Ultrafast ligand rebinding in the heme domain of the oxygen sensors FixL and Dos: General regulatory implications for heme-based sensors

Liebl, Ursula; Bouzhir-Sima, Latifa; Négrerie, Michel; Martin, Jean−Louis; Vos, Marten H.

doi:10.1073/pnas.192311699

Cited by 52 publications

(104 citation statements)

References 44 publications

(69 reference statements)

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“…Although this particular aspect involves further assumptions, it is clear that this confinement will increase the recombination rate constant. This explains the viscosity dependence of NO recombination (15), fast NO recombination in FixL (31), and the increase in CO recombination rate constant in some constrained enviroments as well.…”

Section: Resultsmentioning

confidence: 78%

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Spin-dependent mechanism for diatomic ligand binding to heme

Franzen

2002

Proc. Natl. Acad. Sci. U.S.A.

103

134

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The nature of diatomic ligand recombination in heme proteins is elucidated by using a Landau-Zener model for the electronic coupling in the recombination rate constant. The model is developed by means of explicit potential energy surfaces calculated by using density functional theory (DFT). The interaction of all possible spin states of the three common diatomic ligands, CO, NO, and O2, and high-spin heme iron is compared. The electronic coupling, rebinding barrier, and Landau-Zener force terms can be obtained and used to demonstrate significant differences among the ligands. In particular the intermediate spin states of NO (S ‫؍‬ 3͞2) and O2 (S ‫؍‬ 1) are shown to be bound states. Rapid recombination occurs from these bound states in agreement with experimental data. The slower phases of O2 recombination can be explained by the presence of two higher spin states, S ‫؍‬ 2 and S ‫؍‬ 3, which have a small and relatively large barrier to ligand recombination, respectively. By contrast, the intermediate spin state for CO is not a bound state, and the only recombination pathway for CO involves direct recombination from the S ‫؍‬ 2 state. This process is significantly slower according to the Landau-Zener model. Quantitative estimates of the parameters used in the rate constants provide a complete description that explains rebinding rates that range from femtoseconds to milliseconds at ambient temperature.T he binding of diatomic ligands to heme has been studied for over 100 years (1). The dissociation of carbon monoxide (CO), nitric oxide (NO), and oxygen (O 2 ) from the iron of heme occurs by both a thermal and photolytic process (2-4). In the case of flash photolysis, the fate of the ligand depends on the competition between the intrinsic (or geminate) recombination rate constant and protein relaxation in a docking site roughly 3.5 Å from the iron as well as ligand escape from the protein (5-8). Recombination of these ligands occurs by the reverse of the thermal process. The time dependence of recombination serves as a probe of the intrinsic properties of the diatomic ligand-iron bond formation and dynamic processes that occur in the protein that surrounds the heme cofactor (9-11). The startlingly different recombination dynamics of CO, NO, and O 2 have been attributed to spin states in earlier work (3,12). In the present study, the ground state potential energy surfaces for the potential energy surfaces of all possible spin states are calculated by using density functional theory (DFT) and compared within the context of a Landau-Zener (L-Z) model for the intrinsic recombination process of each of the ligands. The observed recombination kinetics of CO, NO, and O 2 can be influenced by protein dynamics if the intrinsic recombination rate constant is slower than these dynamics (10,(13)(14)(15)(16). When a combination of temperature and viscosity dependence is used, the general time scale for the intrinsic rate constants can be extracted, and it is these rate constants that are compared in the present work.The rebindin...

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Section: Resultsmentioning

confidence: 78%

“…The intrinsic rate constant NO Ϸ 10 ps for NO recombination is Ϸ5 orders of magnitude greater than that for CO. Even more rapid NO recombination has been observed as a single exponential process in heme proteins that have constrained distal structures that restrict NO diffusion (31).…”

mentioning

confidence: 99%

Spin-dependent mechanism for diatomic ligand binding to heme

Franzen

2002

Proc. Natl. Acad. Sci. U.S.A.

103

134

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“…The main rebinding occurs with a time constant of 8 ps; a minor (ϳ10%) ϳ50-ps phase was also observed. For comparison, in Mb a rebinding phase of ϳ5 ps was also observed, but a substantial fraction of the dissociated O 2 did not rebind on the picosecond time scale (33,(35)(36)(37). Thus, in the M80A mutant, the heme environment appeared to act as an effective "cage" not only for CO and NO but also for O 2 .…”

Section: Mutantmentioning

confidence: 94%

Ligand Dynamics in an Electron Transfer Protein

Silkstone

Jasaitis

Wilson

et al. 2007

Journal of Biological Chemistry

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Substitution of the heme coordination residue Met-80 of the electron transport protein yeast iso-1-cytochrome c allows external ligands like CO to bind and thus increase the effective redox potential. This mutation, in principle, turns the protein into a quasi-native photoactivable electron donor. We have studied the kinetic and spectral characteristics of geminate recombination of heme and CO in a series of single M80X (X ‫؍‬ Ala, Ser, Asp, Arg) mutants, using femtosecond transient absorption spectroscopy. In these proteins, all geminate recombination occurs on the picosecond and early nanosecond time scale, in a multiphasic manner, in which heme relaxation takes place on the same time scale. The extent of geminate recombination varies from >99% (Ala, Ser) to ϳ70% (Arg), the latter value being in principle low enough for electron injection studies. The rates and extent of the CO geminate recombination phases are much higher than in functional ligand-binding proteins like myoglobin, presumably reflecting the rigid and hydrophobic properties of the heme environment, which are optimized for electron transfer. Thus, the dynamics of CO recombination in cytochrome c are a tool for studying the heme pocket, in a similar way as NO in myoglobin. We discuss the differences in the CO kinetics between the mutants in terms of the properties of the heme environment and strategies to enhance the CO escape yield. Experiments on double mutants in which Phe-82 is replaced by Asp or Gly as well as the M80D substitution indicate that such steric changes substantially increase the motional freedom-dissociated CO.

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“…It is additionally possible, particularly in the case of the M95H mutant, that the O 2 access channel is widened or the electrostatic character of the O 2 access channel is altered, similar to that observed in myoglobin distal mutants. Liebl et al (39) reported that the decay phase of geminate recombination of O 2 with the isolated PAS domain is 5.3 ps. This value is not significantly different from those obtained with FixL and myoglobin (39).…”

Section: Fig 6 Ft Ir Spectra Of Co Complexes Of the Wild Type (--)mentioning

confidence: 99%

“…Liebl et al (39) reported that the decay phase of geminate recombination of O 2 with the isolated PAS domain is 5.3 ps. This value is not significantly different from those obtained with FixL and myoglobin (39). For myoglobin, the overall k off for O 2 is governed equally by the rate of Fe(II)-O 2 bond disruption and the rate of O 2 dissociation from the protein (38).…”

Section: Fig 6 Ft Ir Spectra Of Co Complexes Of the Wild Type (--)mentioning

confidence: 99%

Binding of Oxygen and Carbon Monoxide to a Heme-regulated Phosphodiesterase from Escherichia coli

Taguchi

Matsui

Igarashi

et al. 2004

Journal of Biological Chemistry

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The heme-regulated phosphodiesterase, Ec DOS, is a redox sensor that uses the heme in its PAS domain to regulate catalysis. The rate of O 2 association (k on ) with full-length Ec DOS is extremely slow at 0. 0019 The phosphodiesterase (PDE) 1 from Escherichia coli, Ec DOS, is composed of an N-terminal heme-bound PAS domain and a C-terminal PDE catalytic domain (1). The basic physicochemical characteristics and function of this enzyme have been partially elucidated by our group and that of Kitagawa et al. (1,2). PDE activity is dependent on the redox state of Ec DOS in that the enzyme is active only when the heme is in the Fe(II) state. Changes in the redox state of the heme bound to the N-terminal PAS domain may induce a subtle conformational change, which intramolecularly transmits signals to the C-terminal PDE domain to initiate and/or regulate catalysis. Ec DOS therefore constitutes a novel class of heme enzymes designated "heme-based sensors" (3-5). These include proteins such as FixL (6, 7), CooA (8, 9), sGC (10, 11), and Hem-AT (12, 13). In these enzymes, association or dissociation of the exogenous axial ligand (O 2 , CO, or NO) from the heme iron leads to protein conformational changes, which in turn transmit signals to other domains to regulate catalysis or binding to DNA. The Ec DOS signal transducing mechanism appears to be unique, since changes in the redox state of the PAS domain, rather than iron coordination chemistry, are responsible for signal transduction (1). However, in other words, signal transduction triggered by ligand binding (CO and NO) is common to Ec DOS and FixL, based on the finding that CO or NO binding abolishes catalysis by Ec DOS (1).The physicochemical properties of the isolated heme-bound PAS domain of Ec DOS were initially characterized by GillesGonzales and colleagues (14). The kinetics of exogenous axial ligand binding to the heme protein and associated equilibrium constants provide useful information on the structure and characteristics of the heme distal site and ligand access channel (16 -19). It is important to study O 2 and CO binding, particularly to full-length Ec DOS, to clarify whether the enzyme is a direct O 2 sensor. These analyses would also be useful in elucidating the structure of the heme distal site and ligand access channel and their relation to the signal transduction mechanism. Based on the amino acid sequence alignment and crystal structure of a similar PAS enzyme, FixL (7,20,21), Met-95 is suggested as a heme axial ligand trans to His-77.In the present study, we report rate and equilibrium constants for O 2 and CO binding to the full-length enzyme in the Fe(II) state, isolated heme-bound PAS domain, and Met-95 * The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.‡ To whom correspondence should be addressed: Institute of Multidisciplinary Research for Advanced Materials, Tohok...

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Ultrafast ligand rebinding in the heme domain of the oxygen sensors FixL and Dos: General regulatory implications for heme-based sensors

Cited by 52 publications

References 44 publications

Spin-dependent mechanism for diatomic ligand binding to heme

Spin-dependent mechanism for diatomic ligand binding to heme

Ligand Dynamics in an Electron Transfer Protein

Binding of Oxygen and Carbon Monoxide to a Heme-regulated Phosphodiesterase from Escherichia coli

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