Republic of Germany, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Peter Hildebrandt
- Contribution from the Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Federal Republic of Germany, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Federico I. Rosell
- Contribution from the Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Federal Republic of Germany, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - A. Grant Mauk
- Contribution from the Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Federal Republic of Germany, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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18
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Gao F, Qin H, Knaff DB, Zhang L, Yu L, Yu CA, Ondrias MR. Q-band resonance Raman spectra of oxidized and reduced mitochondrial bc1 complexes. Biochemistry 1998; 37:9751-8. [PMID: 9657688 DOI: 10.1021/bi9800653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Recently published crystallographic studies of mitochondrial bc1 complexes have stimulated renewed interest in the active site architecture of these important integral membrane proteins. We present resonance Raman spectra obtained via variable excitation within the heme Q-band from samples poised in several different net redox states. Appropriate subtraction and polarization analysis allows the vibrational behavior of the individual heme bL,bH, and c1 sites to be assessed. The spectra of the b hemes are particularly noteworthy. They exhibit evidence for a protonation equilibrium involving heme axial ligands and reveal a marked structural heterogeneity at the heme bH site that most likely involves nonplanar distortions of the macrocycle. The possible implications of these findings for heme functionality are discussed.
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Affiliation(s)
- F Gao
- Department of Chemistry, University of New Mexico, Albuquerque 87131 USA
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19
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Laberge M, Vreugdenhil AJ, Vanderkooi JM, Butler IS. Microperoxidase-11: molecular dynamics and Q-band excited resonance Raman of the oxidized, reduced and carbonyl forms. J Biomol Struct Dyn 1998; 15:1039-50. [PMID: 9669550 DOI: 10.1080/07391102.1998.10508999] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Resonance Raman spectra with Q-band excitation are reported for microperoxidase-11, the cytochrome c analog. Spectra were acquired in the mid-frequency range for the oxidized, and reduced forms of the undecapeptide, as well as for the imidazole and carbonyl complexes. Oxidation and spin state marker bands of the undecapeptides are consistent with a six-coordinate, low spin iron in both oxidation states. Porphyrin core size correlations yield a porphyrin-centre to pyrrole-nitrogen distance of 2.00 A for MP11, suggestive of a six-coordinate species in a distorted heme environment. Molecular dynamics results show that the non-planarity of the heme of the parent cytochrome is conserved in the microperoxidase and its carbonmonoxy analog.
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Affiliation(s)
- M Laberge
- Johnson Research Foundation, Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia 19104, USA.
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20
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Othman S, Fitch J, Cusanovich MA, Desbois A. Influence of conserved amino acids on the structure and environment of the heme of cytochrome c2. A resonance Raman study. Biochemistry 1997; 36:5499-508. [PMID: 9154933 DOI: 10.1021/bi962584g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Resonance Raman spectra using Soret excitations of oxidized and reduced Rhodobacter capsulatus cytochrome c2 at pH 7.5 were studied. The spectra of oxidized cytochrome c2 show three components for the v10 mode at 1638, 1633, and 1629 cm(-1). The intensities of these components are sensitive to the excitation wavelength. This effect is explained in the context of a conformational equilibrium of the ferriheme between a nearly planar structure and two ruffled structures. In the case of reduced cytochrome c2, the absolute frequencies as well as the excitation-dependent frequency dispersion of the v10 mode (1618-1621 cm(-1)) indicate a displacement of the conformational equilibrium of heme toward the more planar structures. To measure the influence of some key amino acid residues on the heme-protein interaction of cytochrome c2, four site-directed mutants of Rb. capsulatus cytochrome c2 have been studied by resonance Raman spectroscopy and their spectra compared with the spectra obtained for the wild type cytochrome. The mutants studied are K14E/K32E, P35A, W67Y, and Y75F. The spectral changes induced by the mutations are interpreted in terms of alterations in the structure and/or environment of the cytochrome c2 heme in the framework of the expected role of the different amino acid residues in the stability and redox potential.
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Affiliation(s)
- S Othman
- Département de Biologie Cellulaire et Moléculaire, CEA et CNRS-URA 2096, CEA/Saclay, Gif-sur-Yvette, France
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Abstract
This paper provides an overview of the usefulness of the resonance Raman (RR) spectroscopy in the determination of the structural and electronic properties of heme(s) included in c-type cytochromes. It reviews the mode assignments presently available for heme c and includes recent RR data on the most important subclasses of c-type cytochromes. It also describes the effects of cytochrome c-oxidase and cytochrome c-reductase associations on the heme vibrational modes of the bound cytochrome c.
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Affiliation(s)
- A Desbois
- Département de Biologie Cellulaire et Moléculaire, Centre d'Etudes de Saclay, Gif-sur-Yvette, France
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22
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Othman S, Le Lirzin A, Desbois A. A heme c-peptide model system for the resonance Raman study of c-type cytochromes: characterization of the solvent-dependence of peptide-histidine-heme interactions. Biochemistry 1993; 32:9781-91. [PMID: 8396971 DOI: 10.1021/bi00088a033] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The visible absorption and Soret-excited resonance Raman spectra of ferrous microperoxidase-8 [MP8(II)], an octapeptide containing a heme c, are reported. These spectroscopies indicate that MP8(II), dissolved in aqueous buffered solutions, forms low-spin six-coordinated complexes in the 7-14 pH range. Intermolecular bonding interactions of MP8(II) in water account for this behavior. On the contrary, when the hemopeptide is dispersed in aqueous solutions containing detergent or an alcohol, the spectroscopic data show that the iron atom of MP8(II) is essentially high-spin five-coordinated in accordance with a monomeric structure of MP8(II). In addition to a high-spin signature to the heme skeletal modes, the high-frequency regions of resonance Raman spectra characterize an electronic influence of the thioether bridges on the frequency of stretching modes of C beta-C beta bonds (nu 2, nu 11, and nu 29). On the other hand, the low-frequency Raman spectra of monomeric MP8(II) at pH 7.5 present significant differences in the 150-250-cm-1 regions depending upon the solvent composition (pH, presence or absence of detergent, alcohol). These effects are attributed to frequency variations of the Fe-N(His)-involving mode which indicate changes in the H-bonding interactions of the axial His and therefore solvent-dependent changes of the octapeptide conformation. Our resonance Raman data further show that the axial His of monomeric MP8(II) could be totally deprotonated in aqueous cetyltrimethylammonium bromide solution at very alkaline pH (pKa = 13.3). The vibrational data (100-1700 cm-1) obtained for the various monomeric forms of MP8(II) are expected to be useful for determining the heme structure and environment in reduced c'-type cytochromes. Comparisons of resonance Raman data with X-ray crystallographic data available for different hemoproteins allow us to evaluate the ionization and H-bonding states of the His bound to the high-spin five-coordinated hemes. These data are discussed in terms of proximal influence of protein-His-heme interactions on the determination and the regulation of a particular biological function.
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Affiliation(s)
- S Othman
- Département de Biologie Cellulaire et Moléculaire, Centre d'Etudes de Saclay, Gif-sur-Yvette, France
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23
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Hobbs JD, Wynn M, Nunez DJ, Malkin R, Knaff DB, Ondrias MR. Structural characterization of heme sites in spinach cytochrome b6f complexes: a resonance Raman study. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1059:37-44. [PMID: 1873297 DOI: 10.1016/s0005-2728(05)80185-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Resonance Raman spectra of cytochrome b6f complexes isolated from spinach chloroplasts have been obtained. Selective resonance enhancements and partial reductions of the complex by redox mediators were used to isolate and identify the contributions of heme b6 and heme f sites to the observed spectra. Corresponding spectra for turnip cytochrome f have also been obtained. Power-dependent photoreduction was observed in cytochrome f of the complex as well as in the isolated cytochrome f during the course of the Raman experiments.
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Affiliation(s)
- J D Hobbs
- Department of Chemistry, University of New Mexico, Albuquerque 87131
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24
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Cartling B. A stochastic model of protein conformational dynamics and electronic–conformational coupling in biological energy transduction. J Chem Phys 1985. [DOI: 10.1063/1.449737] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Cartling B, Holtom GR, Spiro TG. Photoelectron generation and transfer to cytochromecstudied by nanosecond transient absorption spectroscopy. J Chem Phys 1985. [DOI: 10.1063/1.449101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Spiro TG. Resonance Raman spectroscopy as a probe of heme protein structure and dynamics. ADVANCES IN PROTEIN CHEMISTRY 1985; 37:111-59. [PMID: 2998161 DOI: 10.1016/s0065-3233(08)60064-9] [Citation(s) in RCA: 104] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Our understanding of metalloporphyrin resonance Raman spectra has advanced to the point where it is possible to obtain detailed information about the structure of the heme group in situ in heme proteins. The porphyrin skeletal mode frequencies can be analyzed in terms of the ligation and spin state of the heme and may provide information about protein-induced stresses. The high-frequency region of the spectrum also contains bands due to vibrations of the porphyrin peripheral substituents, which are potentially monitors of the protein contacts. In the low-frequency region, it is possible to locate bands, at least in some states of the heme protein, which are associated with vibrations of the axial ligands. They give direct information about the nature of the bonding to exogenous ligands or to the proximal protein residue. Thus, a variety of evidence is potentially available in the resonance Raman spectra from which a fairly complete picture of the heme site can be assembled for a particular protein in its various functional states. Detailed studies have been pursued for paradigmatic heme proteins, including myoglobin, hemoglobin, cytochrome c, horseradish peroxidase, and cytochrome oxidase. These studies provide a substantial data base from which the exploration of lesser known systems can be launched. Another extension of current knowledge to new frontiers is in the time domain, since pulsed lasers now make it feasible to carry out time-resolved resonance Raman studies on heme protein reactions. Time-resolved resonance Raman spectroscopy is capable of elucidating the temporal evolution of heme structure and provides a link between heme chemistry and protein dynamics. This link is being elucidated for hemoglobin and cytochrome c, where specific heme intermediates have been identified following ligand photodissociation or electron transfer.
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27
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Terner J, Reed DE. Resonance raman spectroscopic characterization of the heme coordination and spin state in the alkaline form of horseradis peroxidase. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/0167-4838(84)90064-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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