Reversible thermally induced spin crossover in the myoglobin-nitrito adduct directly monitored by resonance Raman spectroscopy.

Myoglobin has been demonstrated to function as a nitrite reductase to produce nitric oxide during hypoxia. One of the most intriguing aspects of the myoglobin/nitrite interactions revealed so far is the unusual O-binding mode of nitrite to the ferric heme iron, although conflicting data have been reported for the electronic structure of this complex also raising the possibility of linkage isomerism. In this work, we applied resonance Raman spectroscopy in a temperature-dependent approach to investigate the binding of nitrite to ferric myoglobin and the properties of the formed adduct from ambient to low temperatures (293 K to 153 K). At ambient temperature the high spin state of the ferric heme Fe-O-N[double bond, length as m-dash]O species is present and upon decreasing the temperature the low spin state is populated, demonstrating that a thermally-induced spin crossover phenomenon takes place analogous to what has been observed in many transition metal complexes. The observed spin crossover is fully reversible and is not due to linkage isomerism, since the O-binding mode is retained upon the spin transition. The role of the heme pocket environment in controlling the nitrite binding mode and spin transition is discussed.

Linking the Dynamic Changes in the In Vitro Antioxidant Activity of Carob Kibbles upon Roasting to the Chemical and Structural Changes Revealed by FTIR Spectroscopy.

Recent studies have highlighted the potential of utilizing carob kibbles as a bioactive-rich food ingredient associated with substantial health benefits. Roasting is a key process in enhancing the sensory characteristics of carob kibbles, also affecting the bioactive polyphenols and leading to the formation of Maillard reaction products (MRPs), including the polymeric melanoidins that are associated with a high antioxidant potential but remain unexplored in carob. In this work, we employed for the first time attenuated total reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy to probe the dynamic chemical and structural changes upon the roasting of carob kibbles, along with the investigation of the in vitro antioxidant activity through the 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity and the determination of the total polyphenolic, proanthocyanidin, gallic acid and cinnamic acid contents. Roasting significantly enhanced the in vitro antioxidant activity of the polyphenolic carob extracts, with different rates at distinct roasting temperatures. The ATR-FTIR analysis enabled the identification of the changes in the structural features of polyphenolic compounds that were related to the improved antioxidant activity upon roasting. Furthermore, the detection of characteristic signatures for the polymeric melanoidins in the infrared (IR) fingerprint region provided the first evidence for the formation and structural properties of these complex, diverse compounds in roasted carob kibbles.

Anti-Cancer Activity and Phenolic Content of Extracts Derived from Cypriot Carob (Ceratonia siliqua L.) Pods Using Different Solvents.

Extracts derived from the Ceratonia siliqua L. (carob) tree have been widely studied for their ability to prevent many diseases mainly due to the presence of polyphenolic compounds. In this study, we explored, for the first time, the anti-cancer properties of Cypriot carobs. We produced extracts from ripe and unripe whole carobs, pulp and seeds using solvents with different polarities. We measured the ability of the extracts to inhibit proliferation and induce apoptosis in cancer and normal immortalized breast cells, using the MTT assay, cell cycle analysis and Western Blotting. The extracts' total polyphenol content and anti-oxidant action was evaluated using the Folin-Ciocalteu method and the DPPH assay. Finally, we used LC-MS analysis to identify and quantify polyphenols in the most effective extracts. Our results demonstrate that the anti-proliferative capacity of carob extracts varied with the stage of carob maturity and the extraction solvent. The Diethyl-ether and Ethyl acetate extracts derived from the ripe whole fruit had high Myricetin content and also displayed specific activity against cancer cells. Their mechanism of action involved caspase-dependent and independent apoptosis. Our results indicate that extracts from Cypriot carobs may have potential uses in the development of nutritional supplements and pharmaceuticals.

Protein Dynamics of the Sensor Protein HemAT as Probed by Time-Resolved Step-Scan FTIR Spectroscopy.

The heme-based aerotactic transducer (HemAT) is an oxygen-sensor protein consisting of a sensor and a signaling domain in the N- and C-terminal regions, respectively. Time-resolved step-scan FTIR spectroscopy was employed to characterize protein intermediate states obtained by photolysis of the carbon monoxide complexes of sensor-domain, full-length HemAT, and the Y70F (B-helix), L92A (E-helix), T95A (E-helix), and Y133F (G-helix) HemAT mutants. We assign the spectral components to discrete substructures, which originate from a helical structure that is solvated (1638 cm-1) and a native helix that is protected from solvation by interhelix tertiary interactions (1654 cm-1). The full-length protein is characterized by an additional amide I absorbance at 1661 cm-1, which is attributed to disordered structure suggesting that further protein conformational changes occur in the presence of the signaling domain in the full-length protein. The kinetics monitored within the amide I absorbance of the polypeptide backbone in the sensor domain exhibit two distinct relaxation phases (t1 = 24 and t2 = 694 µs), whereas that of the full-length protein exhibits monophasic behavior for all substructures in a time range of t = 1253-2090 µs. These observations can be instrumental in monitoring helix motion and the role of specific mutants in controlling the dynamics in the communication pathway from the sensor to the signaling domain. The kinetics observed for the amide I relaxation for the full-length protein indicate that the discrete substructures within full-length HemAT, unlike those of the sensor domain, relax independently.

Probing the Role of the Heme Distal and Proximal Environment in Ligand Dynamics in the Signal Transducer Protein HemAT by Time-Resolved Step-Scan FTIR and Resonance Raman Spectroscopy.

HemAT is a heme-containing oxygen sensor protein that controls aerotaxis. Time-resolved step-scan FTIR studies were performed on the isolated sensor domain and full-length HemAT proteins as well as on the Y70F (B-helix), L92A (E-helix), T95A (E-helix), and Y133F (G-helix) mutants to elucidate the effect of the site-specific mutations on the ligand dynamics subsequent to CO photolysis. The mutations aimed to perturb H-bonding and electrostatic interactions near the heme Fe-bound gaseous ligand (CO) and the heme proximal environment. Rebinding of CO to the heme Fe is biphasic in the sensor domain and full-length HemAT as well as in the mutants, with the exception of the Y133F mutant protein. The monophasic rebinding of CO in Y133F suggests that in the absence of the H-bond between Y133 and the heme proximal H123 residue the ligand rebinding process is significantly affected. The role of the proximal environment is also probed by resonance Raman photodissociation experiments, in which the Fe-His mode of the photoproduct of sensor domain HemAT-CO is detected at a frequency higher than that of the deoxy form in the difference resonance Raman spectra. The role of the conformational changes of Y133 (G-helix) and the role of the distal L92 and T95 residues (E-helix) in regulating ligand dynamics in the heme pocket are discussed.

Probing nitrite coordination in horseradish peroxidase by resonance Raman spectroscopy: Detection of two binding sites.

Nitrite is a powerful oxidant that affects the activity of peroxidases towards various substrates and leads to heme macrocycle modifications in members of the peroxidase family, such as the horseradish peroxidase (HRP). We have applied resonance Raman spectroscopy to investigate the structural properties of the species formed in the reaction of NO2- with the ferric form of HRP. Our data demonstrate that the heme nitrovinyl group is partially formed at near neutral pH, without coordination of NO2- to the heme Fe. Nitrite coordinates to the heme Fe at acidic pH in the nitro binding mode, characterized by the detection of the ν(Fe-NO2) at 563cm-1, δ(FeNO2) at 822cm-1 and νsym(NO2) at 1272cm-1. The sensitivity of the vibrations of the heme Fe-nitro complex to H/D exchange indicates H-bonding interaction of the heme-bound ligand with the distal environment that determines the NO2- binding mode. A model describing the different modes of NO2- binding in HRP is presented.

Coupling of helix E-F motion with the O-nitrito and 2-nitrovinyl coordination in myoglobin.

Myoglobin (Mb) is known to react slowly with nitirite to form the green pigment by NO2- cordination to the heme Fe in the O-binding nitrito (O1NO2) mode and to the heme 2-vinyl position. Nitrite is a powerful oxidizing agent and a biological reservoir for NO that has been implicated in a variety of aerobic biological systems. Accordingly, it is important to elucidate the nature and variety of NO2- reaction mechanisms with Mb. We have performed principal component analysis (PCA, or essential dynamics) on Molecular Dynamics trajectories of all MbNO2 coordination states to resolve the most important motions in the protein at 298K. We show that the coordination or removal of NO2- to/from the heme iron is associated mainly with a motion of helix E and the coordination of NO2- to the 2-vinyl is associated with a motion of helix F and a correlated motion of helices E-F. This latter correlated motion can be attributed to the interaction of Val68 and Ile107 with the 2-nitrovinyl moiety. The resonance Raman results show that coordination of NO2- to the 2-vinyl is increased at pH6.0 demonstrating that the amide protons in the F helix are not protected from access of solvent water and the helix F motion allows solvent access to the 2-vinyl group, without affecting the coordination to the heme Fe.

Nitrite coordination in myoglobin.

The coordination of nitrite in myoglobin (Mb) has been characterized by resonance Raman spectroscopy and the frequencies of the nitrite bound to the heme Fe as well to the 2-vinyl have been computed by density functional theory (DFT) calculations. The DFT Natural Bond Orbital (NBO) analysis and the extensive isotope-labeling in the resonance Raman experiments indicate that NO2- (O1NO2) is bound to the heme Fe via O1. Based on the vibrational characterization of the reversible transition between low and high spin FeONO/2-nitrovinyl species, we suggest that the key step that triggers the spin-change is the increase of the proximal FeNHis93 bond length. The frequencies of the O and N sensitive bands of the FeONO/2-nitrovinyl species remained largely unchanged in the low- to high-spin transition. Therefore the "greening" process in the reaction of ferric Mb with NO2- proceeds through the FeONO/2-nitrovinyl species, which can exist in either the high or low-spin state.

Spin Crossover in Nitrito-Myoglobin as Revealed by Resonance Raman Spectroscopy.

The myoglobin (Mb) heme Fe-O-N=O and heme Fe-O-N=O/2-nitrovinyl species have been characterized by resonance Raman spectroscopy. In the heme Fe-O-N=O species, the bound nitrite ligand is removed by solvent exchange, thus reforming metmyoglobin (metMb). The high-spin heme Fe-O-N=O unit is converted into a low-spin heme Fe-O-N=O/2-nitrovinyl species that can be reversibly switched between a low- and a high-spin state without removing the bound nitrite ligand, as observed in the case of the heme Fe-O-N=O species. This spin-state change is likely to be accompanied by a general structural rearrangement in the protein-binding pocket. This example is the first of a globin protein that can reversibly change its metal spin state through an internal perturbation. These findings provide a basis for understanding the structure-function relationship of the spin cross found in other metalloenzymes and Fe(III) -porphyrin complexes.

Probing the nitrite and nitric oxide reductase activity of cbb3 oxidase: resonance Raman detection of a six-coordinate ferrous heme-nitrosyl species in the binuclear b3/CuB center.

In this work we report the first spectroscopic evidence demonstrating that cbb3 oxidase catalyzes the reduction of nitrite to nitrous oxide under reducing anaerobic conditions. The reaction proceeds through the formation of a ferrous six-coordinate heme b3-nitrosyl species that has been characterized by resonance Raman spectroscopy.

Probing the ligand recognition and discrimination environment of the globin-coupled oxygen sensor protein YddV by FTIR and time-resolved step-scan FTIR spectroscopy.

YddV is a newly discovered signal transducer heme protein that recognizes O2 and CO. Structural differences in the ligand-bound heme complex in YddV reflect variations in catalytic regulation by O2 and CO. Time-resolved step-scan (TRS(2)) FTIR studies of the wild type and of the important in oxygen recognition and stability of the heme Fe(II)-O2 complex L65M, L65T, Y43A, Y43F and Y43W mutants were performed to determine the site-specific protein dynamics following carbon monoxide (CO) photodissociation. These mutations were designed to perturb the electrostatic field near the iron-bound gaseous ligand (CO) and also to allow us to investigate the communication pathway between the distal residues of the protein and heme. TRS(2)-FTIR spectra of YddV-heme-CO show that the heme propionates are in protonated and deprotonated states. Moreover, the rate of decay of the vibrations of amide I is on a time scale that coincides with the rate of rebinding of CO, which suggests that there is coupling between ligation dynamics in the distal heme environment and (i) relaxation of the protein backbone and (ii) the environment sensed by the heme propionates. The fast recombination rates in L65M, L65T and Y43W imply a significant role of L65 and Y43 in controlling the ligand dynamics. The implications of these results with respect to the role of the heme propionates and the charged or proton-donating residues in the distal pocket, which are crucial for stabilizing bound gaseous ligands, are discussed.

Resonance Raman detection of the myoglobin nitrito heme Fe-O-N=O/2-nitrovinyl species: implications for helix E-helix F interactions.

The description of biological activity in heme proteins responsible for activating small molecules requires identification of ligand movement into the metal and non-metal binding sites. Mechanisms of nitrite reductase activity in globins are difficult to verify without the structures of the bound ligand, but we now have such information from resonance Raman spectroscopy on the myoglobin nitrito heme Fe-O-N=O/2-nitrovinyl species in their natural environment rather than in crystals. Our results indicate that the formation of the nitrito heme Fe-O-N=O/2-nitrovinyl species is pH-dependent. The conditions under which the nitrito heme Fe-O-N=O/2-nitrovinyl species is generated strongly suggest that this form corresponds to an acid induced transformation. We propose that the movement of helices E and F at low pH results in the protonation of nitrito heme Fe-O-N=O by His64 Nε-H(E) to form the nitrous heme Fe-O(H)-N=O species.

The structure of a ferrous heme-nitro species in the binuclear heme a3/CuB center of ba3-cytochrome c oxidase as determined by resonance Raman spectroscopy.

Members of the cytochrome c oxidase family exhibit nitrite reductase activity. In this work, we have characterized a ferrous heme a3-nitro species in ba3-oxidase by resonance Raman spectroscopy. This provides the first evidence for the structure of a nitrite-bound species in the binuclear heme/copper center of cytochrome c oxidases.

The protein effect in the structure of two ferryl-oxo intermediates at the same oxidation level in the heme copper binuclear center of cytochrome c oxidase.

Identification of the intermediates and determination of their structures in the reduction of dioxygen to water by cytochrome c oxidase (CcO) are particularly important to understanding both O2 activation and proton pumping by the enzyme. In this work, we report the products of the rapid reaction of O2 with the mixed valence form (CuA(2+), heme a(3+), heme a3(2+)-CuB(1+)) of the enzyme. The resonance Raman results show the formation of two ferryl-oxo species with characteristic Fe(IV)=O stretching modes at 790 and 804 cm(-1) at the peroxy oxidation level (PM). Density functional theory calculations show that the protein environment of the proximal H-bonded His-411 determines the strength of the distal Fe(IV)=O bond. In contrast to previous proposals, the PM intermediate is also formed in the reaction of Y167F with O2. These results suggest that in the fully reduced enzyme, the proton pumping ν(Fe(IV)=O) = 804 cm(-1) to ν(Fe(IV)=O) = 790 cm(-1) transition (P→F, where P is peroxy and F is ferryl) is triggered not only by electron transfer from heme a to heme a3 but also by the formation of the H-bonded form of the His-411-Fe(IV)=O conformer in the proximal site of heme a3. The implications of these results with respect to the role of an O=Fe(IV)-His-411-H-bonded form to the ring A propionate of heme a3-Asp-399-H2O site and, thus, to the exit/output proton channel (H2O) pool during the proton pumping P→F transition are discussed. We propose that the environment proximal to the heme a3 controls the spectroscopic properties of the ferryl intermediates in cytochrome oxidases.

Observation of ligand transfer in ba3 oxidase from Thermus thermophilus: simultaneous FTIR detection of photolabile heme a3(2+)-CN and transient Cu(B)(2+)-CN complexes.

FTIR and light-minus-dark FTIR spectroscopy have been employed to investigate the reaction of oxidized and fully reduced ba(3) oxidase with cyanide. The characterization of the structures of the bound CN(-) in the binuclear heme Fe-Cu(B) center is essential, given that a central issue in the function of ba(3) oxidase is the extent to which the partially reduced substrates interact with the two metals. In the reaction of oxidized ba(3) oxidase with cyanide the initially formed heme a(3)(3+)-C≡N-Cu(B)(2+) species with ν(CN) frequency at 2152 cm(-1) was replaced by a photolabile complex with a frequency at 2075 cm(-1) characteristic of heme a(3)(2+)-CN(-). Photolysis of the heme a(3)(2+)-CN(-) adduct produced a band at 2146 cm(-1) attributed to the formation of a transient Cu(B)(2+)-CN(-) complex. All forms are pH independent between pH 5.5-9.5 and at pD 7.5 indicating the absence of ionizable groups that influence the properties of the cyanide complexes. In contrast to previous reports, our results show that CN(-) does not bind simultaneously to both heme a(3)(2+) and Cu(B)(2+) to form the mixed valence a(3)(2+)-CN·Cu(B)(2+)CN species. The photolysis products of the heme a(3)(2+)-CN(-)/Cu(B)(2+) and heme a(3)(2+)-CN(-)/Cu(B)(1+) species are different suggesting that relaxation dynamics in the binuclear center following ligand photodissociation are dependent on the oxidation state of Cu(B).

The origin of the Fe(IV)=O intermediates in cytochrome aa(3) oxidase.

The dioxygen reduction mechanism in cytochrome oxidases relies on proton control of the electron transfer events that drive the process. Proton delivery and proton channels in the protein that are relevant to substrate reduction and proton pumping are considered, and the current status of this area is summarized. We propose a mechanism in which the coupling of the oxygen reduction chemistry to proton translocation (P→F transition) is related to the properties of two groups of highly conserved residues, namely, His411/G386-T389 and the heme a(3)-propionateA-D399-H403 chain.

Aldoxime dehydratase: probing the heme environment involved in the synthesis of the carbon-nitrogen triple bond.

Fourier transform infrared (FTIR) spectra, "light" minus "dark" difference FTIR spectra, and time-resolved step-scan (TRS(2)) FTIR spectra are reported for carbonmonoxy aldoxime dehydratase. Two C-O modes of heme at 1945 and 1964 cm(-1) have been identified and remained unchanged in H(2)O/D(2)O exchange and in the pH 5.6-8.5 range, suggesting the presence of two conformations at the active site. The observed C-O frequencies are 5 and 16 cm(-1) lower and higher, respectively, than that obtained previously (Oinuma, K.-I.; et al. FEBS Lett.2004, 568, 44-48). We suggest that the strength of the Fe-His bond and the neutralization of the negatively charged propionate groups modulate the ν(Fe-CO)/ν(CO) back-bonding correlation. The "light" minus "dark" difference FTIR spectra indicate that the heme propionates are in both the protonated and deprotonated forms, and the photolyzed CO becomes trapped within a ligand docking site (ν(CO) = 2138 cm(-1)). The TRS(2)-FTIR spectra show that the rate of recombination of CO to the heme is k(1945 cm(-1)) = 126 ± 20 s(-1) and k(1964 cm(-1)) = 122 ± 20 s(-1) at pH 5.6, and k(1945 cm(-1)) = 148 ± 30 s(-1) and k(1964 cm(-1)) = 158 ± 32 s(-1) at pH 8.5. The rate of decay of the heme propionate vibrations is on a time scale coincident with the rate of rebinding, suggesting that there is a coupling between ligation dynamics in the distal heme environment and the environment sensed by the heme propionates. The implications of these results with respect to the proximal His-Fe heme environment including the propionates and the positively charged or proton-donating residues in the distal pocket which are crucial for the synthesis of nitriles are discussed.

Evidence for the presence of two conformations of the heme a3-Cu(B) pocket of cytochrome caa3 from Thermus thermophilus.

Resonance Raman (RR) and "light" minus "dark" Fourier transform infrared (FTIR) difference spectra are reported for the CO-bound caa(3) oxidase from Thermus thermophilus. Two Fe-CO stretching modes at 518 and 507 cm(-1), the Fe-C-O bending mode at 570 cm(-1), and three C-O modes of heme a(3) at 1958, 1967, and 1973 cm(-1) have been identified in the RR and FTIR spectra, respectively. The FTIR "light" minus "dark" spectrum indicates the formation of Cu(B)CO as revealed by its ν(CO) at 2060/2065 cm(-1). We assign the bands at 518 (ν(Fe-CO)) and 1967/1973 cm(-1) (ν(C-O)) as the α-conformation. We also assign the bands at 507 and 1958 cm(-1) (ν(C-O)) as originating from the ß-conformation of the enzyme. A frequency upshift of the heme a(3) Fe-His mode is observed subsequent to CO photolysis from 209 cm(-1) in the equilibrium deoxy enzyme to 214 cm(-1) in the photoproduct. The caa(3) data, distinctly different from those of ba(3) oxidase, are discussed in terms of the coupling of the α- and ß-conformations that occur in heme-copper oxidases with catalytic function. The dynamics between the heme a(3) and heme a propionates as revealed by the perturbation of the bending vibrations δ(prop) of hemes a and a(3) at 385 and 392 cm(-1), respectively, induced upon CO binding to heme a(3) is discussed in terms of the protonic connectivity between the heme a ring-D propionate/Arg site with that of the heme a(3) ring-D propionate-H(2)O site that leads to the highly conserved in the heme-copper oxidases water pool.

Nitric oxide activation and reduction by heme-copper oxidoreductases and nitric oxide reductase.

The understanding of the dynamics and conformational control involved in the interplay between structure and function of nitric oxide reductase (Nor) and heme-copper oxidoreductases in their function to convert nitric oxide (NO) to nitrous oxide (N2O) is of fundamental importance in bioenergetics. We have applied resonance Raman spectroscopy to investigate the NO ligation/deligation reactions and the extent of communication between the metal centers at the heme a3-CuB site of heme-copper oxidases and of the heme Fe-non-heme Fe in Nor. The present study provides information of the electronic and vibrational structure of intermediates, and thus, it forms the basis for an atomic-level description of the key steps in the N-N bond formation and the N-O bond cleavage mechanism. The present experiments provide evidence as to the validity of the proposed hypothesis of the common evolutionary origin of aerobic respiration and bacterial denitrification.

ICPBCZin: a red emitting ratiometric fluorescent indicator with nanomolar affinity for Zn2+ ions.

A new fluorescent Zn2+ indicator, namely, ICPBCZin was synthesized and the spectral profile of its free and Zn2+ bound forms was studied. The newly synthesized zinc indicator incorporates as chromophore the chromeno [3',2':3,4]pyrido[1,2a] [1,3]benzimidazole moiety and belongs to the dicarboxylate-type of zinc probes. The compound is excited with visible light, exhibits high selectivity for zinc in the presence of calcium and other common biological ions, and its Zn2+ dissociation constant is 4.0 nM. Fluorescence spectra studies of ICPBCZin indicated a clear shift in its emission wavelength maxima upon Zn2+ binding, as it belongs to the class of Photoinduced Charge Transfer (PCT) indicators, along with changes in fluorescence intensity that enable the compound to be used as a ratiometric, visible-excitable Zn2+ probe.