Fragmentation of heme and hemin+ with sequential loss of carboxymethyl groups: A DFT and mass-spectrometry study

Combining experiment and energy landscapes to explore anaerobic heme breakdown in multifunctional hemoproteins

To survive, many pathogens extract heme from their host organism and break down the porphyrin scaffold to sequester the Fe2+ ion via a heme oxygenase. Recent studies have revealed that certain pathogens can anaerobically degrade heme. Our own research has shown that one such pathway proceeds via NADH-dependent heme degradation, which has been identified in a family of hemoproteins from a range of bacteria. HemS, from Yersinia enterocolitica, is the main focus of this work, along with HmuS (Yersinia pestis), ChuS (Escherichia coli) and ShuS (Shigella dysenteriae). We combine experiments, Energy Landscape Theory, and a bioinformatic investigation to place these homologues within a wider phylogenetic context. A subset of these hemoproteins are known to bind certain DNA promoter regions, suggesting not only that they can catalytically degrade heme, but that they are also involved in transcriptional modulation responding to heme flux. Many of the bacterial species responsible for these hemoproteins (including those that produce HemS, ChuS and ShuS) are known to specifically target oxygen-depleted regions of the gastrointestinal tract. A deeper understanding of anaerobic heme breakdown processes exploited by these pathogens could therefore prove useful in the development of future strategies for disease prevention.

Molecular Taphonomy of Heme: Chemical Degradation of Hemin under Presumed Fossilization Conditions

The metalloporphyrin heme acts as the oxygen-complexing prosthetic group of hemoglobin in blood. Heme has been noted to survive for many millions of years in fossils. Here, we investigate its stability and degradation under various conditions expected to occur during fossilization. Oxidative, reductive, aerobic, and anaerobic conditions were studied at neutral and alkaline pH values. Elevated temperatures were applied to accelerate degradation. High-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) identified four main degradation products. The vinyl residues are oxidized to formyl and further to carboxylate groups. In the presence of air or H₂O₂, cleavage of the tetrapyrrole ring occurs, and hematinic acid is formed. The highest stability of heme was observed under anaerobic reductive conditions (half-life 9.5 days), while the lowest stability was found in the presence of H₂O₂ (half-life 1 min). We confirmed that the iron cation plays a crucial role in degradation, since protoporphyrin IX, lacking iron, remained significantly more stable. Under anaerobic, reductive conditions, the above-mentioned degradation products were not observed, suggesting a different degradation pathway. To our knowledge, this is the first molecular taphonomy study on heme, which will be useful for understanding its fate during fossilization.

Biodereplication of Antiplasmodial Extracts: Application of the Amazonian Medicinal Plant Piper coruscans Kunth

Improved methodological tools to hasten antimalarial drug discovery remain of interest, especially when considering natural products as a source of drug candidates. We propose a biodereplication method combining the classical dereplication approach with the early detection of potential antiplasmodial compounds in crude extracts. Heme binding is used as a surrogate of the antiplasmodial activity and is monitored by mass spectrometry in a biomimetic assay. Molecular networking and automated annotation of targeted mass through data mining were followed by mass-guided compound isolation by taking advantage of the versatility and finely tunable selectivity offered by centrifugal partition chromatography. This biodereplication workflow was applied to an ethanolic extract of the Amazonian medicinal plant Piper coruscans Kunth (Piperaceae) showing an IC50 of 1.36 µg/mL on the 3D7 Plasmodium falciparum strain. It resulted in the isolation of twelve compounds designated as potential antiplasmodial compounds by the biodereplication workflow. Two chalcones, aurentiacin (1) and cardamonin (3), with IC50 values of 2.25 and 5.5 µM, respectively, can be considered to bear the antiplasmodial activity of the extract, with the latter not relying on a heme-binding mechanism. This biodereplication method constitutes a rapid, efficient, and robust technique to identify potential antimalarial compounds in complex extracts such as plant extracts.

Ionization and Photofragmentation of Isolated Metalloporphyrin Cations Investigated by VUV Action Spectroscopy*

We investigated the photoionization and fragmentation of isolated metal protoporphyrin IX cations (MPPIX+ with M=Fe, Co, Zn) by means of vacuum-ultraviolet (VUV) action spectroscopy in the energy range of 8.5-35 eV. Experiments were carried out in the gas phase by interfacing an electrospray ionization tandem mass spectrometer with a synchrotron beamline. The mass spectra and partial ion yields show that photoexcitation of the precursor ions predominantly leads to . CH2 COOH radical side-chain losses of the macrocycle with additional methyl radical (. CH3 ) side-chain losses. Ionization, in contrast, leads to the formation of the intact ionized precursor and various doubly charged fragments which are mostly due to side-chain cleavages. Although statistical fragmentation dominates, we found evidence for non-statistical processes such as new fragments involving for example single and double H2 O losses, indicating that different relaxation mechanisms are at play upon photoionization compared to photoexcitation. The measured ionization energies were 9.6±0.2 eV, 9.4±0.2 eV and 9.6±0.2 eV for FePPIX+ , CoPPIX+ and ZnPPIX+ , respectively.

The electronic structure and deexcitation pathways of an isolated metalloporphyrin ion resolved by metal L-edge spectroscopy

The local electronic structure of the metal-active site and the deexcitation pathways of metalloporphyrins are crucial for numerous applications but difficult to access by commonly employed techniques. Here, we applied near-edge X-ray absorption mass spectrometry and quantum-mechanical restricted active space calculations to investigate the electronic structure of the metal-active site of the isolated cobalt(iii) protoporphyrin IX cation (CoPPIX+) and its deexcitation pathways upon resonant absorption at the cobalt L-edge. The experiments were carried out in the gas phase, thus allowing for control over the chemical state and molecular environment of the metalloporphyrin. The obtained mass spectra reveal that resonant excitations of CoPPIX+ at the cobalt L3-edge lead predominantly to the formation of the intact radical dication and doubly charged fragments through losses of charged and neutral side chains from the macrocycle. The comparison between experiment and theory shows that CoPPIX+ is in a 3A2g triplet ground state and that competing excitations to metal-centred non-bonding and antibonding σ* molecular orbitals lead to distinct deexcitation pathways.

Heme Determination and Quantification Methods and Their Suitability for Practical Applications and Everyday Use

Many research institutions, clinical diagnostic laboratories, and blood banks are desperately searching for a possibility to identify and quantify heme in different physiological and pathological settings as well as various research applications. The reasons for this are the toxicity of the heme and the fact that it acts as a hemolytic and pro-inflammatory molecule. Heme only exerts these severe and undesired effects when it is not incorporated in hemoproteins. Upon release from the hemoproteins, it enters a biologically available state (labile heme), in which it is loosely associated with proteins, lipids, nucleic acids, or other molecules. While the current methods and procedures for quantitative determination of heme have been used for many years in different settings, their value is limited by the challenging chemical properties of heme. A major cause of inadequate quantification is the separation of labile and permanently bound heme and its high aggregation potential. Thus, none of the current methods are utilized as a generally applicable, standardized approach. The aim of this Feature is to describe and summarize the most common and frequently used chemical, analytical, and biochemical methods for the quantitative determination of heme. Based on this overview, the most promising approaches for future solutions to heme quantification are highlighted.

The dramatic effect of N-methylimidazole on trans axial ligand binding to ferric heme: experiment and theory

The binding energy of CO, O2 and NO to isolated ferric heme, [FeIIIP]+, was studied in the presence and absence of a σ donor (N-methylimidazole and histidine) as the trans axial ligand. This study combines the experimental determination of binding enthalpies by equilibrium measurements in a low temperature ion trap using the van't Hoff equation and high level DFT calculations. It was found that the presence of N-methylimidazole as the axial ligand on the [FeIIIP]+ porphyrin dramatically weakens the [FeIIIP-ligand]+ bond with an up to sevenfold decrease in binding energy owing to the σ donation by N-methylimidazole to the FeIII(3d) orbitals. This trans σ donor effect is characteristic of ligation to iron in hemes in both ferrous and ferric redox forms; however, to date, this has not been observed for ferric heme.

Quantum chemical mass spectrometry: ab initio prediction of electron ionization mass spectra and identification of new fragmentation pathways

The electron ionization mass spectra of four organic compounds are predicted based on the results of quantum chemical calculations at the DFT/B3LYP/6-311 + G* level of theory. This prediction is performed 'ab initio', i.e. without any prior knowledge of the thermodynamics or kinetics of the reactions under consideration. Using a set of rules determining which routes will be followed, the fragmentation of the molecules' bonds and the complete resulting fragmentation pathways are studied. The most likely fragmentation pathways are identified based on calculated reaction energies ΔE when bond cleavage is considered and on activation energies ΔE^‡ when rearrangements are taken into account; the final intensities of the peaks in the spectrum are estimated from these values. The main features observed in the experimental mass spectra are correctly predicted, as well as a number of minor peaks. In addition, the results of the calculations allow us to propose fragmentation pathways new to empirical mass spectrometry, which have been experimentally verified using tandem mass spectrometry measurements. Copyright © 2016 John Wiley & Sons, Ltd.

Gas-phase spectroscopy of ferric heme-NO complexes

Weakly bound complexes between ferric heme cations and NO were synthesised in the gas phase from ion-molecule reactions, and their absorption measured based on photodissociation yields. The Soret band, which serves as an important marker band for heme-protein spectroscopy, is maximal at 357±5 nm and significantly blue-shifted compared to ferric heme nitrosyl proteins (maxima between 408 and 422 nm). This is in stark contrast to the Q-band absorption where the protein microenvironment is nearly innocent in perturbing the electronic structure of the porphyrin macrocycle. Photodissociation is primarily through loss of NO. In contrast to the Q-band region, two-photon absorption was seen in the Soret band despite NO loss only requiring ∼1 eV. A model based on intersystem crossing to a long-lived triplet state where a barrier has to be surmounted is suggested. Finally, we summarise the measured absorption maxima of heme and its complexes with amino acids and NO.

Partial characterization of a novel amphibian hemoglobin as a model for graduate student investigation on peptide chemistry, mass spectrometry, and atomic force microscopy

Graduate students in chemistry, and in biological and biomedical fields must learn the fundamentals and practices of peptide and protein chemistry as early as possible. A project-oriented approach was conducted by first-year M.Sc and Ph.D students in biological sciences. A blind glass slide containing a cellular smear and an aqueous cellular extract were offered to the students. Qualitative and quantitative cell morphological parameters were analyzed by atomic force microscopy. The fractionation of the aqueous extract was conducted by reversed-phase chromatography followed by analysis of the isolated and partially purified proteins and peptides by mass spectrometry (MS). The proteins were treated by peptidases and the obtained peptide fragments were sequenced by de novo MS/MS, together with peptides already present in the extract. The most abundant protein fractions were identified as the alpha and beta chains of hemoglobin from an amphibian of the Leptodactylus genera. Two of the peptides sequenced by the students were synthesized by the solid-phase methodology, one of those being obtained by the split-and-pool library synthesis method. Thus, the students were able to learn some advanced principles and practices of protein chemistry and bionanotechnology in a 6-weeks project-oriented approach.

Unravelling the intrinsic features of NO binding to iron(II)- and iron(III)-hemes

Electrospray ionization of appropriate precursors is used to deliver [Fe (III)-heme] (+) and [Fe (II)-hemeH] (+) ions as naked species in the gas phase where their ion chemistry has been examined by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. In the naked, four-coordinate [Fe (II)-hemeH] (+) and [Fe (III)-heme] (+) ions, the intrinsic reactivity of iron(II)- and iron(III)-hemes is revealed free from any influence due to axial ligand, counterion, or solvent effects. Ligand (L) addition and ligand transfer equilibria with a series of selected neutrals are attained when [Fe (II)-hemeH] (+), corresponding to protonated Fe (II)-heme, is allowed to react in the FT-ICR cell. A Heme Cation Basicity (HCB) ladder for the various ligands toward [Fe (II)-hemeH] (+), corresponding to -Delta G degrees for the process [Fe (II)-hemeH] (+) + L --> [Fe (II)-hemeH(L)] (+) and named HCB (II), can thus be established. The so-obtained HCB (II) values are compared with the corresponding HCB (III) values for [Fe (III)-heme] (+). In spite of pronounced differences displayed by various ligands, NO shows a quite similar HCB of about 67 kJ mol (-1) at 300 K toward both ions, estimated to correspond to a binding energy of 124 kJ mol (-1). Density Functional Theory (DFT) computations confirm the experimental results, yielding very similar values of NO binding energies to [Fe (II)-hemeH] (+) and [Fe (III)-heme] (+), equal to 140 and 144 kJ mol (-1), respectively. The kinetic study of the NO association reaction supports the equilibrium HCB data and reveals that the two species share very close rate constant values both for the forward and for the reverse reaction. These gas phase results diverge markedly from the kinetics and thermodynamic behavior of NO binding to iron(II)- and iron(III)-heme proteins and model complexes in solution. The requisite of either a very labile or a vacant coordination site on iron for a facile addition of NO to occur, suggested to explain the bias for typically five-coordinate iron(II) species in solution, is fully supported by the present work.

Electron-capture-induced dissociation of protoporphyrin IX ions

Electron-capture induced dissociation of protoporphyrin cations and anions has been studied. The cations captured two electrons in two successive collisions and were converted to the corresponding even-electron anions. About one fifth of the ions lost a hydrogen atom to become radical anions but otherwise very little fragmentation was observed. The anions captured an electron to become dianions. No hydrogen loss occurred, and the only fragmentation channel observed was loss of CO2H, to give a doubly charged carbanion. Our results indicate that protoporphyrin ions are very efficient in accommodating one or even two electrons in the lowest unoccupied molecular orbital of the porphyrin macrocycle, and that electron capture induces only limited dissociation.

A new technique for time-resolved daughter ion mass spectrometry on the microsecond to millisecond time scale using an electrostatic ion storage ring

A new method for time-resolved daughter ion mass spectrometry is presented, based on the electrostatic ion storage ring in Aarhus, ELISA. Ions with high internal energy, e.g., as a result of photoexcitation, dissociate and the yield of neutrals is monitored as a function of time. This gives information on lifetimes in the microsecond to millisecond time range but no information on the fragment masses. To determine the dissociation channels, we have introduced pulsed supplies with switching times of a few microseconds. This allows rapid switching from storage of parent ions to storage of daughter ions, which are dumped into a detector after a number of revolutions in the ring. A fragment mass spectrum is obtained by monitoring the daughter ion signal as a function of the ring voltages. This technique allows identification of the dissociation channels and determination of the time dependent competition between these channels.

Theoretical DFT Study of Fragmentation and Association of Heme and Hemin

The electronic and geometric structures, energy stability, and normal vibrational frequencies of heme, hemine, and their stepwise fragmentation products (with successive loss of two carboxymethyl, four methyl, and two vinyl peripheral groups) in the states with different multiplicity were calculated using the density functional theory (the B3LYP method) with several basis sets. At the same level, the structure and stability of neutral and positively charged dimers of the ferri- and ferroporphyrines were also computed. The computational results are compared with available experimental data. The trends in the behavior of these properties of heme and hemin are analyzed upon the stepwise fragmentation and association and with a change in the multiplicity and external charge. The structure and energetic stability of complexes of the species with molecular oxygen are discussed.

A Mass Spectrometric Investigation of Native and Oxidatively Inactivated Chloroperoxidase

The enzyme chloroperoxidase (CPO) found in Caldariomyces fumago is able to catalyze several stereoselective oxidation reactions by using a clean oxidant, usually hydrogen peroxide (H(2)O(2)), without the need for expensive cofactor generation. CPO's lack of operational stability, however, is a major limitation for its commercial use. In the present study, a capillary-LC on-line trypsin-digestion system combined with reversed-phase chromatography and mass spectrometric detection was optimized for studying the primary sequence of CPO. Samples containing native CPO, CPO treated with H(2)O(2), and CPO oxidatively inactivated by the use of indole and H(2)O(2) were analyzed and compared. Three oxidized peptides were found in the samples treated with H(2)O(2). Two additional oxidized peptides were found in the CPO samples that were completely inactivated, one of which contained an oxidized cysteine residue, Cys50, which is an essential amino acid due to its function as the axial ligand to the iron in the heme--the prosthetic group in CPO. In addition, the heme group was absent in the inactivated samples but was readily detected in other samples.

How large is the [Fe(III)(protoporphyrin IX)]+ ion (hemin+) in the gas phase?

Comparison of the collision cross-section of the [Fe(III)-protoporphyrin IX]+ ion, hemin+, measured by means of ion-mobility experiments and the cross-sections calculated from theoretical structures based on density functional theory reveals that hemin+, in the gas phase, contains intramolecular hydrogen bonding between its two propionic acid side-chains.

Dissociation of heme from gaseous myoglobin ions studied by infrared multiphoton dissociation spectroscopy and Fourier-transform ion cyclotron resonance mass spectrometry

Detachment of heme prosthetic groups from gaseous myoglobin ions has been studied by collision-induced dissociation and infrared multiphoton dissociation in combination with Fourier-transform ion cyclotron resonance mass spectrometry. Multiply charged holomyoglobin ions (hMbn+) were generated by electrospray ionization and transferred to an ion cyclotron resonance cell, where the ions of interest were isolated and fragmented by either collision with Ar atoms or irradiation with 3 mum photons, producing apomyoglobin ions (aMbn+). Both charged heme loss (with [Fe(III)-heme]+ and aMb(n-1)+ as the products) and neutral heme loss (with [Fe(II)-heme] and aMbn+ as the products) were detected concurrently for hMbn+ produced from a myoglobin solution pretreated with reducing reagents. By reference to Ea = 0.9 eV determined by blackbody infrared radiative dissociation for charged heme loss of ferric hMbn+, an activation energy of 1.1 eV was deduced for neutral heme loss of ferrous hMbn+ with n = 9 and 10.