Accessibility of the distal heme face, rather than Fe-His bond strength, determines the heme-nitrosyl coordination number of cytochromes c': evidence from spectroscopic studies

A Heme Pocket Aromatic Quadrupole Modulates Gas Binding to Cytochrome c'-β: Implications for NO Sensors

The structural basis by which gas-binding heme proteins control their interactions with NO, CO, and O₂, is fundamental to enzymology, biotechnology and human health. Cytochromes c´ (cyts c´) are a group of putative NO-binding heme proteins that fall into two families: the well characterised four alpha helix bundle fold (cyts c´-α) and an unrelated family with a largely beta sheet fold (cyts c´-β) resembling that of cytochromes P460. A recent structure of cyt c´-β from Methylococcus capsulatus Bath (McCP-β) revealed two heme pocket phenylalanine residues (Phe 32 and Phe 61) positioned near the distal gas binding site. This feature, dubbed the "Phe cap", is highly conserved within the sequences of other cyts c´-β, but is absent in their close homologues, the hydroxylamine oxidizing cytochromes P460, although some do contain a single Phe residue. Here we report an integrated structural, spectroscopic, and kinetic characterization of McCP-β complexes with diatomic gases, focusing on the interaction of the Phe cap with NO and CO. Significantly, crystallographic and resonance Raman data show that orientation of the electron rich aromatic ring face of Phe 32 towards distally-bound NO or CO is associated with weakened backbonding and higher off rates. Moreover, we propose that an aromatic quadrupole also contributes to the unusually weak backbonding reported for some heme-based gas sensors, including the mammalian NO-sensor, soluble guanylate cyclase (sGC). Collectively, this study sheds light on the influence of highly conserved distal Phe residues on heme-gas complexes of cytochrome c'-β, including the potential for aromatic quadrupoles to modulate NO and CO binding in other heme proteins.

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

Structure and reactivity of chlorite dismutase nitrosyls

Ferric nitrosyl ({FeNO}6) and ferrous nitrosyl ({FeNO}7) complexes of the chlorite dismutases (Cld) from Klebsiella pneumoniae and Dechloromonas aromatica have been characterized using UV-visible absorbance and Soret-excited resonance Raman spectroscopy. Both of these Clds form kinetically stable {FeNO}6 complexes and they occupy a unique region of ν(Fe-NO)/ν(N-O) correlation space for proximal histidine liganded heme proteins, characteristic of weak Fe-NO and N-O bonds. This location is attributed to admixed FeIII-NO character of the {FeNO}6 ground state. Cld {FeNO}6 complexes undergo slow reductive nitrosylation to yield {FeNO}7 complexes. The effects of proximal and distal environment on reductive nitroylsation rates for these dimeric and pentameric Clds are reported. The ν(Fe-NO) and ν(N-O) frequencies for Cld {FeNO}7 complexes reveal both six-coordinate (6c) and five-coordinate (5c) nitrosyl hemes. These 6c and 5c forms are in a pH dependent equilibrium. The 6c and 5c {FeNO}7 Cld frequencies provided positions of both Clds on their respective ν(Fe-NO) vs ν(N-O) correlation lines. The 6c {FeNO}7 complexes fall below (along the ν(Fe-NO) axis) the correlation line that reports hydrogen-bond donation to NNO, which is consistent with a relatively weak Fe-NO bond. Kinetic and spectroscopic evidence is consistent with the 5c {FeNO}7 Clds having NO coordinated on the proximal side of the heme, analogous to 5c {FeNO}7 hemes in proteins known to have NO sensing functions.

A nitric oxide-binding heterodimeric cytochrome c complex from the anammox bacterium Kuenenia stuttgartiensis binds to hydrazine synthase

Anaerobic ammonium oxidation (anammox) is a microbial process responsible for significant nitrogen loss from the oceans and other ecosystems. The redox reactions at the heart of anammox are catalyzed by large multiheme enzyme complexes that rely on small cytochrome c proteins for electron shuttling. Among the most highly abundant of these cytochromes is a unique heterodimeric complex composed of class I and class II c-type cytochromes called NaxLS, which has distinctive biochemical and spectroscopic properties. Here, we present the 1.7 Å resolution crystal structure of this complex from the anammox organism Kuenenia stuttgartiensis (KsNaxLS). The structure reveals that the heme irons in each subunit exhibit a rare His/Cys ligation, which, as we show by substitution, causes the observed unusual spectral properties. Unlike its individual subunits, the KsNaxLS complex binds nitric oxide (NO) only at the distal heme side, forming 6cNO adducts. This is likely due to steric immobilization of the proximal heme-binding motifs upon complex formation, a finding that may be of functional relevance, because NO is an intermediate in the central anammox metabolism. Pulldown experiments with K. stuttgartiensis cell-free extract showed that the KsNaxLS complex binds specifically to one of the central anammox enzyme complexes, hydrazine synthase, which uses NO as one of its substrates. It is therefore possible that the KsNaxLS complex plays a role in binding the volatile NO to retain it in the cell for transfer to hydrazine synthase. Alternatively, we propose that KsNaxLS may shuttle electrons to this enzyme complex.

Structural and functional insights into thermally stable cytochrome c' from a thermophile

Thermophilic Hydrogenophilus thermoluteolus cytochrome c′ (PHCP) exhibits higher thermal stability than a mesophilic counterpart, Allochromatium vinosum cytochrome c′ (AVCP), which has a homo‐dimeric structure and ligand‐binding ability. To understand the thermal stability mechanism and ligand‐binding ability of the thermally stable PHCP protein, the crystal structure of PHCP was first determined. It formed a homo‐dimeric structure, the main chain root mean square deviation (rmsd) value between PHCP and AVCP being 0.65 Å. In the PHCP structure, six specific residues appeared to strengthen the heme‐related and subunit–subunit interactions, which were not conserved in the AVCP structure. PHCP variants having altered subunit–subunit interactions were more severely destabilized than ones having altered heme‐related interactions. The PHCP structure further revealed a ligand‐binding channel and a penta‐coordinated heme, as observed in the AVCP protein. A spectroscopic study clearly showed that some ligands were bound to the PHCP protein. It is concluded that the dimeric PHCP from the thermophile is effectively stabilized through heme‐related and subunit–subunit interactions with conservation of the ligand‐binding ability.

Brief Summary

We report the X‐ray crystal structure of cytochrome c′ (PHCP) from thermophilic Hydrogenophilus thermoluteolus. The high thermal stability of PHCP was attributed to heme‐related and subunit–subunit interactions, which were confirmed by a mutagenesis study. The ligand‐binding ability of PHCP was examined by spectrophotometry. PHCP acquired the thermal stability with conservation of the ligand‐binding ability. This study furthers the understanding of the stability and function of cytochromes c.

PDB Code(s): 5B3I

Engineering proximal vs. distal heme-NO coordination via dinitrosyl dynamics: implications for NO sensor design

Proximal vs. distal heme-NO coordination is a novel strategy for selective gas response in heme-based NO-sensors. In the case of Alcaligenes xylosoxidans cytochrome c' (AXCP), formation of a transient distal 6cNO complex is followed by scission of the trans Fe-His bond and conversion to a proximal 5cNO product via a putative dinitrosyl species. Here we show that replacement of the AXCP distal Leu16 residue with smaller or similar sized residues (Ala, Val or Ile) traps the distal 6cNO complex, whereas Leu or Phe residues lead to a proximal 5cNO product with a transient or non-detectable distal 6cNO precursor. Crystallographic, spectroscopic, and kinetic measurements of 6cNO AXCP complexes show that increased distal steric hindrance leads to distortion of the Fe-N-O angle and flipping of the heme 7-propionate. However, it is the kinetic parameters of the distal NO ligand that determine whether 6cNO or proximal 5cNO end products are formed. Our data support a 'balance of affinities' mechanism in which proximal 5cNO coordination depends on relatively rapid release of the distal NO from the dinitrosyl precursor. This mechanism, which is applicable to other proteins that form transient dinitrosyls, represents a novel strategy for 5cNO formation that does not rely on an inherently weak Fe-His bond. Our data suggest a general means of engineering selective gas response into biologically-derived gas sensors in synthetic biology.

Conformational control of the binding of diatomic gases to cytochrome c'

The cytochromes c' (CYTcp) are found in denitrifying, methanotrophic and photosynthetic bacteria. These proteins are able to form stable adducts with CO and NO but not with O2. The binding of NO to CYTcp currently provides the best structural model for the NO activation mechanism of soluble guanylate cyclase. Ligand binding in CYTcps has been shown to be highly dependent on residues in both the proximal and distal heme pockets. Group 1 CYTcps typically have a phenylalanine residue positioned close to the distal face of heme, while for group 2, this residue is typically leucine. We have structurally, spectroscopically and kinetically characterised the CYTcp from Shewanella frigidimarina (SFCP), a protein that has a distal phenylalanine residue and a lysine in the proximal pocket in place of the more common arginine. Each monomer of the SFCP dimer folds as a 4-alpha-helical bundle in a similar manner to CYTcps previously characterised. SFCP exhibits biphasic binding kinetics for both NO and CO as a result of the high level of steric hindrance from the aromatic side chain of residue Phe 16. The binding of distal ligands is thus controlled by the conformation of the phenylalanine ring. Only a proximal 5-coordinate NO adduct, confirmed by structural data, is observed with no detectable hexacoordinate distal NO adduct.

Cytochromes c': Structure, Reactivity and Relevance to Haem-Based Gas Sensing

Cytochromes c' are a group of class IIa cytochromes with pentacoordinate haem centres and are found in photosynthetic, denitrifying and methanotrophic bacteria. Their function remains unclear, although roles in nitric oxide (NO) trafficking during denitrification or in cellular defence against nitrosoative stress have been proposed. Cytochromes c' are typically dimeric with each c-type haem-containing monomer folding as a four-α-helix bundle. Their hydrophobic and crowded distal sites impose severe restrictions on the binding of distal ligands, including diatomic gases. By contrast, NO binds to the proximal haem face in a similar manner to that of the eukaryotic NO sensor, soluble guanylate cyclase and bacterial analogues. In this review, we focus on how structural features of cytochromes c' influence haem spectroscopy and reactivity with NO, CO and O2. We also discuss the relevance of cytochrome c' to understanding the mechanisms of gas binding to haem-based sensor proteins.

Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy

It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularly when applied in situ at macromolecular crystallography beamlines, allow spectroscopic investigations of redox and ligand states and the identification of reaction intermediates in protein crystals during the collection of structural data. Single-crystal resonance Raman spectroscopy was carried out in combination with macromolecular crystallography on Swiss Light Source beamline X10SA using cytochrome c' from Alcaligenes xylosoxidans. This allowed the fingerprinting and validation of different redox and ligand states, identification of vibrational modes and identification of intermediates together with monitoring of radiation-induced changes. This combined approach provides a powerful tool to obtain complementary data and correctly assign the true oxidation and ligand state(s) in redox-protein crystals.

Vibrational spectroscopic analyses of unique yellow feather pigments (spheniscins) in penguins

Many animals extract, synthesize and refine chemicals for colour display, where a range of compounds and structures can produce a diverse colour palette. Feather colours, for example, span the visible spectrum and mostly result from pigments in five chemical classes (carotenoids, melanins, porphyrins, psittacofulvins and metal oxides). However, the pigment that generates the yellow colour of penguin feathers appears to represent a sixth, poorly characterized class of feather pigments. This pigment class, here termed 'spheniscin', is displayed by half of the living penguin genera; the larger and richer colour displays of the pigment are highly attractive. Using Raman and mid-infrared spectroscopies, we analysed yellow feathers from two penguin species (king penguin, Aptenodytes patagonicus; macaroni penguin, Eudyptes chrysolophus) to further characterize spheniscin pigments. The Raman spectrum of spheniscin is distinct from spectra of other feather pigments and exhibits 17 distinctive spectral bands between 300 and 1700 cm(-1). Spectral bands from the yellow pigment are assigned to aromatically bound carbon atoms, and to skeletal modes in an aromatic, heterocyclic ring. It has been suggested that the penguin pigment is a pterin compound; Raman spectra from yellow penguin feathers are broadly consistent with previously reported pterin spectra, although we have not matched it to any known compound. Raman spectroscopy can provide a rapid and non-destructive method for surveying the distribution of different classes of feather pigments in the avian family tree, and for correlating the chemistry of spheniscin with compounds analysed elsewhere. We suggest that the sixth class of feather pigments may have evolved in a stem-lineage penguin and endowed modern penguins with a costly plumage trait that appears to be chemically unique among birds.

Picosecond binding of the His ligand to four-coordinate heme in cytochrome c': a one-way gate for releasing proximal NO

We provide a direct demonstration of a "kinetic trap" mechanism in the proximal 5-coordinate heme-nitrosyl complex (5c-NO) of cytochrome c' from Alcaligenes xylosoxidans (AXCP) in which picosecond rebinding of the endogenous His ligand following heme-NO dissociation acts as a one-way gate for the release of proximal NO into solution. This demonstration is based upon picosecond transient absorption changes following NO photodissociation of the proximal 5c-NO AXCP complex. We have determined the absolute transient absorption spectrum of 4-coordinate ferrous heme to which NO rebinds with a time constant τ(NO) = 7 ps (k(NO) = 1.4 × 10(11) s(-1)) and shown that rebinding of the proximal histidine to the 4-coordinate heme takes place with a time constant τ(His) = 100 ± 10 ps (k(His) = 10(10) s(-1)) after the release of NO from the proximal heme pocket. This rapid His reattachment acts as a one-way gate for releasing proximal NO by precluding direct proximal NO rebinding once it has left the proximal heme pocket and requiring NO rebinding from solution to proceed via the distal heme face.

How do heme-protein sensors exclude oxygen? Lessons learned from cytochrome c', Nostoc puntiforme heme nitric oxide/oxygen-binding domain, and soluble guanylyl cyclase

SIGNIFICANCE

Ligand selectivity for dioxygen (O(2)), carbon monoxide (CO), and nitric oxide (NO) is critical for signal transduction and is tailored specifically for each heme-protein sensor. Key NO sensors, such as soluble guanylyl cyclase (sGC), specifically recognized low levels of NO and achieve a total O(2) exclusion. Several mechanisms have been proposed to explain the O(2) insensitivity, including lack of a hydrogen bond donor and negative electrostatic fields to selectively destabilize bound O(2), distal steric hindrance of all bound ligands to the heme iron, and restriction of in-plane movements of the iron atom.

RECENT ADVANCES

Crystallographic structures of the gas sensors, Thermoanaerobacter tengcongensis heme-nitric oxide/oxygen-binding domain (Tt H-NOX(1)) or Nostoc puntiforme (Ns) H-NOX, and measurements of O(2) binding to site-specific mutants of Tt H-NOX and the truncated β subunit of sGC suggest the need for a H-bonding donor to facilitate O(2) binding.

CRITICAL ISSUES

However, the O(2) insensitivity of full length sGC with a site-specific replacement of isoleucine by a tyrosine on residue 145 and the very slow autooxidation of Ns H-NOX and cytochrome c' suggest that more complex mechanisms have evolved to exclude O(2) but retain high affinity NO binding. A combined graphical analysis of ligand binding data for libraries of heme sensors, globins, and model heme shows that the NO sensors dramatically inhibit the formation of six-coordinated NO, CO, and O(2) complexes by direct distal steric hindrance (cyt c'), proximal constraints of in-plane iron movement (sGC), or combinations of both following a sliding scale rule. High affinity NO binding in H-NOX proteins is achieved by multiple NO binding steps that produce a high affinity five-coordinate NO complex, a mechanism that also prevents NO dioxygenation.

FUTURE DIRECTIONS

Knowledge advanced by further extensive test of this "sliding scale rule" hypothesis should be valuable in guiding novel designs for heme based sensors.

Carbon monoxide poisoning is prevented by the energy costs of conformational changes in gas-binding haemproteins

Carbon monoxide (CO) is a product of haem metabolism and organisms must evolve strategies to prevent endogenous CO poisoning of haemoproteins. We show that energy costs associated with conformational changes play a key role in preventing irreversible CO binding. AxCYTcp is a member of a family of haem proteins that form stable 5c-NO and 6c-CO complexes but do not form O(2) complexes. Structure of the AxCYTcp-CO complex at 1.25 Å resolution shows that CO binds in two conformations moderated by the extent of displacement of the distal residue Leu16 toward the haem 7-propionate. The presence of two CO conformations is confirmed by cryogenic resonance Raman data. The preferred linear Fe-C-O arrangement (170 ± 8°) is accompanied by a flip of the propionate from the distal to proximal face of the haem. In the second conformation, the Fe-C-O unit is bent (158 ± 8°) with no flip of propionate. The energetic cost of the CO-induced Leu-propionate movements is reflected in a 600 mV (57.9 kJ mol(-1)) decrease in haem potential, a value in good agreement with density functional theory calculations. Substitution of Leu by Ala or Gly (structures determined at 1.03 and 1.04 Å resolutions) resulted in a haem site that binds CO in the linear mode only and where no significant change in redox potential is observed. Remarkably, these variants were isolated as ferrous 6c-CO complexes, attributable to the observed eight orders of magnitude increase in affinity for CO, including an approximately 10,000-fold decrease in the rate of dissociation. These new findings have wide implications for preventing CO poisoning of gas-binding haem proteins.

Distal-to-proximal NO conversion in hemoproteins: the role of the proximal pocket

Hemoproteins play central roles in the formation and utilization of nitric oxide (NO) in cellular signaling, as well as in protection against nitrosative stress. Key to heme-nitrosyl function and reactivity is the Fe coordination number (5 or 6). For (five-coordinate) 5c-NO complexes, the potential for NO to bind on either heme face exists, as in the microbial cytochrome c' from Alcaligenes xylosoxidans (AxCYTcp), which forms a stable proximal 5c-NO complex via a distal six-coordinate NO intermediate and a putative dinitrosyl species. Strong parallels between the NO-binding kinetics of AxCYTcp, the eukaryotic NO sensor soluble guanylate cyclase, and the ferrocytochrome c/cardiolipin complex have led to the suggestion that a distal-to-proximal NO switch could contribute to the selective ligand responses in gas-sensing hemoproteins. The proximal NO-binding site in AxCYTcp is close to a conserved basic (Arg124) residue that is postulated to modulate NO reactivity. We have replaced Arg124 by five different amino acids and have determined high-resolution (1.07-1.40 Å) crystallographic structures with and without NO. These, together with kinetic and resonance Raman data, provide new insights into the mechanism of distal-to-proximal heme-NO conversion, including the determinants of Fe-His bond scission. The Arg124Ala variant allowed us to determine the structure of an analog of the previously unobserved key 5c-NO distal intermediate species. The very high resolution structures combined with the extensive spectroscopic and kinetic data have allowed us to provide a fresh insight into heme reactivity towards NO, a reaction that is of wide importance in biology.

Electronic structure and dynamics of nitrosyl porphyrins

Nitric oxide (NO) is a signaling molecule employed to regulate essential physiological processes. Thus, there is great interest in understanding the interaction of NO with heme, which is found at the active site of many proteins that recognize NO, as well as those involved in its creation and elimination. We summarize what we have learned from investigations of the structure, vibrational properties, and conformational dynamics of NO complexes with ferrous porphyrins, as well as computational investigations in support of these experimental studies. Multitemperature crystallographic data reveal variations in the orientational disorder of the nitrosyl ligand. In some cases, equilibria among NO orientations can be analyzed using the van't Hoff relationship and the free energy and enthalpy of the solid-state transitions evaluated experimentally. Density functional theory (DFT) calculations predict that intrinsic barriers to torsional rotation are smaller than thermal energies at physiological temperatures, and the coincidence of observed NO orientations with minima in molecular mechanics potentials indicates that nonbonded interactions with other chemical groups control the conformational freedom of the bound NO. In favorable cases, reduced disorder at low temperatures exposes subtle structural features including off-axis tilting of the Fe-NO bond and anisotropy of the equatorial Fe-N bonds. We also present the results of nuclear resonance vibrational spectroscopy measurements on oriented single crystals of [Fe(TPP)(NO)] and [Fe(TPP)(1-MeIm)(NO)]. These describe the anisotropic vibrational motion of iron in five- and six-coordinate heme-NO complexes and reveal vibrations of all Fe-ligand bonds as well as low-frequency molecular distortions associated with the doming of the heme upon ligand binding. A quantitative comparison with predicted frequencies, amplitudes, and directions facilitates identification of the vibrational modes but also suggests that commonly used DFT functionals are not fully successful at capturing the trans interaction between the axial NO and imidazole ligands. This supports previous conclusions that heme-NO complexes exhibit an unusual degree of variability with respect to the computational method, and we speculate that this variability hints at a genuine electronic instability that a protein can exploit to tune its reactivity. We anticipate that ongoing characterization of heme-NO complexes will deepen our understanding of their structure, dynamics, and reactivity.

Is the redox state of the ci heme of the cytochrome b6f complex dependent on the occupation and structure of the Qi site and vice versa?

Oxidoreductases of the cytochrome bc(1)/b(6)f family transfer electrons from a liposoluble quinol to a soluble acceptor protein and contribute to the formation of a transmembrane electrochemical potential. The crystal structure of cyt b(6)f has revealed the presence in the Q(i) site of an atypical c-type heme, heme c(i). Surprisingly, the protein does not provide any axial ligand to the iron of this heme, and its surrounding structure suggests it can be accessed by exogenous ligand. In this work we describe a mutagenesis approach aimed at characterizing the c(i) heme and its interaction with the Q(i) site environment. We engineered a mutant of Chlamydomonas reinhardtii in which Phe(40) from subunit IV was substituted by a tyrosine. This results in a dramatic slowing down of the reoxidation of the b hemes under single flash excitation, suggesting hindered accessibility of the heme to its quinone substrate. This modified accessibility likely originates from the ligation of the heme iron by the phenol(ate) side chain introduced by the mutation. Indeed, it also results in a marked downshift of the c(i) heme midpoint potential (from +100 mV to -200 mV at pH 7). Yet the overall turnover rate of the mutant cytochrome b(6)f complex under continuous illumination was found similar to the wild type one, both in vitro and in vivo. We propose that, in the mutant, a change in the ligation state of the heme upon its reduction could act as a redox switch that would control the accessibility of the substrate to the heme and trigger the catalysis.

Reversible NO motion in crystalline [Fe(Porph)(1-MeIm)(NO)] derivatives

The synthesis, characterization, and X-ray structures of three low-spin (nitrosyl)iron(II) tetraarylporphyrinates, [Fe(TpXPP)(NO)(1-MeIm)], where X = F (in a triclinic and a monoclinic form) and OCH(3) are reported. All three molecules, at 100 K, have a single orientation of NO. These structures are the first examples of ordered NO's in [Fe(Porph)(NO)(1-MeIm)] complexes. The three new derivatives have similar structural features including a previously unnoted "bowing" of the N(NO)-Fe-N(Im) angle caused by a concerted tilting of the axial Fe-N(NO) and Fe-N(Im) bonds. Structural features such as the displacement of Fe out of the mean porphyrin plane toward NO, tilting of the Fe-N(NO) bond off the heme normal, and the asymmetry of the Fe-N(por) bonds further strengthen and confirm observations from earlier studies. The [Fe(TpXPP)(NO)(1-MeIm)] complexes were also studied at temperatures between 125 and 350 K to investigate temperature-dependent variations and trends in the coordination group geometry. At varying temperatures (above 150 K), all three derivatives display a second orientation of the NO ligand. The population and depopulation of this second orientation are thermally driven, with no apparent hysteresis. Crystal packing appears to be the significant feature in defining the order/disorder of the NO ligand. The length of the bond trans to NO, Fe-N(Im), was also found to be sensitive to temperature variation. The Fe-N(Im) bond length increases with increased temperature, whereas no other bonds change appreciably. The temperature-dependent Fe-N(Im) bond length change and cell volume changes are consistent with a "soft" Fe-N(Im) bond. Variable-temperature measurements show that the N-O stretching frequency changes with the Fe-N(Im) bond length. Temperature-dependent changes in the Fe-NIm bond length and N-O stretching frequency were also found to be completely reversible with no apparent hysteresis.

Delivery of nitric oxide for analysis of the function of cytochrome c'

On delivery of nitric oxide (NO) to protein samples (e.g., cytochrome c'), for spectroscopic experiments it is important to avoid exposure to oxygen and to remove contaminants from the NO gas. We describe a number of techniques for steady-state UV/Vis spectrophotometry and pre-steady-state stopped-flow spectrophotometry analysis of cytochrome c'.

Electron paramagnetic resonance and Mössbauer spectroscopy of intact mitochondria from respiring Saccharomyces cerevisiae

Mitochondria from respiring cells were isolated under anaerobic conditions. Microscopic images were largely devoid of contaminants, and samples consumed O(2) in an NADH-dependent manner. Protein and metal concentrations of packed mitochondria were determined, as was the percentage of external void volume. Samples were similarly packed into electron paramagnetic resonance tubes, either in the as-isolated state or after exposure to various reagents. Analyses revealed two signals originating from species that could be removed by chelation, including rhombic Fe(3+) (g = 4.3) and aqueous Mn(2+) ions (g = 2.00 with Mn-based hyperfine). Three S = 5/2 signals from Fe(3+) hemes were observed, probably arising from cytochrome c peroxidase and the a(3):Cu(b) site of cytochrome c oxidase. Three Fe/S-based signals were observed, with averaged g values of 1.94, 1.90 and 2.01. These probably arise, respectively, from the [Fe(2)S(2)](+) cluster of succinate dehydrogenase, the [Fe(2)S(2)](+) cluster of the Rieske protein of cytochrome bc (1), and the [Fe(3)S(4)](+) cluster of aconitase, homoaconitase or succinate dehydrogenase. Also observed was a low-intensity isotropic g = 2.00 signal arising from organic-based radicals, and a broad signal with g (ave) = 2.02. Mössbauer spectra of intact mitochondria were dominated by signals from Fe(4)S(4) clusters (60-85% of Fe). The major feature in as-isolated samples, and in samples treated with ethylenebis(oxyethylenenitrilo)tetraacetic acid, dithionite or O(2), was a quadrupole doublet with DeltaE (Q) = 1.15 mm/s and delta = 0.45 mm/s, assigned to [Fe(4)S(4)](2+) clusters. Substantial high-spin non-heme Fe(2+) (up to 20%) and Fe(3+) (up to 15%) species were observed. The distribution of Fe was qualitatively similar to that suggested by the mitochondrial proteome.

Quantitative vibrational dynamics of iron in carbonyl porphyrins

We use nuclear resonance vibrational spectroscopy and computational predictions based on density functional theory (DFT) to explore the vibrational dynamics of (57)Fe in porphyrins that mimic the active sites of histidine-ligated heme proteins complexed with carbon monoxide. Nuclear resonance vibrational spectroscopy yields the complete vibrational spectrum of a Mössbauer isotope, and provides a valuable probe that is not only selective for protein active sites but quantifies the mean-squared amplitude and direction of the motion of the probe nucleus, in addition to vibrational frequencies. Quantitative comparison of the experimental results with DFT calculations provides a detailed, rigorous test of the vibrational predictions, which in turn provide a reliable description of the observed vibrational features. In addition to the well-studied stretching vibration of the Fe-CO bond, vibrations involving the Fe-imidazole bond, and the Fe-N(pyr) bonds to the pyrrole nitrogens of the porphyrin contribute prominently to the observed experimental signal. All of these frequencies show structural sensitivity to the corresponding bond lengths, but previous studies have failed to identify the latter vibrations, presumably because the coupling to the electronic excitation is too small in resonance Raman measurements. We also observe the FeCO bending vibrations, which are not Raman active for these unhindered model compounds. The observed Fe amplitude is strongly inconsistent with three-body oscillator descriptions of the FeCO fragment, but agrees quantitatively with DFT predictions. Over the past decade, quantum chemical calculations have suggested revised estimates of the importance of steric distortion of the bound CO in preventing poisoning of heme proteins by carbon monoxide. Quantitative agreement with the predicted frequency, amplitude, and direction of Fe motion for the FeCO bending vibrations provides direct experimental support for the quantum chemical description of the energetics of the FeCO unit.

Differential sensing of protein influences by NO and CO vibrations in heme adducts

Heme proteins bind the gaseous ligands XO (X = C, N, O) via backbonding from Fe d(pi) electrons. Backbonding is modulated by distal interactions of the bound ligand with the surrounding protein and by variations in the strength of the trans proximal ligand. Vibrational modes associated with FeX and XO bond stretching coordinates report on these interactions, but the interpretive framework developed for CO adducts, involving anticorrelations of nuFeC and nuCO, has seemed not to apply to NO adducts. We have now obtained an excellent anticorrelation of nuFeN and nuNO, via resonance Raman spectroscopy on (N-methylimidazole)Fe(II)TPP-Y(NO), where TPP-Y is tetraphenylporphine with electron-donating or -withdrawing substituents, Y, that modulate the backbonding; the problem of laser-induced dissociation of the axial base was circumvented by using frozen solutions. New data are also reported for CO adducts. The anticorrelations are supported by DFT calculations of structures and spectra. When protein data are examined, the NO adducts show large deviations from the modeled anticorrelation when there are distal H-bonds or positive charges. These deviations are proposed to result from closing of the FeNO angle due to a shift in the valence isomer equilibrium toward the Fe(III)(NO-) form, an effect that is absent in CO adducts. The differing vibrational patterns of CO and NO adducts provide complementary information with respect to protein interactions, which may help to elucidate the mechanisms of ligand discrimination and signaling in heme sensor proteins.

Molecular basis for nitric oxide dynamics and affinity with Alcaligenes xylosoxidans cytochrome c

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.

Nitric oxide binding to prokaryotic homologs of the soluble guanylate cyclase beta1 H-NOX domain

The heme cofactor in soluble guanylate cyclase (sGC) is a selective receptor for NO, an important signaling molecule in eukaryotes. The sGC heme domain has been localized to the N-terminal 194 amino acids of the beta1 subunit of sGC and is a member of a family of conserved hemoproteins, called the H-NOX family (Heme-Nitric Oxide and/or OXygen-binding domain). Three new members of this family have now been cloned and characterized, two proteins from Legionella pneumophila (L1 H-NOX and L2 H-NOX) and one from Nostoc punctiforme (Np H-NOX). Like sGC, L1 H-NOX forms a 5-coordinate Fe(II)-NO complex. However, both L2 H-NOX and Np H-NOX form temperature-dependent mixtures of 5- and 6-coordinate Fe(II)-NO complexes; at low temperature, they are primarily 6-coordinate, and at high temperature, the equilibrium is shifted toward a 5-coordinate geometry. This equilibrium is fully reversible with temperature in the absence of free NO. This process is analyzed in terms of a thermally labile proximal Fe(II)-His bond and suggests that in both the 5- and 6-coordinate Fe(II)-NO complexes of L2 H-NOX and Np H-NOX, NO is bound in the distal heme pocket of the H-NOX fold. NO dissociation kinetics for L1 H-NOX and L2 H-NOX have been determined and support a model in which NO dissociates from the distal side of the heme in both 5- and 6-coordinate complexes.

Role of Heme Iron Coordination and Protein Structure in the Dynamics and Geminate Rebinding of Nitric Oxide to the H93G Myoglobin Mutant

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.

ENDOR of NO-Ligated Cytochrome c‘

The five-coordinate NO-bound heme in cytochrome c' from an overexpressing variant of denitrifying R. sphaeroides 2.4.3 was investigated by proton, nitrogen, and deuterium Q-band ENDOR (electron nuclear double resonance). ENDOR was a direct probe of the unpaired electron density on the nitrogen of NO and, as measured across the EPR line shape, showed a hyperfine coupling range from 36 to 44 MHz for 14NO and 51 to 63 MHz for 15NO. The smallest NO coupling occurred at an electronic g-tensor axis perpendicular to the FeNO plane, and the largest hyperfine coupling occurred in the FeNO plane where the highest nitrogen valence spin density is located. The isotropic component of the NO hyperfine coupling indicated that the electron spin on the NO is not simply in a pi orbital having only 2p character but is in an orbital having 2s and 2p character in a 1:2 ratio. ENDOR frequencies from heme meso-protons, assigned with reference to porphyrin models, were determined to result from an anisotropic hyperfine tensor. This tensor indicated the orientation of the heme with respect to the FeNO plane and showed that the FeNO plane bisects the heme N-Fe-N 90 degrees angle. ENDOR provided additional structural information through dipolar couplings, as follows: (1) to the nearest proton of the Phe14 ring, approximately 3.1 A away from the heme iron, where Phe14 is positioned to occlude binding of NO as a 6th (distal) ligand; (2) to exchangeable deuterons assigned to Arg127 which may H-bond with the proximal NO ligand.

Unexpected NO-dependent DNA binding by the CooA homolog from Carboxydothermus hydrogenoformans

CooA, the CO-sensing heme protein from Rhodospirillum rubrum, regulates the expression of genes that encode a CO-oxidation system, allowing R. rubrum to use CO as a sole energy source. To better understand the gas-sensing regulation mechanism used by R. rubrum CooA and its homologs in other organisms, we characterized spectroscopically and functionally the Fe(II), Fe(II)-NO, and Fe(II)-CO forms of CooA from Carboxydothermus hydrogenoformans. Surprisingly, and unlike R. rubrum CooA, C. hydrogenoformans CooA binds NO to form a six-coordinate Fe(II)-NO heme that is active for DNA binding in vitro and in vivo. In contrast, R. rubrum CooA, which is exquisitely specific for CO, forms a five-coordinate Fe(II)-NO adduct that is inactive for DNA binding. Based on analyses of protein variants and temperature studies, NO-dependent DNA binding by C. hydrogenoformans CooA is proposed to result from a greater apparent stability of the six-coordinate Fe(II)-NO adduct at room temperature. Results from the present study strengthen the proposal that CO specificity in the CooA activation mechanism is based on the requirement for a small, neutral distal ligand, which in turn affects the relative positioning of the ligand-bound heme.