Resonance Raman studies of dioxygen and carbon monoxide binding to imidazole-appended hemes.

Resonance Raman spectroscopy has been employed to probe the effects of proximal base strain on the bonding of O2 and CO in three synthetic hemins with covalently linked imidazole ligands. The strain is introduced by varying the length of the imidazole-containing side chain and by restricting the side chain flexibility with a phenyl ring. These hemins are abbreviated as "long," "short," and "stiff" hemins, respectively. In the deoxy state, the iron-imidazole stretching frequencies [nu(Fe--N epsilon)] for long, short, and stiff hemins are detected at 200, 207, and 204 cm-1, respectively. The strain induced in the iron-imidazole bond by the short hemin results in a higher nu(Fe--N epsilon) frequency, in contrast to the strain induced by sterically hindered 2-methylimidazole or 1,2-dimethylimidazole complexes in which the Fe--N epsilon bond is tilted and lengthened, but the imidazole ring remains perpendicular to the heme plane. However, in the short hemin, the plane of the imidazole ring may not be perpendicular to the plane of the porphyrin, altering the amount of pi-interaction (hence the strength of Fe--N epsilon bond) and the nature of normal mode containing Fe--N epsilon bond stretching. Upon CO binding, we have observed the nu(Fe--CO) stretching frequencies at 497 (long), 499 (short), and 496 cm-1 (stiff), somewhat lower than those reported by Mitchell et al. (Inorg. Chem., 1985, 24:967) for the chelated-heme X CO complexes (i.e., 501-506 cm-1). This is the first report of an iron-oxygen-associated vibration observed in solution for an unprotected heme.(ABSTRACT TRUNCATED AT 250 WORDS)     

Resonance Raman enhancement of the Mn-N-O bending mode in nitrosyl manganese "strapped" and "open" heme complexes

Resonance Raman spectra of the MnII-NO moiety in synthetic nitrosyl manganese heme complexes with and without steric hindrance are reported. The "strapped" hemes having a hydrocarbon strap (variable length) across one face of the heme hinder the perpendicular bonding of a linear ligand. These complexes were employed to investigate the effects of ligand distortion (primarily tilting) on Mn-NO stretching, Mn-N-O bending, and N-O stretching modes. It is demonstrated that ligand distortion in the MnII-NO system is a valid mechanism for causing the resonance enhancement of the Mn-N-O bending mode, similar to that observed in the FeII-CO system (Yu, N.-T., E. A. Kerr, B. Ward, and C. K. Chang. 1983. Biochemistry. 22:4534-4540). More interesting is the observation of the delta(Mn-N-O) enhancement caused by the tilting of the trans Mn-N epsilon bond in the "open" heme complexes (e.g., heme-5 and proto-1X dimethylester) with 1,2-dimethylimidazole or piperidine as a base. The nu(Mn-NO) and nu(N-O) modes exhibit an increase and a decrease, respectively, as the strap length decreases (hence the steric hindrance increases). Both nu(Mn-NO) and nu(N-O) frequencies are insensitive to the strength of the trans base. The results from "strapped" and "open" model heme systems imply that the Mn-N-O geometry is essentially linear and perpendicular in the nitrosyl complexes of monomeric manganese insect hemoglobin CTT IV and sperm whale myoglobin. The unusually low nu(N-O) frequency in the manganese myoglobin complex may be caused by the distal histidine-NO interaction. The delta(Mn-N-O) enhancement in both nitrosyl manganese CTT IV and nitrosyl manganese myoglobin may be caused by a tilting of the Mn"-Nf (proximal histidine) bond.     

Resonance Raman studies of Escherichia coli sulfite reductase hemoprotein. 3. Bound ligand vibrational modes

The vibrations of the bound diatomic heme ligands CO, CN-, and NO are investigated by resonance Raman spectroscopy in various redox states of Escherichia coli sulfite reductase hemoprotein, and assignments are generated by use of isotopically labeled ligands. For the fully reduced CO complex (ferrous siroheme, reduced Fe4S4 cluster) at room temperature, nu CO is observed at 1904 cm-1, shifting to 1920 cm-1 upon oxidation of the cluster. The corresponding delta FeCO modes are identified at 574 and 566 cm-1, respectively, by virtue of the zigzag pattern of their isotopic shifts. In frozen solution, two species are observed for the cluster-oxidized state, with nu CO at 1910 and 1936 cm-1 and nu FeC at 532 and 504 cm-1, respectively; nu FeC for the fully reduced species is identified at 526 cm-1 in the frozen state. For the ferrous siroheme-NO complex (cluster oxidized), nu NO is identified at 1555 cm-1 in frozen solution and a low-frequency mode is identified at 558 cm-1; this stretching mode is significantly lower than that observed in Mb-NO. For the ferric siroheme cyanide complexes evidence of two ligand-bonding forms is observed, with modes at 451/390 and 451/352 cm-1; they are distinguished by a reversal of the isotopic shift patterns of the upper and lower modes and could arise from a linear and a bent Fe-C unit, respectively. For the ferrous siroheme cyanide complex isotope-sensitive modes observed at 495 and 452 cm-1 are assigned to the FeCN- bending and FeC stretching vibrations, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)     

Resonance Raman and ligand binding studies of the oxygen-sensing signal transducer protein HemAT from Bacillus subtilis

HemAT-Bs is a heme-containing signal transducer protein responsible for aerotaxis of Bacillus subtilis. The recombinant HemAT-Bs expressed in Escherichia coli was purified as the oxy form in which oxygen was bound to the ferrous heme. Oxygen binding and dissociation rate constants were determined to be k(on) = 32 microm(-1) s(-1) and k(off) = 23 s(-1), respectively, revealing that HemAT-Bs has a moderate oxygen affinity similar to that of sperm whale myoglobin (Mb). The rate constant for autoxidation at 37 degrees C was 0.06 h(-1), which is also close to that of Mb. Although the electronic absorption spectra of HemAT-Bs were similar to those of Mb, HemAT-Bs showed some unique characteristics in its resonance Raman spectra. Oxygen-bound HemAT-Bs gave the nu(Fe-O(2)) band at a noticeably low frequency (560 cm(-1)), which suggests a unique hydrogen bonding between a distal amino acid residue and the proximal atom of the bound oxygen molecule. Deoxy HemAT-Bs gave the nu(Fe-His) band at a higher frequency (225 cm(-1)) than those of ordinary His-coordinated deoxy heme proteins. CO-bound HemAT-Bs gave the nu(Fe-CO) and nu(C-O) bands at 494 and 1964 cm(-1), respectively, which fall on the same nu(C-O) versus nu(Fe-CO) correlation line as that of Mb. Based on these results, the structural and functional properties of HemAT-Bs are discussed.     

Resonance Raman studies and structure of a sulfide complex of methemerythrin.

The complex of sulfide and methemerythrin has been characterized by resonance Raman spectroscopy. At pH 8.0 the complex contains two irons and one S2- at the active site. The resonance Raman spectrum of the sulfidomethemerythrin complex contains only one vibration, at 444 cm-1. This vibration is assigned to an iron-sulfide stretch. The possibility that sulfidomethemerythrin contains a mu-sulfido bridge. FeIII-S2-FeIII, analogous to the proposed mu-oxo bridge in azidomethemerythrin is discussed.     

Resonance Raman and lifetime studies on regioselectively deuteriated ruthenium(II) polypyridyl complexes.

Two series of ruthenium(II) polypyridyl complexes [Ru(bipy)(2)(phpytr)](+) and [Ru(bipy)(2)(phpztr)](+) (where Hphpytr = 2-(5-phenyl-1H-[1,2,4]triazol-3-yl)-pyridine and Hphpztr = 2-(5-phenyl-1H-[1,2,4]triazol-3-yl)-pyrazine) are examined by electrochemistry, UV/Vis, emission, resonance Raman, transient resonance Raman and transient absorption spectroscopy, in order to obtain a more comprehensive understanding of their excited state electronic properties. The interpretation of the results obtained is facilitated by the availability of several isotopologues of each of the complexes examined. For the pyridine-1,2,4-triazolato based complex the lowest emissive excited state is exclusively bipy based, however, for the pyrazine based complexes excited state localisation on particular ligands shows considerable solvent and pH dependency.     

Effect of ultrasound and ionizing radiation on a sterically hindered cyclic secondary amine: an ESR study.

The possible use of 2,2,6,6-tetramethyl-4-piperidone (TMPone) for the detection of singlet oxygen was investigated by gamma radiolysis and sonolysis of oxygen-saturated aqueous solutions. Formation of 2,2,6,6-tetra-methyl-4-piperidone-N-oxyl (TAN) was observed with both gamma radiolysis and sonolysis with a similar dependence on the concentration of TMPone up to 20 mM and a strong dependence on pH. In oxygen-saturated solutions the sonolysis of TMPone leads to the formation of the cyclic hydroxylamine (approx. 30% of the yield of TAN) while radiolysis does not. In the low pH range (5-6.5) and at high concentrations of OH radical scavengers (azide or formate), TAN is produced by sonolysis but not by radiolysis. Sonolysis of argon-saturated solutions of TMPone produces methyl radicals due to the high-temperature regions of the collapsing cavitation bubbles. The methyl radicals were detected by ESR (electron spin resonance) and spin trapping with 3,5-dibromo-2,6-dideuterio-4-nitroso-benzene sulfonate. Since the reaction of singlet oxygen with TMPone is also strongly dependent on pH, it does not seem likely that TMPone could be used for the detection of singlet oxygen in sonochemistry.     

Copper(II) nitrato and chloro complexes with sterically hindered tridentate ligands: Influence of ligand framework and charge on their structure and physicochemical properties

Copper(II) coordination complexes of the neutral ligand, tris(3-tert-butyl-5-methyl-1-pyrazolyl)methane (L2′), i.e. the copper(II) nitrato complexes [Cu(L2′)(NO₃)][Cu(NO₃)₄]_1/2 (1) and [Cu(L2′)(NO₃)](ClO₄) (2) and the copper(II) chloro complex [Cu(L2′)(Cl)](ClO₄) (3), and its anionic borate analogue, hydrotris(3-tert-butyl-5-methyl-1-pyrazolyl)borate (L2⁻), i.e. the copper(II) nitrato complex [Cu(L2)(NO₃)] (4) and the copper(II) chloro complex [Cu(L2)(Cl)] (5), were synthesized in order to investigate the influence of ligand framework and charge on their structure and physicochemical properties. While X-ray crystallography did not show any definitive trends in terms of copper(II) atom geometry in four-coordinate copper(II) chloro complexes 3 and 5, different structural trends were observed in five-coordinate copper(II) nitrato complexes 1, 2, and 4. These complexes were also characterized by spectroscopic techniques, namely, UV-Vis, ESR, IR/far-IR, and X-ray absorption spectroscopy.     

Resonance Raman studies of cytochrome P450BM3 and its complexes with exogenous ligands.

Resonance Raman spectra are reported for both the heme domain and holoenzyme of cytochrome P450BM3 in the resting state and for the ferric NO, ferrous CO, and ferrous NO adducts in the absence and presence of the substrate, palmitate. Comparison of the spectrum of the palmitate-bound form of the heme domain with that of the holoenzyme indicates that the presence of the flavin reductase domain alters the structure of the heme domain in such a way that water accessibility to the distal pocket is greater for the holoenzyme, a result that is consistent with analogous studies of cytochrome P450cam. The data for the exogenous ligand adducts are compared to those previously reported for corresponding derivatives of cytochrome P450cam and document significant and important differences for the two proteins. Specifically, while the binding of substrate induces relatively dramatic changes in the nu(Fe-XY) modes of the ferrous CO, ferric NO, and ferrous NO derivatives of cytochrome P450cam, no significant changes are observed for the corresponding derivatives of cytochrome P450BM3 upon binding of palmitate. In fact, the spectral data for substrate-free cytochrome P450BM3 provide evidence for distortion of the Fe-XY fragment, even in the absence of substrate. This apparent distortion, which is nonexistent in the case of substrate-free cytochrome P450cam, is most reasonably attributed to interaction of the Fe-XY fragment with the F87 phenylalanine side chain. This residue is known to lie very close to the heme iron in the substrate-free derivative of cytochrome P450BM3 and has been suggested to prevent hydroxylation of the terminal, omega, position of long-chain fatty acids.     

Structural studies on bioactive compounds. Part 29: palladium catalysed arylations and alkynylations of sterically hindered immunomodulatory 2-amino-5-halo-4,6-(disubstituted)pyrimidines

The immunological agent bropirimine 5 is a tetra-substituted pyrimidine with anticancer and interferon-inducing properties. Synthetic routes to novel 5-aryl analogues of bropirimine have been developed and their potential molecular recognition properties analysed by molecular modelling methods. Sterically challenged 2-amino-5-halo-6-phenylpyrimidin-4-ones (halo = Br or I) are poor substrates for palladium catalysed Suzuki cross-coupling reactions with benzeneboronic acid because the basic conditions of the reaction converts the amphoteric pyrimidinones to their unreactive enolic forms. Palladium-mediated reductive dehalogenation of the pyrimidinone substrates effectively competes with cross-coupling. 2-Amino-5-halo-4-methoxy-6-phenylpyrimidines can be converted to a range of 5-aryl derivatives with the 5-iodopyrimidines being the most efficient substrates. Hydrolysis of the 2-amino-5-aryl-4-methoxy-6-phenylpyrimidines affords the required pyrimidin-4-ones in high yields. Semi-empirical quantum mechanical calculations show how the nature of the 5-substituent influences the equilibrium between the 1H- and 3H-tautomeric forms, and the rotational freedom about the bond connecting the 6-phenyl group and the pyrimidine ring. Both of these factors may influence the biological properties of these compounds.     

Resonance Raman and magnetic circular dichroism studies of reduced [2Fe-2S] proteins.

The structural and electronic properties of the [2Fe-2S] clusters in reduced putidaredoxin, Spinacea oleracea ferredoxin, and Clostridium pasteurianum [2Fe-2S] ferredoxin have been investigated by resonance Raman and variable temperature magnetic circular dichroism spectroscopies. Both techniques are shown to provide diagnostic fingerprints for identifying [2Fe-2S]+ clusters in more complex multicomponent metalloenzymes. The Fe-S stretching modes of oxidized and reduced putidaredoxin are assigned via 34S and D2O isotope shifts and previous normal mode calculations for adrenodoxin (Han, S., Czernuszewicz, R. S., Kimura, T., Adams, M. W. W., and Spiro, T. G. (1989) J. Am. Chem. Soc. 111, 3505-3511). The close similarity in the resonance Raman spectra of reduced [2Fe-2S] centers, in terms of both the vibrational frequencies and enhancement profiles of the Fe-S stretching modes, permits these assignments to be generalized to all clusters of this type. Modes primarily involving Fe(III)-S(Cys) stretching are identified in all three reduced [2Fe-2S] proteins, and the frequencies are rationalized in terms of the conformation of the cysteine residues ligating the Fe(III) site of the localized valence reduced cluster. D2O isotope shifts indicate few, if any, amide NH-S hydrogen bond interactions involving the cysteines ligating the Fe(III) site. Preliminary resonance Raman excitation profiles suggest assignments for the complex pattern of electronic bands that comprise the low temperature magnetic circular dichroism spectra of the reduced proteins. S----Fe(III) and Fe(II)----S charge transfer, Fe d-d, and Fe(II)----Fe(III) intervalence bands are identified.     

Resonance Raman studies of cytochrome c' support the binding of NO and CO to opposite sides of the heme: implications for ligand discrimination in heme-based sensors

Resonance Raman (RR) studies have been conducted on Alcaligenes xylosoxidans cytochrome c', a mono-His ligated hemoprotein which reversibly binds NO and CO but not O(2). Recent crystallographic characterization of this protein has revealed the first example of a hemoprotein which can utilize both sides of its heme (distal and proximal) for binding exogenous ligands to its Fe center. The present RR investigation of the Fe coordination and heme pocket environments of ferrous, carbonyl, and nitrosyl forms of cytochrome c' in solution fully supports the structures determined by X-ray crystallography and offers insights into mechanisms of ligand discrimination in heme-based sensors. Ferrous cytochrome c' reacts with CO to form a six-coordinate heme-CO complex, whereas reaction with NO results in cleavage of the proximal linkage to give a five-coordinate heme-NO adduct, despite the relatively high stretching frequency (231 cm(-1)) of the ferrous Fe-N(His) bond. RR spectra of the six-coordinate CO adduct indicate that CO binds to the Fe in a nonpolar environment in line with its location in the hydrophobic distal heme pocket. On the other hand, RR data for the five-coordinate NO adduct suggest a positively polarized environment for the NO ligand, consistent with its binding close to Arg 124 on the opposite (proximal) side of the heme. Parallels between certain physicochemical properties of cytochrome c' and those of heme-based sensor proteins raise the possibility that the latter may also utilize both sides of their hemes to discriminate between NO and CO binding.     

Resonance Raman study on cytochrome c peroxidase and its intermediate. Presence of the Fe(IV) = O bond in compound ES and heme-linked ionization

Resonance Raman spectra of ferrous and ferric cytochrome c peroxidase and Compound ES and their pH dependences were investigated in resonance with Soret band. The Fe(IV) = O stretching Raman line of Compound ES was assigned to a broad band around 767 cm-1, which was shifted to 727 cm-1 upon 18O substitution. The 18O-isotopic frequency shift was recognized for Compound ES derived in H218O, but not in H216O. This clearly indicated occurrence of an oxygen exchange between the Fe(IV) = O heme and bulk water. The Fe(IV) = O stretching Raman band was definitely more intense and of higher frequency in D2O than in H2O as in Compound II of horseradish peroxidase, but in contrast with this its frequency was unaltered between pH 4 and 11. The Fe(II)-histidine stretching Raman line was assigned on the basis of the frequency shift observed for 54Fe isotopic substitution. From the intensity analysis of this band, the pKa of the heme-linked ionization of ferrocytochrome c peroxidase was determined to be 7.3. The Raman spectrum of ferricytochrome c peroxidase strongly suggested that the heme is placed under an equilibrium between the 5- and 6-coordinate high-spin structures. At neutral pH it is biased to the 5-coordinate structure, but at the acidic side of the transition of pKa = 5.5 the 6-coordinate heme becomes dominant. F- was bound to the heme iron at pH 6, but Cl- was bound only at acidic pH. Acidification by HNO3, H2SO4, CH3COOH, HBr, or HI resulted in somewhat different populations of the 5- and 6-coordinate forms when they were compared at pH 4.3. Accordingly, it is inferred that a water molecule which is suggested to occupy the sixth coordination position of the heme iron is not coordinated to the heme iron at pH 6 but that protonation of the pKa = 5.5 residue induces an appreciable structural change, allowing the coordination of the water molecule to the heme iron.     

Multinuclear magnetic resonance studies of Escherichia coli adenylate kinase in free and bound forms. Resonance assignment, secondary structure and ligand binding.

The crystal structure of Escherichia coli adenylate kinase (AKe) revealed three main components: a CORE domain, composed of a five-stranded parallel beta-sheet surrounded by alpha-helices, and two peripheral domains involved in covering the ATP in the active site (LID) and binding of the AMP (NMPbind). We initiated a long-term NMR study aiming to characterize the solution structure, binding mechanism and internal dynamics of the various domains. Using single (15N) and double-labeled (13C and 15N) samples and double- and triple-resonance NMR experiments we assigned 97% of the 1H, 13C and 15N backbone resonances, and proton and 13Cbeta resonances for more than 40% of the side chains in the free protein. Analysis of a 15N-labeled enzyme in complex with the bi-substrate analogue [P1,P5-bis(5'-adenosine)-pentaphosphate] (Ap5A) resulted in the assignment of 90% of the backbone 1H and 15N resonances and 42% of the side chain resonances. Based on short-range NOEs and 1H and 13C secondary chemical shifts, we identified the elements of secondary structure and the topology of the beta-strands in the unliganded form. The alpha-helices and the beta-strands of the parallel beta-sheet in solution have the same limits (+/- 1 residue) as those observed in the crystal. The first helix (alpha1) appears to have a frayed N-terminal side. Significant differences relative to the crystal were noticed in the LID domain, which in solution exhibits four antiparallel beta-strands. The secondary structure of the nucleoside-bound form, as deduced from intramolecular NOEs and the 1Halpha chemical shifts, is similar to that of the free enzyme. The largest chemical shift differences allowed us to map the regions of protein-ligand contacts. 1H/2H exchange experiments performed on free and Ap5A-bound enzymes showed a general decrease of the structural flexibility in the complex which is accompanied by a local increased flexibility on the N-side of the parallel beta-sheet.     

Effects of an interchain disulfide bond on tropomyosin structure: intrinsic fluorescence and circular dichroism studies

An interchain disulfide crosslink was introduced into rabbit skeletal tropomyosin (TM) at Cys190 by two different methods under non-denaturing conditions. The effects of the crosslink on the structure of tropomyosin were investigated by fluorescence and circular dichroism methods as a function of temperature and guanidine · hydrochloride concentration. Four different preparations were studied: Nbs₂-TM, red-TM crosslinked with Ellman's reagent, 5,5′-dithiobis(2-nitrobenzoate); O₂-TM, TM whose SH groups were air-oxidized; red-TM, TM reduced with dithiothreitol; IA-TM, red-TM whose SH groups were blocked with iodoacetamide. Sodium dodecyl sulfate/polyacrylamide gel electrophoresis studies indicated that SS crosslinks were quantitatively introduced between the subunits of TM for Nbs₂-TM and O₂-TM. In the completely folded state (below 25 °C or in the absence of denaturant) and in the unfolded state (above 65 °C or greater than 4 m-guanidine · hydrochloride) all of the samples had the same Tyr fluorescence quantum yield, accessibility to acrylamide fluorescence quenching, fluorescence polarization and mean residue rotation at 222 nm. Thermal and denaturant-induced unfolding profiles at pH 7.5 were obtained for each sample with measurements of these parameters. The main transition at about 45 °C or 2 m-guanidine · hydrochloride was shifted about +7 deg. C and 0.8 m in guanidine · hydrochloride, respectively, for the crosslinked samples as compared to the uncrosslinked samples. In addition, a destabilizing pretransition was observed in the 30 to 45 °C region or the 0 to 2 m-guanidine · hydrochloride region only for the crosslinked samples when polarization or ellipticity was measured. Studies of the ability of Nbs₂ to crosslink red-TM as a function of guanidine · hydrochloride concentration indicated that the chains separate at Cys190 between 0 and 2 m-guanidine · hydrochloride before they dissociate. Thus, the effect of the SS crosslink at Cys190 on the conformation of TM at physiological temperatures appears to be related to the inherent instability of the molecule in this region of the sequence.     

Roles of Arg-97 and Phe-113 in regulation of distal ligand binding to heme in the sensor domain of Ec DOS protein. Resonance Raman and mutation study

The direct oxygen sensor protein isolated from Escherichia coli (Ec DOS) is a heme-based signal transducer protein responsible for phosphodiesterase (PDE) activity. Binding of O(2), CO, or NO to a reduced heme significantly enhances the PDE activity toward 3',5'-cyclic diguanylic acid. We report stationary and time-resolved resonance Raman spectra of the wild-type and several mutants (Glu-93 --> Ile, Met-95 --> Ala, Arg-97 --> Ile, Arg-97 --> Ala, Arg-97 --> Glu, Phe-113 --> Leu, and Phe-113 --> Thr) of the heme-containing PAS domain of Ec DOS. For the CO- and NO-bound forms, both the hydrogen-bonded and non-hydrogen-bonded conformations were found, and in the former Arg-97 forms a hydrogen bond with the heme-bound external ligand. The resonance Raman results revealed significant interactions of Arg-97 and Phe-113 with a ligand bound to the sixth coordination site of the heme and profound structural changes in the heme propionates upon dissociation of CO. Mutation of Phe-113 perturbed the PDE activities, and the mutation of Arg-97 and Phe-113 significantly influenced the transient binding of Met-95 to the heme upon photodissociation of CO. This suggests that the electrostatic interaction of Arg-97 and steric interaction of Phe-113 are crucial for regulating the competitive recombination of Met-95 and CO to the heme. On the basis of these results, we propose a model for the role of the heme propionates in communicating the heme structural changes to the protein moiety.