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Yoo BK, Kruglik SG, Lambry JC, Lamarre I, Raman CS, Nioche P, Negrerie M. The H-NOX protein structure adapts to different mechanisms in sensors interacting with nitric oxide. Chem Sci 2023; 14:8408-8420. [PMID: 37564404 PMCID: PMC10411614 DOI: 10.1039/d3sc01685d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
Some classes of bacteria within phyla possess protein sensors identified as homologous to the heme domain of soluble guanylate cyclase, the mammalian NO-receptor. Named H-NOX domain (Heme-Nitric Oxide or OXygen-binding), their heme binds nitric oxide (NO) and O2 for some of them. The signaling pathways where these proteins act as NO or O2 sensors appear various and are fully established for only some species. Here, we investigated the reactivity of H-NOX from bacterial species toward NO with a mechanistic point of view using time-resolved spectroscopy. The present data show that H-NOXs modulate the dynamics of NO as a function of temperature, but in different ranges, changing its affinity by changing the probability of NO rebinding after dissociation in the picosecond time scale. This fundamental mechanism provides a means to adapt the heme structural response to the environment. In one particular H-NOX sensor the heme distortion induced by NO binding is relaxed in an ultrafast manner (∼15 ps) after NO dissociation, contrarily to other H-NOX proteins, providing another sensing mechanism through the H-NOX domain. Overall, our study links molecular dynamics with functional mechanism and adaptation.
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Affiliation(s)
- Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Sergei G Kruglik
- Laboratoire Jean Perrin, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS 75005 Paris France
| | - Jean-Christophe Lambry
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Isabelle Lamarre
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - C S Raman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore Maryland 21201 USA
| | - Pierre Nioche
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, UMR S1124, Centre Universitaire des Saints-Pères, Université Paris Descartes 75006 Paris France
- Structural and Molecular Analysis Platform, BioMedTech Facilities, INSERM US36-CNRS-UMS2009, Paris Université Paris France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
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Abstract
This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.
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3
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Distorted five-coordinate square pyramidal geometry of a cadmium(II) complex containing a 2-methylimidazole ligand: Crystal structure and axial ligand effect on spectroscopic properties. Polyhedron 2019. [DOI: 10.1016/j.poly.2019.114107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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4
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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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5
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Cote Y, Nominé Y, Ramirez J, Hellwig P, Stote RH. Peptide-Protein Binding Investigated by Far-IR Spectroscopy and Molecular Dynamics Simulations. Biophys J 2017. [PMID: 28636914 DOI: 10.1016/j.bpj.2017.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular dynamics (MD) simulations and far-infrared (far-IR) spectroscopy were combined to study peptide binding by the second PDZ domain (PDZ1) of MAGI1, which has been identified as an important target for the Human Papilloma Virus. PDZ1 recognizes and binds to the C-terminal end of the E6 protein from high-risk Human Papilloma Virus. The far-IR spectra of two forms of the protein, an unbound APO form and a HOLO form (where the PDZ1 is bound to an 11-residue peptide derived from the C terminus of HPV16 E6), were obtained. MD simulations were used to determine the most representative structure of each form and these were used to compute their respective IR spectra by normal mode analysis. Far-UV circular dichroism spectroscopy was used to confirm the secondary structure content and the stability through temperature-dependent studies. Both the experimental and calculated far-IR spectra showed a red shift of the low-frequency peaks upon peptide binding. The calculations show that this is coincident with an increased number of hydrogen bonds formed as the peptide augments the protein β-sheet. We further identified the contribution of surface-bound water molecules to bands in the far-IR and, through the calculations, identified potential pathways for allosteric communication. Together, these results demonstrate the utility of combining far-IR experiments and MD studies to study peptide binding by proteins.
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Affiliation(s)
- Yoann Cote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 UMR 7104 CNRS, Université de Strasbourg, Illkirch, France
| | - Yves Nominé
- Équipe Labellisée Ligue Contre le Cancer, Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 UMR 7104 CNRS, Université de Strasbourg, Illkirch, France
| | - Juan Ramirez
- Equipe Oncoprotéines, Ecole Supérieure de Biotechnologie de Strasbourg, Biotechnologie et Signalisation Cellulaire, UMR 7242, CNRS, Université de Strasbourg, Illkirch, France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, CNRS, Strasbourg, France
| | - Roland H Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 UMR 7104 CNRS, Université de Strasbourg, Illkirch, France.
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6
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Sun Y, Benabbas A, Zeng W, Muralidharan S, Boon EM, Champion PM. Kinetic Control of O2 Reactivity in H-NOX Domains. J Phys Chem B 2016; 120:5351-8. [PMID: 27229134 DOI: 10.1021/acs.jpcb.6b03348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transient absorption, resonance Raman, and vibrational coherence spectroscopies are used to investigate the mechanisms of NO and O2 binding to WT Tt H-NOX and its P115A mutant. Vibrational coherence spectra of the oxy complexes provide clear evidence for the enhancement of an iron-histidine mode near 217 cm(-1) following photoexcitation, which indicates that O2 can be dissociated in these proteins. However, the quantum yield of O2 photolysis is low, particularly in the wild type (≲3%). Geminate recombination of O2 and NO in both of these proteins is very fast (∼1.4 × 10(11) s(-1)) and highly efficient. We show that the distal heme pocket of the H-NOX system forms an efficient trap that limits the O2 off-rate and determines the overall affinity. The distal pocket hydrogen bond, which appears to be stronger in the P115A mutant, may help retard the O2 ligand from escaping into the solvent following either photoinduced or thermal dissociation. This, along with a strengthening of the Fe-O2 bond that is correlated with the significant heme ruffing and saddling distortions, explains the unusually high O2 affinity of WT Tt H-NOX and the even higher affinity found in the P115A mutant.
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Affiliation(s)
- Yuhan Sun
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Weiqiao Zeng
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Sandhya Muralidharan
- Department of Chemistry and the Institute of Chemical Biology and Drug Discovery, Stony Brook University , Stony Brook, New York 11794, United States
| | - Elizabeth M Boon
- Department of Chemistry and the Institute of Chemical Biology and Drug Discovery, Stony Brook University , Stony Brook, New York 11794, 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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Karunakaran V, Sun Y, Benabbas A, Champion PM. Investigations of the low frequency modes of ferric cytochrome c using vibrational coherence spectroscopy. J Phys Chem B 2014; 118:6062-70. [PMID: 24823442 PMCID: PMC4059251 DOI: 10.1021/jp501298c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Femtosecond vibrational coherence
spectroscopy is used to investigate
the low frequency vibrational dynamics of the electron transfer heme
protein, cytochrome c (cyt c). The
vibrational coherence spectra of ferric cyt c have
been measured as a function of excitation wavelength within the Soret
band. Vibrational coherence spectra obtained with excitation between
412 and 421 nm display a strong mode at ∼44 cm–1 that has been assigned to have a significant contribution from heme
ruffling motion in the electronic ground state. This assignment is
based partially on the presence of a large heme ruffling distortion
in the normal coordinate structural decomposition (NSD) analysis of
the X-ray crystal structures. When the excitation wavelength is moved
into the ∼421–435 nm region, the transient absorption
increases along with the relative intensity of two modes near ∼55
and 30 cm–1. The intensity of the mode near 44 cm–1 appears to minimize in this region and then recover
(but with an opposite phase compared to the blue excitation) when
the laser is tuned to 443 nm. These observations are consistent with
the superposition of both ground and excited state coherence in the
421–435 nm region due to the excitation of a weak porphyrin-to-iron
charge transfer (CT) state, which has a lifetime long enough to observe
vibrational coherence. The mode near 55 cm–1 is
suggested to arise from ruffling in a transient CT state that has
a less ruffled heme due to its iron d6 configuration.
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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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8
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Sun Y, Karunakaran V, Champion PM. Investigations of the low-frequency spectral density of cytochrome c upon equilibrium unfolding. J Phys Chem B 2013; 117:9615-25. [PMID: 23863217 DOI: 10.1021/jp404881k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The equilibrium unfolding process of ferric horse heart cytochrome c (cyt c), induced by guanidinium hydrochloride (GdHCl), was studied using UV-vis absorption spectroscopy, resonance Raman spectroscopy, and vibrational coherence spectroscopy (VCS). The unfolding process was successfully fit using a three-state model which included the fully folded (N) and unfolded (U) states, along with an intermediate (I) assigned to a Lys bound heme. The VCS spectra revealed for the first time several low-frequency heme modes that are sensitive to cyt c unfolding: γ(a) (~50 cm(-1)), γ(b) (~80 cm(-1)), γ(c) (~100 cm(-1)), and ν(s)(His-Fe-His) at 205 cm(-1). These out-of-plane modes have potential functional relevance and are activated by protein-induced heme distortions. The free energies for the N-I and the I-U transitions at pH 7.0 and 20 °C were found to be 4.6 kcal/M and 11.6 kcal/M, respectively. Imidazole was also introduced to replace the methionine ligand so the unfolding can be modeled as a two-state system. The intensity of the mode γ(b)~80 cm(-1) remains nearly constant during the unfolding process, while the amplitudes of the other low frequency modes track with spectral changes observed at higher frequency. This confirms that the heme deformation changes are coupled to the protein tertiary structural changes that take place upon unfolding. These studies also reveal that damping of the coherent oscillations depends sensitively on the coupling between heme and the surrounding water solvent.
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Affiliation(s)
- Yuhan Sun
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
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9
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Ganim Z. Single-molecule vibrational spectroscopy adds structural resolution to the optical trap. Biophys J 2013; 104:4-5. [PMID: 23332052 DOI: 10.1016/j.bpj.2012.09.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 09/12/2012] [Accepted: 09/20/2012] [Indexed: 12/01/2022] Open
Abstract
The ability to apply forces on single molecules with an optical trap is combined with the endogenous structural resolution of Raman spectroscopy in an article in this issue, and applied to measure the Raman spectrum of ds-DNA during force-extension.
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Affiliation(s)
- Ziad Ganim
- Physik Department, Technische Universität München, Garching, Germany.
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10
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Benabbas A, Karunakaran V, Youn H, Poulos TL, Champion PM. Effect of DNA binding on geminate CO recombination kinetics in CO-sensing transcription factor CooA. J Biol Chem 2012; 287:21729-40. [PMID: 22544803 DOI: 10.1074/jbc.m112.345090] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbon monoxide oxidation activator (CooA) proteins are heme-based CO-sensing transcription factors. Here we study the ultrafast dynamics of geminate CO rebinding in two CooA homologues, Rhodospirillum rubrum (RrCooA) and Carboxydothermus hydrogenoformans (ChCooA). The effects of DNA binding and the truncation of the DNA-binding domain on the CO geminate recombination kinetics were specifically investigated. The CO rebinding kinetics in these CooA complexes take place on ultrafast time scales but remain non-exponential over many decades in time. We show that this non-exponential kinetic response is due to a quenched enthalpic barrier distribution resulting from a distribution of heme geometries that is frozen or slowly evolving on the time scale of CO rebinding. We also show that, upon CO binding, the distal pocket of the heme in the CooA proteins relaxes to form a very efficient hydrophobic trap for CO. DNA binding further tightens the narrow distal pocket and slightly weakens the iron-proximal histidine bond. Comparison of the CO rebinding kinetics of RrCooA, truncated RrCooA, and DNA-bound RrCooA proteins reveals that the uncomplexed and inherently flexible DNA-binding domain adds additional structural heterogeneity to the heme doming coordinate. When CooA forms a complex with DNA, the flexibility of the DNA-binding domain decreases, and the distribution of the conformations available in the heme domain becomes restricted. The kinetic studies also offer insights into how the architecture of the heme environment can tune entropic barriers in order to control the geminate recombination of CO in heme proteins, whereas spin selection rules play a minor or non-existent role.
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Affiliation(s)
- Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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11
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Barabanschikov A, Demidov A, Kubo M, Champion PM, Sage JT, Zhao J, Sturhahn W, Alp EE. Spectroscopic identification of reactive porphyrin motions. J Chem Phys 2011; 135:015101. [PMID: 21744919 PMCID: PMC3144962 DOI: 10.1063/1.3598473] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Accepted: 05/18/2011] [Indexed: 11/14/2022] Open
Abstract
Nuclear resonance vibrational spectroscopy (NRVS) reveals the vibrational dynamics of a Mössbauer probe nucleus. Here, (57)Fe NRVS measurements yield the complete spectrum of Fe vibrations in halide complexes of iron porphyrins. Iron porphine serves as a useful symmetric model for the more complex spectrum of asymmetric heme molecules that contribute to numerous essential biological processes. Quantitative comparison with the vibrational density of states (VDOS) predicted for the Fe atom by density functional theory calculations unambiguously identifies the correct sextet ground state in each case. These experimentally authenticated calculations then provide detailed normal mode descriptions for each observed vibration. All Fe-ligand vibrations are clearly identified despite the high symmetry of the Fe environment. Low frequency molecular distortions and acoustic lattice modes also contribute to the experimental signal. Correlation matrices compare vibrations between different molecules and yield a detailed picture of how heme vibrations evolve in response to (a) halide binding and (b) asymmetric placement of porphyrin side chains. The side chains strongly influence the energetics of heme doming motions that control Fe reactivity, which are easily observed in the experimental signal.
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Affiliation(s)
- Alexander Barabanschikov
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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13
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Meyer-Ilse J, Akimov D, Dietzek B. Femtosecond Coherence Spectroscopic Study of the Onset of Chemical Denaturation of Myoglobin upon Addition of Minor Amounts of Urea. Z PHYS CHEM 2011. [DOI: 10.1524/zpch.2011.0082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractThe interaction of urea with myoglobin, as a benchmark system for heme-containing proteins, is studiedviafemtosecond coherence spectroscopy. The work focuses on the effect of urea on the appearance of low-wavenumber oscillations, which are a measure of the geometrical structure of the heme group and its interaction with the polypeptide chain. Pursuing this approach, structural alterations (i.e.changes in the vibrational dynamics of the heme group) are detected at denaturant concentrations below the full denaturation limit of 6 M urea for myoglobin. In particular, the low-wavenumber oscillation associated with the heme-doming (i.e.the out-off-plane vibration of the propyrin macrocycle) is found to appear spectrally shifted with a concentration of only 3 M urea. These results suggest that the local environment around the heme is already altered despite the fact that macroscopic unfolding as manifested in the thermodynamic properties of the polypeptide chain is not complete at these urea concentrations.
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Affiliation(s)
- Julia Meyer-Ilse
- Friedrich-Schiller-Univesrität Jena, Institute of Physical Chemistry, Jena, Deutschland
| | - Denis Akimov
- Institute of Photonic Technology Jena e.V., Jena, Deutschland
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Karunakaran V, Denisov I, Sligar SG, Champion PM. Investigation of the low frequency dynamics of heme proteins: native and mutant cytochrome P450(cam) and redox partner complexes. J Phys Chem B 2011; 115:5665-77. [PMID: 21391540 DOI: 10.1021/jp112298y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Vibrational coherence spectroscopy (VCS) is used to investigate the low-frequency dynamics of camphor-free and camphor-bound cytochrome P450(cam) (CYP 101) and its L358P mutant. The low-frequency heme vibrations are found to be perturbed upon binding to the electron transfer partner putidaredoxin (Pdx). A strong correlation between the "detuned" vibrational coherence spectrum, which monitors frequencies between 100 and 400 cm(-1), and the lower frequency part of the Raman spectrum is also demonstrated. The very low frequency region ≤200 cm(-1), uniquely accessed by open-band VCS measurements, reveals a mode near 103 cm(-1) in P450(cam) when camphor is not present in the distal pocket. This reflects the presence of a specific heme distortion, such as saddling or ruffling, in the substrate-free state where water is coordinated to the low-spin iron atom. Such distortions are likely to retard the rate of electron transfer to the substrate-free protein. The presence of strong mode near ∼33 cm(-1) in the camphor-bound form suggests a significant heme-doming distortion, which is supported by analysis using normal coordinate structural decomposition. Pdx also displays a strong coherent vibration near 30 cm(-1) that in principle could be involved in vibrational resonance with its electron transfer target. A splitting of the 33 cm(-1) feature and intensification of a mode near 78 cm(-1) appear when the P450(cam)/Pdx complex is formed. These observations are consistent with vibrational mixing and heme geometric distortions upon Pdx binding that are coincident with the increased thiolate electron donation to the heme. The appearance of a mode near 65 cm(-1) in the coherence spectra of the L358P mutant is comparable to the mode at 78 cm(-1) seen in the P450(cam)/Pdx complex and is consistent with the view that the heme and its environment in the L358P mutant are similar to the Pdx-bound native protein. Resonance Raman spectra are presented for both P450(cam) and the L358P mutant and the changes are correlated with an increased amount of thiolate electron donation to the heme in the mutant sample.
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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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15
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Karunakaran V, Benabbas A, Sun Y, Zhang Z, Singh S, Banerjee R, Champion PM. Investigations of low-frequency vibrational dynamics and ligand binding kinetics of cystathionine beta-synthase. J Phys Chem B 2010; 114:3294-306. [PMID: 20155941 DOI: 10.1021/jp909700r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Vibrational coherence spectroscopy is used to study the low frequency dynamics of the truncated dimer of human cystathionine beta-synthase (CBS). CBS is a pyridoxal-5'-phosphate-dependent heme enzyme with cysteine and histidine axial ligands that catalyzes the condensation of serine and homocysteine to form cystathionine. A strong correlation between the "detuned" coherence spectrum (which probes higher frequencies) and the Raman spectrum is demonstrated, and a rich pattern of modes below 200 cm(-1) is revealed. Normal coordinate structural decomposition (NSD) of the ferric CBS crystal structure predicts the enhancement of normal modes with significant heme "doming", "ruffling", and "saddling" content, and they are observed in the coherence spectra near approximately 40, approximately 60, and approximately 90 cm(-1). When pH is varied, the relative intensities and frequencies of the low frequency heme modes indicate the presence of a unique protein-induced heme structural perturbation near pH 7 that differs from what is observed at higher or lower pH. For ferric CBS, we observe a new mode near approximately 25 cm(-1), possibly involving the response of the protein, which exhibits a phase jump of approximately pi for excitation on the blue and red side of the Soret band maximum. The low frequency vibrational coherence spectrum of ferrous CBS is also presented, along with our efforts to probe its NO-bound complex. The CO geminate rebinding kinetics of CBS are similar to the CO-bound form of the gene activator protein CooA, but with the appearance of a significant additional kinetic inhomogeneity. Analysis of this inhomogeneity suggests that it arises from the two subunits of CBS and leads to a factor of approximately 20 for the ratio of the average CO geminate rebinding rates of the two subunits.
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Affiliation(s)
- Venugopal Karunakaran
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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16
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Benabbas A, Ye X, Kubo M, Zhang Z, Maes EM, Montfort WR, Champion PM. Ultrafast dynamics of diatomic ligand binding to nitrophorin 4. J Am Chem Soc 2010; 132:2811-20. [PMID: 20121274 DOI: 10.1021/ja910005b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nitrophorin 4 (NP4) is a heme protein that stores and delivers nitric oxide (NO) through pH-sensitive conformational change. This protein uses the ferric state of a highly ruffled heme to bind NO tightly at low pH and release it at high pH. In this work, the rebinding kinetics of NO and CO to NP4 are investigated as a function of iron oxidation state and the acidity of the environment. The geminate recombination process of NO to ferrous NP4 at both pH 5 and pH 7 is dominated by a single approximately 7 ps kinetic phase that we attribute to the rebinding of NO directly from the distal pocket. The lack of pH dependence explains in part why NP4 cannot use the ferrous state to fulfill its function. The kinetic response of ferric NP4NO shows two distinct phases. The relative geminate amplitude of the slower phase increases dramatically as the pH is raised from 5 to 8. We assign the fast phase of NO rebinding to a conformation of the ferric protein with a closed hydrophobic pocket. The slow phase is assigned to the protein in an open conformation with a more hydrophilic heme pocket environment. Analysis of the ultrafast kinetics finds the equilibrium off-rate of NO to be proportional to the open state population as well as the pH-dependent amplitude of escape from the open pocket. When both factors are considered, the off-rate increases by more than an order of magnitude as the pH changes from 5 to 8. The recombination of CO to ferrous NP4 is observed to have a large nonexponential geminate amplitude with rebinding time scales of approximately 10(-11)-10(-9) s at pH 5 and approximately 10(-10)-10(-8) s at pH 7. The nonexponential CO rebinding kinetics at both pH 5 and pH 7 are accounted for using a simple model that has proven effective for understanding CO binding in a variety of other heme systems (Ye, X.; et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14682).
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Affiliation(s)
- Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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17
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Zhang Y, Straub JE. Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. III. The nu(4) and nu(7) modes of nonplanar nickel porphyrin models. J Chem Phys 2009; 130:215101. [PMID: 19508100 DOI: 10.1063/1.3147704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The time scales and pathways of vibrational energy relaxation (VER) of the nu(4) and nu(7) modes of three nickel porphyrin models, nickel porphine (NiP), nickel protoporphyrin IX (Ni-heme), and nickel octaethylporphyrin (NiOEP), were studied using a non-Markovian time-dependent perturbation theory at the B3LYP/6-31G(d) level. When NiP is calculated with D(4h) symmetry, it has the planar structure and the same VER properties as ferrous iron porphine (FeP). The porphine cores of both Ni-heme and NiOEP were distorted from a planar geometry, assuming a nonplanar structure, similar to that of the heme structure in cytochrome c. The VER time scales of Ni-heme are found to be similar to those predicted for a planar iron heme, but the derived pathways have distinctly different features. In particular, the strong coupling between the nu(7) mode and the overtone of the approximately 350 cm(-1) gamma(7) mode, observed for planar porphyrins, is absent in both nonplanar nickel porphyrins. Direct energy exchange between the nu(4) and nu(7) modes is not observed in NiOEP, but is found to play an essential role in the VER of the nu(4) mode in Ni-heme. The Ni-heme isopropionate groups are involved in the dominant VER pathways of both the nu(4) and nu(7) modes of Ni-heme. However, in contrast with VER pathways derived in planar iron heme, the isopropionate groups are not observed to play an essential role relative to other side chains in spatially directing the vibrational energy flow.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
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Zhang Y, Fujisaki H, Straub JE. Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model. J Chem Phys 2009; 130:025102. [DOI: 10.1063/1.3055277] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Gruia F, Ionascu D, Kubo M, Ye X, Dawson J, Osborne RL, Sligar SG, Denisov I, Das A, Poulos TL, Terner J, Champion PM. Low-frequency dynamics of Caldariomyces fumago chloroperoxidase probed by femtosecond coherence spectroscopy. Biochemistry 2008; 47:5156-67. [PMID: 18407660 DOI: 10.1021/bi7025485] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrafast laser spectroscopy techniques are used to measure the low-frequency vibrational coherence spectra and nitric oxide rebinding kinetics of Caldariomyces fumago chloroperoxidase (CPO). Comparisons of the CPO coherence spectra with those of other heme species are made to gauge the protein-specific nature of the low-frequency spectra. The coherence spectrum of native CPO is dominated by a mode that appears near 32-33 cm(-1) at all excitation wavelengths, with a phase that is consistent with a ground-state Raman-excited vibrational wavepacket. On the basis of a normal coordinate structural decomposition (NSD) analysis, we assign this feature to the thiolate-bound heme doming mode. Spectral resolution of the probe pulse ("detuned" detection) reveals a mode at 349 cm(-1), which has been previously assigned using Raman spectroscopy to the Fe-S stretching mode of native CPO. The ferrous species displays a larger degree of spectral inhomogeneity than the ferric species, as reflected by multiple shoulders in the optical absorption spectra. The inhomogeneities are revealed by changes in the coherence spectra at different excitation wavelengths. The appearance of a mode close to 220 cm(-1) in the coherence spectrum of reduced CPO excited at 440 nm suggests that a subpopulation of five coordinated histidine-ligated hemes is present in the ferrous state at a physiologically relevant pH. A significant increase in the amplitude of the coherence signal is observed for the resonance with the 440 nm subpopulation. Kinetics measurements reveal that nitric oxide binding to ferric and ferrous CPO can be described as a single-exponential process, with rebinding time constants of 29.4 +/- 1 and 9.3 +/- 1 ps, respectively. This is very similar to results previously reported for nitric oxide binding to horseradish peroxidase.
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Affiliation(s)
- Flaviu Gruia
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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Gruia F, Kubo M, Ye X, Ionascu D, Lu C, Poole RK, Yeh SR, Champion PM. Coherence spectroscopy investigations of the low-frequency vibrations of heme: effects of protein-specific perturbations. J Am Chem Soc 2008; 130:5231-44. [PMID: 18355013 DOI: 10.1021/ja7104027] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Femtosecond coherence spectroscopy is used to probe the low-frequency (20-200 cm(-1)) vibrational modes of heme proteins in solution. Horseradish peroxidase (HRP), myoglobin (Mb), and Campylobacter jejuni globin (Cgb) are compared and significant differences in the coherence spectra are revealed. It is concluded that hydrogen bonding and ligand charge do not strongly affect the low-frequency coherence spectra and that protein-specific deformations of the heme group lower its symmetry and control the relative spectral intensities. Such deformations potentially provide a means for proteins to tune heme reaction coordinates, so that they can perform a broad array of specific functions. Native HRP displays complex spectral behavior above approximately 50 cm(-1) and very weak activity below approximately 50 cm(-1). Binding of the substrate analog, benzhydroxamic acid, leads to distinct changes in the coherence and Raman spectra of HRP that are consistent with the stabilization of a heme water ligand. The CN derivatives of the three proteins are studied to make comparisons under conditions of uniform heme coordination and spin-state. MbCN is dominated by a doming mode near 40 cm(-1), while HRPCN displays a strong oscillation at higher frequency (96 cm(-1)) that can be correlated with the saddling distortion observed in the X-ray structure. In contrast, CgbCN displays low-frequency coherence spectra that contain strong modes near 30 and 80 cm(-1), probably associated with a combination of heme doming and ruffling. HRPNO displays a strong doming mode near 40 cm(-1) that is activated by photolysis. The damping of the coherent motions is significantly reduced when the heme is shielded from solvent fluctuations by the protein material and reduced still further when T approximately < 50 K, as pure dephasing processes due to the protein-solvent phonon bath are frozen out.
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Affiliation(s)
- Flaviu Gruia
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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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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