1
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Gaffney KJ. Capturing photochemical and photophysical transformations in iron complexes with ultrafast X-ray spectroscopy and scattering. Chem Sci 2021; 12:8010-8025. [PMID: 34194691 PMCID: PMC8208315 DOI: 10.1039/d1sc01864g] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/25/2021] [Indexed: 12/31/2022] Open
Abstract
Light-driven chemical transformations provide a compelling approach to understanding chemical reactivity with the potential to use this understanding to advance solar energy and catalysis applications. Capturing the non-equilibrium trajectories of electronic excited states with precision, particularly for transition metal complexes, would provide a foundation for advancing both of these objectives. Of particular importance for 3d metal compounds is characterizing the population dynamics of charge-transfer (CT) and metal-centered (MC) electronic excited states and understanding how the inner coordination sphere structural dynamics mediate the interaction between these states. Recent advances in ultrafast X-ray laser science has enabled the electronic excited state dynamics in 3d metal complexes to be followed with unprecedented detail. This review will focus on simultaneous X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS) studies of iron coordination and organometallic complexes. These simultaneous XES-XSS studies have provided detailed insight into the mechanism of light-induced spin crossover in iron coordination compounds, the interaction of CT and MC excited states in iron carbene photosensitizers, and the mechanism of Fe-S bond dissociation in cytochrome c.
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Affiliation(s)
- Kelly J Gaffney
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Stanford University Menlo Park California 94025 USA
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2
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Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c. Nat Commun 2021; 12:1086. [PMID: 33597529 PMCID: PMC7889893 DOI: 10.1038/s41467-021-21423-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
The dynamics of photodissociation and recombination in heme proteins represent an archetypical photochemical reaction widely used to understand the interplay between chemical dynamics and reaction environment. We report a study of the photodissociation mechanism for the Fe(II)-S bond between the heme iron and methionine sulfur of ferrous cytochrome c. This bond dissociation is an essential step in the conversion of cytochrome c from an electron transfer protein to a peroxidase enzyme. We use ultrafast X-ray solution scattering to follow the dynamics of Fe(II)-S bond dissociation and 1s3p (Kβ) X-ray emission spectroscopy to follow the dynamics of the iron charge and spin multiplicity during bond dissociation. From these measurements, we conclude that the formation of a triplet metal-centered excited state with anti-bonding Fe(II)-S interactions triggers the bond dissociation and precedes the formation of the metastable Fe high-spin quintet state.
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3
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Ko YK, Yabushita A, Kobayashi T. Primary Electronic and Vibrational Dynamics of Cytochrome c Observed by Sub-10 fs NUV Laser Pulses. J Phys Chem B 2020; 124:8249-8258. [PMID: 32852960 DOI: 10.1021/acs.jpcb.0c05959] [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
The primary reaction mechanism of cytochrome c (Cyt c) was elucidated for two redox forms of ferric (oxidized) and ferrous (reduced) Cyt c by measuring their transient absorption (TA) spectra using a homemade sub-10 fs broadband NUV laser pulses system. The TA traces measured in the broad probe wavelength region were analyzed by the global analysis method to study the electronic dynamics. The difference of relaxation dynamics dependent on the excitation bandwidth enabled us to elucidate that the 2.5 ps component in ferrous Cyt c can be assigned to intramolecular vibration energy redistribution and not to vibrational cooling, which was not clear until this work. The temporal resolution of 10 fs observes TA signal modulation caused by the molecular vibration in the time domain, which can be used to calculate the instantaneous frequency of the molecular vibration mode. The observed vibrational dynamics has visualized that the heme structure changes in 0.8 ps for ferric Cyt c and in >1.0 ps for ferrous Cyt c. These estimated lifetimes of vibrational dynamics reflect vibrational relaxation in the ground state of ferric Cyt c and electronic transition from the S2 state to the S1 state in ferrous Cyt c, respectively.
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Affiliation(s)
- Ying Kuan Ko
- Department of Electrophysics, National Chiao-Tung University, Hsinchu 300, Taiwan, R.O.C
| | - Atsushi Yabushita
- Department of Electrophysics, National Chiao-Tung University, Hsinchu 300, Taiwan, R.O.C
| | - Takayoshi Kobayashi
- Department of Electrophysics, National Chiao-Tung University, Hsinchu 300, Taiwan, R.O.C
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4
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Négrerie M. Iron transitions during activation of allosteric heme proteins in cell signaling. Metallomics 2020; 11:868-893. [PMID: 30957812 DOI: 10.1039/c8mt00337h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.
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Affiliation(s)
- Michel Négrerie
- Laboratoire d'Optique et Biosciences, INSERM, CNRS, Ecole Polytechnique, 91120 Palaiseau, France.
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5
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Ferrante C, Batignani G, Pontecorvo E, Montemiglio LC, Vos MH, Scopigno T. Ultrafast Dynamics and Vibrational Relaxation in Six-Coordinate Heme Proteins Revealed by Femtosecond Stimulated Raman Spectroscopy. J Am Chem Soc 2020; 142:2285-2292. [PMID: 31917551 PMCID: PMC7735705 DOI: 10.1021/jacs.9b10560] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Identifying
the structural rearrangements during photoinduced reactions is a fundamental
challenge for understanding from a microscopic perspective the dynamics
underlying the functional mechanisms of heme proteins. Here, femtosecond
stimulated Raman spectroscopy is applied to follow the ultrafast evolution
of two different proteins, each bearing a six-coordinate heme with
two amino acid axial ligands. By exploiting the sensitivity of Raman
spectra to the structural configuration, we investigate the effects
of photolysis and the binding of amino acid residues in cytochrome c and neuroglobin. By comparing the system response for
different time delays and Raman pump resonances, we show how detailed
properties of atomic motions and energy redistribution can be unveiled.
In particular, we demonstrate substantially faster energy flow from
the dissociated heme to the protein moiety in cytochrome c, which we assign to the presence of covalent heme–protein
bonds.
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Affiliation(s)
- Carino Ferrante
- Center for Life Nano Science @Sapienza , Istituto Italiano di Tecnologia , Rome I-00161 , Italy
| | | | | | | | - Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM , Institut Polytechnique de Paris , 91128 Palaiseau , France
| | - Tullio Scopigno
- Center for Life Nano Science @Sapienza , Istituto Italiano di Tecnologia , Rome I-00161 , Italy
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6
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Benabbas A, Champion PM. Adiabatic Ligand Binding in Heme Proteins: Ultrafast Kinetics of Methionine Rebinding in Ferrous Cytochrome c. J Phys Chem B 2018; 122:11431-11439. [PMID: 30230843 DOI: 10.1021/acs.jpcb.8b07355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of methionine geminate recombination following photodissociation in ferrous cytochrome c is investigated over a broad temperature range. The kinetic response, above the solvent glass transition ( Tg), is nearly monoexponential and displays a weak temperature dependence. Below Tg, the rebinding kinetics are nonexponential and can be explained using a quenched distribution of enthalpic rebinding barriers, arising from a relatively narrow distribution of heme out-of-plane displacements. The Arrhenius prefactor of this (Δ S = 2) reaction is ∼1011 s-1, which is similar to what has been found for the (Δ S = 1) NO binding reaction in heme proteins. This observation, along with other examples of ultrafast CO binding, provides strong evidence that ligand binding to heme is an adiabatic reaction with a spin-independent prefactor. In order to simultaneously account for the adiabatic nature of the reaction as well as the temperature dependence of both ultrafast CO and methionine geminate rebinding, it is proposed that a spin triplet state intersects and strongly couples to the reactant ( S = 2) and product ( S = 0) state surfaces in the transition state region along the reaction coordinate. It is also suggested that the nature of the intersecting triplet state and the reaction path may depend upon the proximity of the photolyzed ligand relative to the iron atom. At temperatures below ∼60 K, the kinetic data suggest that there is either an unexpected retardation of the heme photoproduct relaxation or that heavy atom quantum mechanical tunneling becomes significant.
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Affiliation(s)
- Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Paul M Champion
- Department of Physics and Center for Interdisciplinary Research on Complex Systems , Northeastern University , Boston , Massachusetts 02115 , United States
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7
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Vos MH, Reeder BJ, Daldal F, Liebl U. Ultrafast photochemistry of the bc 1 complex. Phys Chem Chem Phys 2018; 19:6807-6813. [PMID: 28218331 DOI: 10.1039/c7cp00193b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present a full investigation of ultrafast light-induced events in the membraneous cytochrome bc1 complex by transient absorption spectroscopy. This energy-transducing complex harbors four redox-active components per monomer: heme c1, two 6-coordinate b-hemes and a [2Fe-2S] cluster. Using excitation of these components in different ratios under various excitation conditions, probing in the full visible range and under three well-defined redox conditions, we demonstrate that for all ferrous hemes of the complex photodissociation of axial ligands takes place and that they rebind in 5-7 ps, as in other 6-coordinate heme proteins, including cytoglobin, which is included as a reference in this study. By contrast, the signals are not consistent with photooxidation of the b hemes. This conclusion contrasts with a recent assessment based on a more limited data set. The binding kinetics of internal and external ligands are indicative of a rigid heme environment, consistent with the electron transfer function. We also report, for the first time, photoactivity of the very weakly absorbing iron-sulfur center. This yields the unexpected perspective of studying photochemistry, initiated by excitation of iron-sulfur clusters, in a range of protein complexes.
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Affiliation(s)
- Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM, 91128 Palaiseau Cedex, France.
| | | | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ursula Liebl
- LOB, Ecole Polytechnique, CNRS, INSERM, 91128 Palaiseau Cedex, France.
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8
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Kruglik SG, Yoo BK, Lambry JC, Martin JL, Negrerie M. Structural changes and picosecond to second dynamics of cytochrome c in interaction with nitric oxide in ferrous and ferric redox states. Phys Chem Chem Phys 2017; 19:21317-21334. [DOI: 10.1039/c7cp02634j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
After dissociation NO rebinds to Cyt c in 10 ps whereas Met80 rebinds in 5 μs after NO release from Cyt c. A complete view of heme – NO dynamics within 12 orders of magnitude of time in Cyt c is presented.
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Affiliation(s)
- Sergei G. Kruglik
- Laboratoire Jean Perrin
- Sorbonne Universités
- UPMC Univ. Paris 06
- CNRS
- 75005 Paris
| | - Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
| | | | - Jean-Louis Martin
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
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9
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Ahn YO, Lee HJ, Kaluka D, Yeh SR, Rousseau DL, Ädelroth P, Gennis RB. The two transmembrane helices of CcoP are sufficient for assembly of the cbb3-type heme-copper oxygen reductase from Vibrio cholerae. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1231-9. [PMID: 26116881 DOI: 10.1016/j.bbabio.2015.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 06/17/2015] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Abstract
The C-family (cbb3) of heme-copper oxygen reductases are proton-pumping enzymes terminating the aerobic respiratory chains of many bacteria, including a number of human pathogens. The most common form of these enzymes contains one copy each of 4 subunits encoded by the ccoNOQP operon. In the cbb3 from Rhodobacter capsulatus, the enzyme is assembled in a stepwise manner, with an essential role played by an assembly protein CcoH. Importantly, it has been proposed that a transient interaction between the transmembrane domains of CcoP and CcoH is essential for assembly. Here, we test this proposal by showing that a genetically engineered form of cbb3 from Vibrio cholerae (CcoNOQP(X)) that lacks the hydrophilic domain of CcoP, where the two heme c moieties are present, is fully assembled and stable. Single-turnover kinetics of the reaction between the fully reduced CcoNOQP(X) and O2 are essentially the same as the wild type enzyme in oxidizing the 4 remaining redox-active sites. The enzyme retains approximately 10% of the steady state oxidase activity using the artificial electron donor TMPD, but has no activity using the physiological electron donor cytochrome c4, since the docking site for this cytochrome is presumably located on the absent domain of CcoP. Residue E49 in the hydrophobic domain of CcoP is the entrance of the K(C)-channel for proton input, and the E49A mutation in the truncated enzyme further reduces the steady state activity to less than 3%. Hence, the same proton channel is used by both the wild type and truncated enzymes.
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Affiliation(s)
- Young O Ahn
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Hyun Ju Lee
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Daniel Kaluka
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Denis L Rousseau
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA.
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10
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Chauvet AAP, Al Haddad A, Kao WC, van Mourik F, Hunte C, Chergui M. Photo-induced dynamics of the heme centers in cytochrome bc1. Phys Chem Chem Phys 2015; 17:2143-51. [DOI: 10.1039/c4cp04805a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The ultrafast response of cytochromebc1is investigated for the first time,viatransient absorption spectroscopy.
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Affiliation(s)
- Adrien A. P. Chauvet
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Laboratoire de Spectroscopie Ultrarapide
- ISIC
- 1015 Lausanne
- Switzerland
| | - André Al Haddad
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Laboratoire de Spectroscopie Ultrarapide
- ISIC
- 1015 Lausanne
- Switzerland
| | - Wei-Chun Kao
- Albert-Ludwigs-Universität Freiburg
- BIOSS Centre for Biological Signalling Studies
- Institute for Biochemistry and Biology
- 79104 Freiburg
- Germany
| | - Frank van Mourik
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Laboratoire de Spectroscopie Ultrarapide
- ISIC
- 1015 Lausanne
- Switzerland
| | - Carola Hunte
- Albert-Ludwigs-Universität Freiburg
- BIOSS Centre for Biological Signalling Studies
- Institute for Biochemistry and Biology
- 79104 Freiburg
- Germany
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Laboratoire de Spectroscopie Ultrarapide
- ISIC
- 1015 Lausanne
- Switzerland
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11
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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
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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.
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Affiliation(s)
- Venugopal Karunakaran
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
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12
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Zaidi S, Hassan MI, Islam A, Ahmad F. The role of key residues in structure, function, and stability of cytochrome-c. Cell Mol Life Sci 2014; 71:229-55. [PMID: 23615770 PMCID: PMC11113841 DOI: 10.1007/s00018-013-1341-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 02/06/2023]
Abstract
Cytochrome-c (cyt-c), a multi-functional protein, plays a significant role in the electron transport chain, and thus is indispensable in the energy-production process. Besides being an important component in apoptosis, it detoxifies reactive oxygen species. Two hundred and eighty-five complete amino acid sequences of cyt-c from different species are known. Sequence analysis suggests that the number of amino acid residues in most mitochondrial cyts-c is in the range 104 ± 10, and amino acid residues at only few positions are highly conserved throughout evolution. These highly conserved residues are Cys14, Cys17, His18, Gly29, Pro30, Gly41, Asn52, Trp59, Tyr67, Leu68, Pro71, Pro76, Thr78, Met80, and Phe82. These are also known as "key residues", which contribute significantly to the structure, function, folding, and stability of cyt-c. The three-dimensional structure of cyt-c from ten eukaryotic species have been determined using X-ray diffraction studies. Structure analysis suggests that the tertiary structure of cyt-c is almost preserved along the evolutionary scale. Furthermore, residues of N/C-terminal helices Gly6, Phe10, Leu94, and Tyr97 interact with each other in a specific manner, forming an evolutionary conserved interface. To understand the role of evolutionary conserved residues on structure, stability, and function, numerous studies have been performed in which these residues were substituted with different amino acids. In these studies, structure deals with the effect of mutation on secondary and tertiary structure measured by spectroscopic techniques; stability deals with the effect of mutation on T m (midpoint of heat denaturation), ∆G D (Gibbs free energy change on denaturation) and folding; and function deals with the effect of mutation on electron transport, apoptosis, cell growth, and protein expression. In this review, we have compiled all these studies at one place. This compilation will be useful to biochemists and biophysicists interested in understanding the importance of conservation of certain residues throughout the evolution in preserving the structure, function, and stability in proteins.
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Affiliation(s)
- Sobia Zaidi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
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13
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Rebinding kinetics of dissociated amino acid ligand and carbon monoxide to ferrous microperoxidase-11 in aqueous solution. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4788-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Zhang P, Małolepsza E, Straub JE. Dynamics of Methionine Ligand Rebinding in Cytochrome c. J Phys Chem B 2012; 116:6980-90. [DOI: 10.1021/jp300783j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ping Zhang
- Department
of Chemistry, Boston University, Boston,
Massachusetts 02215, United States
| | - Edyta Małolepsza
- Department
of Chemistry, Boston University, Boston,
Massachusetts 02215, United States
| | - John E. Straub
- Department
of Chemistry, Boston University, Boston,
Massachusetts 02215, United States
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15
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Ye S, Markelz A. Hydration Effects on Energy Relaxation of Ferric Cytochrome C Films after Soret-Band Photoexcitation. J Phys Chem B 2010; 114:15151-7. [DOI: 10.1021/jp104217j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shuji Ye
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China 230026, and Department of Physics, University at Buffalo, SUNY, 239 Fronczak Hall, Buffalo, New York 14260-1500, United States
| | - Andrea Markelz
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China 230026, and Department of Physics, University at Buffalo, SUNY, 239 Fronczak Hall, Buffalo, New York 14260-1500, United States
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16
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Stocks BB, Konermann L. Time-dependent changes in side-chain solvent accessibility during cytochrome c folding probed by pulsed oxidative labeling and mass spectrometry. J Mol Biol 2010; 398:362-73. [PMID: 20230834 DOI: 10.1016/j.jmb.2010.03.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 03/08/2010] [Accepted: 03/08/2010] [Indexed: 11/28/2022]
Abstract
The current work employs a novel approach for characterizing structural changes during the refolding of acid-denatured cytochrome c (cyt c). At various time points (ranging from 10 ms to 5 min) after a pH jump from 2 to 7, the protein is exposed to a microsecond hydroxyl radical (.OH) pulse that induces oxidative labeling of solvent-exposed side chains. Most of the covalent modifications appear as +16-Da adducts that are readily detectable by mass spectrometry. The overall extent of labeling decreases as folding proceeds, reflecting dramatic changes in the accessibility of numerous residues. Peptide mapping and tandem mass spectrometry reveal that the side chains of C14, C17, H33, F46, Y48, W59, M65, Y67, Y74, M80, I81, and Y97 are among the dominant sites of oxidation. Temporal changes in the accessibility of these residues are consistent with docking of the N- and C-terminal helices as early as 10 ms. However, structural reorganization at the helix interface takes place up to at least 1 s. Initial misligation of the heme iron by H33 leads to distal crowding, giving rise to low solvent accessibility of the displaced (native) M80 ligand and the adjacent I81. W59 retains a surprisingly high level of accessibility long into the folding process, indicating the presence of packing defects in the hydrophobically collapsed core. Overall, the results of this work are consistent with previous hydrogen/deuterium exchange studies that proposed a foldon-mediated mechanism. The structural data obtained by .OH labeling monitor the packing and burial of side chains, whereas hydrogen/deuterium exchange primarily monitors the formation of secondary structure elements. Hence, the two approaches yield complementary information. Considering the very short time scale of pulsed oxidative labeling, an extension of the approach used here to sub-millisecond folding studies should be feasible.
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Affiliation(s)
- Bradley B Stocks
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
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17
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Zhang Y, Straub JE. Diversity of solvent dependent energy transfer pathways in heme proteins. J Phys Chem B 2009; 113:825-30. [PMID: 19115811 DOI: 10.1021/jp807499y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The time scales and pathways of heme cooling in both reduced cytochrome c and oxidized cytochrome c following heme photoexcitation were studied using molecular dynamics simulation. Five different solvent models, including normal water, heavy water, normal glycerol, deuterated glycerol, and a nonpolar solvent, were used in the simulation. Single exponential decay of the excess kinetic energy of the heme following photoexcitation was observed in all systems studied. The simulated time scale for heme cooling in normal water agrees with recent experimental results. In contrast to heme cooling in myoglobin, no solvent dependence was observed for the time scale for heme cooling in cytochrome c. The diversity of solvent dependence results from the different local heme environments in the two proteins. In myoglobin, it has been established that the dominant mechanism for heme cooling is direct energy transfer from the heme to the solvent. In cytochrome c, direct interaction between heme and protein residues forms the dominant energy transfer pathway. This distinction is dictated by protein topology and linked to function.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, Boston University, Boston, Massachusetts, 02215, USA
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18
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Vos MH, Battistoni A, Lechauve C, Marden MC, Kiger L, Desbois A, Pilet E, de Rosny E, Liebl U. Ultrafast heme-residue bond formation in six-coordinate heme proteins: implications for functional ligand exchange. Biochemistry 2008; 47:5718-23. [PMID: 18454557 DOI: 10.1021/bi800288z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A survey is presented of picosecond kinetics of heme-residue bond formation after photolysis of histidine, methionine, or cysteine, in a broad range of ferrous six-coordinate heme proteins. These include human neuroglobin, a bacterial heme-binding superoxide dismutase (SOD), plant cytochrome b 559, the insect nuclear receptor E75, horse heart cytochrome c and the heme domain of the bacterial sensor protein Dos. We demonstrate that the fastest and dominant phase of binding of amino acid residues to domed heme invariably takes place with a time constant in the narrow range of 5-7 ps. Remarkably, this is also the case in the heme-binding SOD, where the heme is solvent-exposed. We reason that this fast phase corresponds to barrierless formation of the heme-residue bond from a configuration close to the bound state. Only in proteins where functional ligand exchange occurs, additional slower rebinding takes place on the time scale of tens of picoseconds after residue dissociation. We propose that the presence of these slower phases reflects flexibility in the heme environment that allows external ligands (O2, CO, NO, . . .) to functionally replace the internal residue after thermal dissociation of the heme-residue bond.
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Affiliation(s)
- Marten H Vos
- Laboratoire d'Optique et Biosciences, CNRS, Ecole Polytechnique, F-91128 Palaiseau, France.
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19
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Yamashita T, Bouzhir-Sima L, Lambry JC, Liebl U, Vos MH. Ligand Dynamics and Early Signaling Events in the Heme Domain of the Sensor Protein Dos from Escherichia coli. J Biol Chem 2008; 283:2344-52. [DOI: 10.1074/jbc.m708123200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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20
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Kubo M, Uchida T, Nakashima S, Kitagawa T. Construction of a subnanosecond time-resolved, high-resolution ultraviolet resonance Raman measurement system and its application to reveal the dynamic structures of proteins. APPLIED SPECTROSCOPY 2008; 62:30-37. [PMID: 18230205 DOI: 10.1366/000370208783412573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A subnanosecond time-resolved ultraviolet (UV) resonance Raman system has been developed to study protein structural dynamics. The system is based on a 1 kHz Nd:YLF-pumped Ti:Sapphire regenerative amplifier with harmonic generation that can deliver visible (412, 440, 458, and 488 nm) and UV (206, 220, 229, and 244 nm) pulses. A subnanosecond (0.2 ns) tunable near-infrared pulse from a custom-made Ti:Sapphire oscillator is used to seed the regenerative amplifier. A narrow linewidth of the subnanosecond pulse offers the advantage of high resolution of UV resonance Raman spectra, which is critical to obtain site-specific information on protein structures. By combination with a 1 m single spectrograph equipped with a 3600 grooves/mm holographic grating and a custom-made prism prefilter, the present system achieves excellent spectral (<10 cm(-1)) and frequency (approximately 1 cm(-1)) resolutions with a relatively high temporal resolution (<0.5 ns). We also report the application of this system to two heme proteins, hemoglobin A and CooA, with the 440 nm pump and 220 nm probe wavelengths. For hemoglobin A, a structural change during the transition to the earliest intermediate upon CO photodissociation is successfully observed, specifically, nanosecond cleavage of the A-E interhelical hydrogen bonds within each subunit at Trpalpha14 and Trpbeta15 residues. For CooA, on the other hand, rapid structural distortion (<0.5 ns) by CO photodissociation and nanosecond structural relaxation following CO geminate recombination are observed through the Raman bands of Phe and Trp residues located near the heme. These results demonstrate the high potential of this instrument to detect local protein motions subsequent to photoreactions in their active sites.
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Affiliation(s)
- Minoru Kubo
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
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21
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Investigations of vibrational coherence in the low-frequency region of ferric heme proteins. Biophys J 2007; 94:2252-68. [PMID: 18065461 DOI: 10.1529/biophysj.107.122119] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Femtosecond coherence spectroscopy is applied to a series of ferric heme protein samples. The low-frequency vibrational spectra that are revealed show dominant oscillations near 40 cm(-1). MbCN is taken as a typical example of a histidine-ligated, six-coordinate, ferric heme and a comprehensive spectroscopic analysis is carried out. The results of this analysis reveal a new heme photoproduct species, absorbing near 418 nm, which is consistent with the photolysis of the His(93) axial ligand. The photoproduct undergoes subsequent rebinding/recovery with a time constant of approximately 4 ps. The photoproduct lineshapes are consistent with a photolysis quantum yield of 75-100%, although the observation of a relatively strong six-coordinate heme coherence near 252 cm(-1) (assigned to nu(9) in the MbCN Raman spectrum) suggests that the 75% lower limit is much more likely. The phase and amplitude excitation profiles of the low-frequency mode at 40 cm(-1) suggest that this mode is strongly coupled to the MbCN photoproduct species and it is assigned to the doming mode of the transient penta-coordinated material. The absolute phase of the 40 cm(-1) mode is found to be pi/2 on the red side of 418 nm and it jumps to 3pi/2 as excitation is tuned to the blue side of 418 nm. The absolute phase of the 40 cm(-1) signal is not explained by the standard theory for resonant impulsive stimulated Raman scattering. New mechanisms that give a dominant momentum impulse to the resonant wavepacket, rather than a coordinate displacement, are discussed. The possibilities of heme iron atom recoil after photolysis, as well as ultrafast nonradiative decay, are explored as potential ways to generate the strong momentum impulse needed to understand the phase properties of the 40 cm(-1) mode.
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22
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Ultrafast dynamics of ligands within heme proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1777:15-31. [PMID: 17996720 DOI: 10.1016/j.bbabio.2007.10.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2007] [Revised: 10/10/2007] [Accepted: 10/15/2007] [Indexed: 11/21/2022]
Abstract
Physiological bond formation and bond breaking events between proteins and ligands and their immediate consequences are difficult to synchronize and study in general. However, diatomic ligands can be photodissociated from heme, and thus in heme proteins ligand release and rebinding dynamics and trajectories have been studied on timescales of the internal vibrations of the protein that drive many biochemical reactions, and longer. The rapidly expanding number of characterized heme proteins involved in a large variety of functions allows comparative dynamics-structure-function studies. In this review, an overview is given of recent progress in this field, and in particular on initial sensing processes in signaling proteins, and on ligand and electron transfer dynamics in oxidases and cytochromes.
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23
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Negrerie M, Cianetti S, Vos MH, Martin JL, Kruglik SG. Ultrafast heme dynamics in ferrous versus ferric cytochrome c studied by time-resolved resonance Raman and transient absorption spectroscopy. J Phys Chem B 2007; 110:12766-81. [PMID: 16800612 DOI: 10.1021/jp0559377] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cytochrome c (Cyt c) is a heme protein involved in electron transfer and also in apoptosis. Its heme iron is bisaxially ligated to histidine and methionine side chains and both ferric and ferrous redox states are physiologically relevant, as well as a ligand exchange between internal residue and external diatomic molecule. The photodissociation of internal axial ligand was observed for several ferrous heme proteins including Cyt c, but no time-resolved studies have been reported on ferric Cyt c. To investigate how the oxidation state of the heme influences the primary photoprocesses, we performed a comprehensive comparative study on horse heart Cyt c by subpicosecond time-resolved resonance Raman and femtosecond transient absorption spectroscopy. We found that in ferric Cyt c, in contrast to ferrous Cyt c, the photodissociation of an internal ligand does not take place, and relaxation dynamics is dominated by vibrational cooling in the ground electronic state of the heme. The intermolecular vibrational energy transfer was found to proceed in a single phase with a temperature decay of approximately 7 ps in both ferric and ferrous Cyt c. For ferrous Cyt c, the instantaneous photodissociation of the methionine side chain from the heme iron is the dominant event, and its rebinding proceeds in two phases, with time constants of approximately 5 and approximately 16 ps. A mechanism of this process is discussed, and the difference in photoinduced coordination behavior between ferric and ferrous Cyt c is explained by an involvement of the excited electronic state coupled with conformational relaxation of the heme.
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Affiliation(s)
- Michel Negrerie
- Laboratory for Optics and Biosciences, CNRS UMR 7645, Ecole Polytechnique, 91128 Palaiseau Cedex, France
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24
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Kruglik SG, Jasaitis A, Hola K, Yamashita T, Liebl U, Martin JL, Vos MH. Subpicosecond oxygen trapping in the heme pocket of the oxygen sensor FixL observed by time-resolved resonance Raman spectroscopy. Proc Natl Acad Sci U S A 2007; 104:7408-13. [PMID: 17446273 PMCID: PMC1863486 DOI: 10.1073/pnas.0700445104] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dissociation of oxygen from the heme domain of the bacterial oxygen sensor protein FixL constitutes the first step in hypoxia-induced signaling. In the present study, the photodissociation of the heme-O2 bond was used to synchronize this event, and time-resolved resonance Raman (TR(3)) spectroscopy with subpicosecond time resolution was implemented to characterize the heme configuration of the primary photoproduct. TR(3) measurements on heme-oxycomplexes are highly challenging and have not yet been reported. Whereas in all other known six-coordinated heme protein complexes with diatomic ligands, including the oxymyoglobin reported here, heme iron out-of-plane motion (doming) occurs faster than 1 ps after iron-ligand bond breaking; surprisingly, no sizeable doming is observed in the oxycomplex of the Bradyrhizobium japonicum FixL sensor domain (FixLH). This assessment is deduced from the absence of the iron-histidine band around 217 cm(-1) as early as 0.5 ps. We suggest that efficient ultrafast oxygen rebinding to the heme occurs on the femtosecond time scale, thus hindering heme doming. Comparing WT oxy-FixLH, mutant proteins FixLH-R220H and FixLH-R220Q, the respective carbonmonoxy-complexes, and oxymyoglobin, we show that a hydrogen bond of the terminal oxygen atom with the residue in position 220 is responsible for the observed behavior; in WT FixL this residue is arginine, crucially implicated in signal transmission. We propose that the rigid O2 configuration imposed by this residue, in combination with the hydrophobic and constrained properties of the distal cavity, keep dissociated oxygen in place. These results uncover the origin of the "oxygen cage" properties of this oxygen sensor protein.
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Affiliation(s)
- Sergei G. Kruglik
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
- Laboratoire de Biophysique Moléculaire, Cellulaire, et Tissulaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7033, University Pierre & Marie Curie, Genopole Campus 1, Batiment Genavenir 8, 5 Rue Henri Desbrueres, 91030 Evry, France
| | - Audrius Jasaitis
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
| | - Klara Hola
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
| | - Taku Yamashita
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
| | - Ursula Liebl
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
| | - Jean-Louis Martin
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
| | - Marten H. Vos
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
- To whom correspondence should be addressed at the † address. E-mail:
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25
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Kruglik SG, Lambry JC, Cianetti S, Martin JL, Eady RR, Andrew CR, Negrerie M. Molecular basis for nitric oxide dynamics and affinity with Alcaligenes xylosoxidans cytochrome c. J Biol Chem 2006; 282:5053-5062. [PMID: 17158883 DOI: 10.1074/jbc.m604327200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial heme protein cytochrome ć from Alcaligenes xylosoxidans (AXCP) reacts with nitric oxide (NO) to form a 5-coordinate ferrous nitrosyl heme complex. The crystal structure of ferrous nitrosyl AXCP has previously revealed that NO is bound in an unprecedented manner on the proximal side of the heme. To understand how the protein structure of AXCP controls NO dynamics, we performed absorption and Raman time-resolved studies at the heme level as well as a molecular computational dynamics study at the entire protein structure level. We found that after NO dissociation from the heme iron, the structure of the proximal heme pocket of AXCP confines NO close to the iron so that an ultrafast (7 ps) and complete (99 +/- 1%) geminate rebinding occurs, whereas the proximal histidine does not rebind to the heme iron on the timescale of NO geminate rebinding. The distal side controls the initial NO binding, whereas the proximal heme pocket controls its release. These dynamic properties allow the trapping of NO within the protein core and represent an extreme behavior observed among heme proteins.
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Affiliation(s)
- Sergei G Kruglik
- Ecole Polytechnique, Laboratoire d'Optique et Biosciences, CNRS UMR 7645, 91128 Palaiseau Cedex, France; BioMoCeTi, CNRS UMR 7033, University Pierre and Marie Curie, Genopole Campus 1, 91030 Evry, France
| | - Jean-Christophe Lambry
- Ecole Polytechnique, Laboratoire d'Optique et Biosciences, CNRS UMR 7645, 91128 Palaiseau Cedex, France; INSERM, U696, 91128 Palaiseau Cedex, France
| | - Simona Cianetti
- Ecole Polytechnique, Laboratoire d'Optique et Biosciences, CNRS UMR 7645, 91128 Palaiseau Cedex, France
| | - Jean-Louis Martin
- Ecole Polytechnique, Laboratoire d'Optique et Biosciences, CNRS UMR 7645, 91128 Palaiseau Cedex, France; INSERM, U696, 91128 Palaiseau Cedex, France
| | - Robert R Eady
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom, and
| | - Colin R Andrew
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850
| | - Michel Negrerie
- Ecole Polytechnique, Laboratoire d'Optique et Biosciences, CNRS UMR 7645, 91128 Palaiseau Cedex, France; INSERM, U696, 91128 Palaiseau Cedex, France.
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26
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Droghetti E, Oellerich S, Hildebrandt P, Smulevich G. Heme coordination states of unfolded ferrous cytochrome C. Biophys J 2006; 91:3022-31. [PMID: 16877519 PMCID: PMC1578467 DOI: 10.1529/biophysj.105.079749] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural changes of ferrous Cyt-c that are induced by binding to SDS micelles, phospholipid vesicles, DeTAB, and GuHCl as well as by high temperatures and changes in the pH have been studied by RR and UV-Vis absorption spectroscopies. Four species have been identified in which the native methionine-80 ligand is removed from the heme iron. This coordination site is either occupied by a histidine (His-33 or His-26) to form a 6cLS configuration, which is the prevailing species in GuHCl at pH 7.0 and ambient temperature, or remains vacant to yield a 5cHS configuration. The three identified 5cHS species differ with respect to the hydrogen-bond interactions of the proximal histidine ligand (His-18) and include a nonhydrogen-bonded, a hydrogen-bonded, and a deprotonated imidazole ring. These structural motifs have been found irrespective of the unfolding conditions used. An unambiguous spectroscopic distinction of these 5cHS species is possible on the basis of the Fe-N(imidazole) stretching vibrations, the RR bands in the region between 1300 and 1650 cm(-1), and the electronic transitions in the Soret- and Q-band regions. In acid and neutral solutions, the species with a hydrogen-bonded and a nonhydrogen-bonded His-18 prevail, whereas in alkaline solutions a configuration with a deprotonated His-18 ligand is also observed. Upon lowering the pH or increasing the temperature in GuHCl solutions, the structure on the proximal side of the heme is perturbed, resulting in a loss of the hydrogen-bond interactions of the His-18 ligand. Conversely, the hydrogen-bonded His-18 of ferrous Cyt-c is stabilized by electrostatic interactions which increase in strength from phospholipid vesicles to SDS micelles. The results here suggest that unfolding of Cyt-c is initiated by the rupture of the Fe-Met-80 bond and structural reorganizations on the distal side of the heme pocket, whereas the proximal part is only affected in a later stage of the denaturation process.
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Affiliation(s)
- Enrica Droghetti
- Dipartimento di Chimica, Università di Firenze, Sesto Fiorentino FI, Italy
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27
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Negrerie M, Kruglik SG, Lambry JC, Vos MH, Martin JL, Franzen S. Role of Heme Iron Coordination and Protein Structure in the Dynamics and Geminate Rebinding of Nitric Oxide to the H93G Myoglobin Mutant. J Biol Chem 2006; 281:10389-98. [PMID: 16476730 DOI: 10.1074/jbc.m513375200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The influence of the heme iron coordination on nitric oxide binding dynamics was investigated for the myoglobin mutant H93G (H93G-Mb) by picosecond absorption and resonance Raman time-resolved spectroscopies. In the H93G-Mb, the glycine replacing the proximal histidine does not interact with the heme iron so that exogenous substituents like imidazole may coordinate to the iron at the proximal position. Nitrosylation of H93G-Mb leads to either 6- or 5-coordinate species depending on the imidazole concentration. At high concentrations, (imidazole)-(NO)-6-coordinate heme is formed, and the photoinduced rebinding kinetics reveal two exponential picosecond phases ( approximately 10 and approximately 100 ps) similar to those of wild type myoglobin. At low concentrations, imidazole is displaced by the trans effect leading to a (NO)-5-coordinate heme, becoming 4-coordinate immediately after photolysis as revealed from the transient Raman spectrum. In this case, NO rebinding kinetics remain bi-exponential with no change in time constant of the fast component whose amplitude increases with respect to the 6-coordinate species. Bi-exponential NO geminate rebinding in 5-coordinate H93G-Mb is in contrast with the single-exponential process reported for nitrosylated soluble guanylate cyclase (Negrerie, M., Bouzhir, L., Martin, J. L., and Liebl, U. (2001) J. Biol. Chem. 276, 46815-46821). Thus, our data show that the iron coordination state or the heme iron out-of-plane motion are not at the origin of the bi-exponential kinetics, which depends upon the protein structure, and that the 4-coordinate state favors the fast phase of NO geminate rebinding. Consequently, the heme coordination state together with the energy barriers provided by the protein structure control the dynamics and affinity for NO-binding enzymes.
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Affiliation(s)
- Michel Negrerie
- INSERM U696, Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Palaiseau F91120, 91128 Palaiseau Cedex, France.
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28
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Silkstone G, Jasaitis A, Vos MH, Wilson MT. Geminate carbon monoxide rebinding to a c-type haem. Dalton Trans 2005:3489-94. [PMID: 16234930 DOI: 10.1039/b508183c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A chemically modified form of cytochrome c(cyt. c), termed carboxymethyl cytochrome c(cm cyt. c), possesses a vacant sixth coordination site to the haem iron that is available to bind external ligands. We present data on the rapid flash photolysis of CO from the ferrous haem iron of cm cyt. c and describe the kinetics and spectral transitions that accompany the recombination. This was achieved using 30-femtosecond laser pulses and a white light continuum to monitor spectral transitions. Whereas the photo-dissociation quantum yield is close to 1, the yield of CO escape from the protein (the apparent quantum yield, varphi) relative to myoglobin (varphi=1) is small due to rapid geminate recombination of CO. On ligand photo-dissociation the haem undergoes a spin-state transition from low-spin ferrous CO bound to penta-coordinate high-spin. Subsequently the system reverts to the CO bound form. The data were fitted with a minimum number of exponentials using global analysis. Recombination of CO with the haem iron of cm cyt. c is multiphasic (tau=16 ps, 120 ps and 1 ns), involving three spectrally distinct components. The fraction of haem (0.11) not recombining with CO within 4 ns is similar to the value of varphi(0.12) measured on the same preparation by the "pulse method" (M. Brunori, G. Giacometti, E. Antonini and J. Wyman, Proc. Natl. Acad. Sci. USA, 1973, 70, 3141-3144, ). This implies that no further geminate recombination occurs at t>4 ns. This unusually efficient CO-haem geminate recombination indicates the sterically hindered ("caged") nature of the distal haem pocket in cm cyt. c from which it is difficult for CO to escape. The large geminate phase may be contrasted with the behaviour of myoglobin in which geminate recombination is small. This is in general agreement with the well-documented extensive structural dynamics in myoglobin that allow ligand passage, and a higher structural rigidity in cyt. c imposed by the restraints of minimising reorganisation energy for electron transfer (M. Brunori, D. Bourgeois and D. Vallone, J. Struct. Biol., 2004, 147, 223-234, ). The high pH ferrous form of cm cyt. c is a low-spin species having a lysine bound to the central iron atom of the haem (M. Brunori, M. Wilson and E. Antonini, J. Biol. Chem., 1972, 247, 6076-6081; G. Silkstone, G. Stanway, P. Brzezinski and M. Wilson, Biophys. Chem., 2002, 98, 65-77, ). This high pH (pH approximately 8) form of deoxy cm cyt. c undergoes photo-dissociation of lysine (although the proximal histidine is possible) after photo-excitation. Recombination occurs with a time constant (tau) of approximately 7 ps. This is similar to that observed for the geminate rebinding of the Met80 residue in native ferrous cyt. c(tau approximately 6 ps) following its photo-dissociation (S. Cianetti, M. Negrerie, M. Vos, J.-L. Martin and S. Kruglik, J. Am. Chem. Soc., 2004, 126, 13 932-13 933; W. Wang, X. Ye, A. Demidov, F. Rosca, T. Sjodin, W. Cao, M. Sheeran and P. Champion, J. Phys. Chem., 2000, 104, 10 789-10 801, ).
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Affiliation(s)
- G Silkstone
- University of Essex, Colchester, UK CO4 3SQ.
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