Conservation of the conformation of the porphyrin macrocycle in hemoproteins

Probing the versatility of cytochrome c by spectroscopic means: A Laudatio on resonance Raman spectroscopy

Over the last 50 years resonance Raman spectroscopy has become an invaluable tool for the exploration of chromophores in biological macromolecules. Among them, heme proteins and metal complexes have attracted considerable attention. This interest results from the fact that resonance Raman spectroscopy probes the vibrational dynamics of these chromophores without direct interference from the surrounding. However, the indirect influence via through-bond and through-space chromophore-protein interactions can be conveniently probed and analyzed. This review article illustrates this point by focusing on class 1 cytochrome c, a comparatively simple heme protein generally known as electron carrier in mitochondria. The article demonstrates how through selective excitation of resonance Raman active modes information about the ligation, the redox state and the spin state of the heme iron can be obtained from band positions in the Raman spectra. The investigation of intensities and depolarization ratios emerged as tools for the analysis of in-plane and out-of-plane deformations of the heme macrocycle. The article further shows how resonance Raman spectroscopy was used to characterize partially unfolded states of oxidized cytochrome c. Finally, it describes its use for exploring structural changes due to the protein's binding to anionic surfaces like cardiolipin containing membranes.

Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis

Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.

Complexes of N-Confused Porphyrin Derivatives as Ortho-Metallating Ligands. Synthesis, Structure, Redox Properties, and Chirality

A family of transition metal complexes of meso-aryl-2-aza-21-carbaporphyrin (N-confused porphyrin, NCP) derivatives acting as ortho-metallating ligands for ruthenium(II), rhodium(III), and iridium(III) is synthesized and characterized by XRD, spectroscopic, and electrochemical methods. The chirality of these systems is shown by the separation of the enantiomers and analyzed by circular dichroism and DFT. A preliminary catalytic study indicates the activity of the iridium(III) ortho-metallated complexes in the N-heterocyclization of primary amines with diols.

Computational Exploration of Minimum Energy Reaction Pathway of N2O Formation from Intermediate I of P450nor Using an Active Center Model

P450nor is a heme-containing enzyme that catalyzes the conversion of nitric oxide (NO) to nitrous oxide (N2O). Its catalytic mechanism has attracted attention in chemistry, biology, and environmental engineering. The catalytic cycle of P450nor is proposed to consist of three major steps. The reaction mechanism for the last step, N2O generation, remains unknown. In this study, the reaction pathway of the N2O generation from the intermediate I was explored with the B3LYP calculations using an active center model after the examination of the validity of the model. In the validation, we compared the heme distortions between P450nor and other oxidoreductases, suggesting a small effect of protein environment on the N2O generation reaction in P450nor. We then evaluated the electrostatic environment effect of P450nor on the hydride affinity to the active site with quantum mechanics/molecular mechanics (QM/MM) calculations, confirming that the affinity was unchanged with or without the protein environment. The active center model for P450nor showed that the N2O generation process in the enzymatic reaction undergoes a reasonable barrier height without protein environment. Consequently, our findings strongly suggest that the N2O generation reaction from the intermediate I depends sorely on the intrinsic reactivity of the heme cofactor bound on cysteine residue.

Molecular Interactions Identified by Two-Dimensional Analysis-Detailed Insight into the Molecular Interactions of the Antimalarial Artesunate with the Target Structure β-Hematin by Means of 2D Raman Correlation Spectroscopy

A thorough understanding of the interaction of endoperoxide antimalarial agents with their biological target structures is of utmost importance for the tailored design of future efficient antimalarials. Detailed insights into molecular interactions between artesunate and β-hematin were derived with a combination of resonance Raman spectroscopy, two-dimensional correlation analysis, and density functional theory calculations. Resonance Raman spectroscopy with three distinct laser wavelengths enabled the specific excitation of different chromophore parts of β-hematin. The resonance Raman spectra of the artesunate-β-hematin complexes were thoroughly analyzed with the help of high-resolution and highly sensitive two-dimensional correlation spectroscopy. Spectral changes in the peak properties were found with increasing artesunate concentration. Changes in the low-frequency, morphology-sensitive Raman bands indicated a loss in crystallinity of the drug-target complexes. Differences in the high-wavenumber region were assigned to increased distortions of the planarity of the structure of the target molecule due to the appearance of various coexisting alkylation species. Evidence for the appearance of high-valent ferryl-oxo species could be observed with the help of differences in the peak properties of oxidation-state sensitive Raman modes. To support those findings, the relaxed ground-state structures of ten possible covalent mono- and di-meso(Cm)-alkylated hematin-dihydroartemisinyl complexes were calculated using density functional theory. A very good agreement with the experimental peak properties was achieved, and the out-of-plane displacements along the lowest-frequency normal coordinates were investigated by normal coordinate structural decomposition analysis. The strongest changes in all data were observed in vibrations with a high participation of Cm-parts of β-hematin.

Molecular Geometry and Electronic Structure of Copper Corroles

Copper corroles are known for their unique multiconfigurational electronic structures in the ground state, which arise from the transfer of electrons from the π orbitals of the corrole to the d-orbital of copper. While density functional theory (DFT) provides reasonably good molecular geometries, the determination of the ground spin state and the associated energetics is heavily influenced by functional choice, particularly the percentage of the Hartree-Fock exchange. Using extended multireference perturbation theory methods (XMS-CASPT2), the functional choice can be assessed. The molecular geometries and electronic structures of both the unsubstituted and the meso-triphenyl copper corroles were investigated. A minimal active space was employed for structural characterization, while larger active spaces are required to examine the electronic structure. The XMS-CASPT2 investigations conclusively identify the ground electronic state as a multiconfigurational singlet (S0) with three dominant electronic configurations in its lowest energy and characteristic saddled structure. In contrast, the planar geometry corresponds to the triplet state (T0), which is approximately 5 kcal/mol higher in energy compared to the S0 state for both the bare and substituted copper corroles. Notably, the planarity of the T0 geometry is reduced in the substituted corrole compared with that in the unsubstituted one. By analyzing the potential energy surface (PES) between the S0 and T0 geometries using XMS-CASPT2, the multiconfigurational electronic structure is shown to transition toward a single electron configuration as the saddling angle decreases (i.e., as one approaches the planar geometry). Despite the ability of the functionals to reproduce the minimum energy structures, only the TPSSh-D3 PES is reasonably close to the XMS-CASPT2 surface. Significant deviations along the PES are observed with other functionals.

Cyclic iron tetra N-heterocyclic carbenes: synthesis, properties, reactivity, and catalysis

Cyclic iron tetracarbenes are an emerging class of macrocyclic iron N-heterocyclic carbene (NHC) complexes. They can be considered as an organometallic compound class inspired by their heme analogs, however, their electronic properties differ, e.g. due to the very strong σ-donation of the four combined NHCs in equatorial coordination. The ligand framework of iron tetracarbenes can be readily modified, allowing fine-tuning of the structural and electronic properties of the complexes. The properties of iron tetracarbene complexes are discussed quantitatively and correlations are established. The electronic nature of the tetracarbene ligand allows the isolation of uncommon iron(III) and iron(IV) species and reveals a unique reactivity. Iron tetracarbenes are successfully applied in C-H activation, CO₂ reduction, aziridination and epoxidation catalysis and mechanisms as well as decomposition pathways are described. This review will help researchers evaluate the structural and electronic properties of their complexes and target their catalyst properties through ligand design.

Heme-Protein Interactions and Functional Relevant Heme Deformations: The Cytochrome c Case

Heme proteins are known to perform a plethora of biologically important functions. This article reviews work that has been conducted on various class I cytochrome c proteins over a period of nearly 50 years. The article focuses on the relevance of symmetry-lowering heme-protein interactions that affect the function of the electron transfer protein cytochrome c. The article provides an overview of various, mostly spectroscopic studies that explored the electronic structure of the heme group in these proteins and how it is affected by symmetry-lowering deformations. In addition to discussing a large variety of spectroscopic studies, the article provides a theoretical framework that should enable a comprehensive understanding of the physical chemistry that underlies the function not only of cytochrome c but of all heme proteins.

1,3-Dipolar cycloaddition of polycyclic azomethine ylide to norcorroles: towards dibenzoullazine-fused derivatives

A 1,3-cycloaddition reaction of 2-(tert-butyl)-8H-isoquinolino[4,3,2-de]phenanthridin-9-ium chloride to Ni^II norcorrole in the presence of base is shown to produce a family of chiral derivatives of polycyclic system(s) fused with pyrrole subunit(s) of the macrocycle. Dehydrogenation of the cycloaddition products gave rise to dibenzoullazine ortho-fused antiaromatic porphyrinoids.

Comparing Properties of Common Bioinorganic Ligands with Switchable Variants of Cytochrome c

Ligand substitution at the metal center is common in catalysis and signal transduction of metalloproteins. Understanding the effects of particular ligands, as well as the polypeptide surrounding, is critical for uncovering mechanisms of these biological processes and exploiting them in the design of bioinspired catalysts and molecular devices. A series of switchable K79G/M80X/F82C (X = Met, His, or Lys) variants of cytochrome (cyt) c was employed to directly compare the stability of differently ligated proteins and activation barriers for Met, His, and Lys replacement at the ferric heme iron. Studies of these variants and their nonswitchable counterparts K79G/M80X have revealed stability trends Met < Lys < His and Lys < His < Met for the protein Fe^III-X and Fe^II-X species, respectively. The differences in the hydrogen-bonding interactions in folded proteins and in solvation of unbound X in the unfolded proteins explain these trends. Calculations of free energy of ligand dissociation in small heme model complexes reveal that the ease of the Fe^III-X bond breaking increases in the series amine < imidazole < thioether, mirroring trends in hardness of these ligands. Experimental rate constants for X dissociation in differently ligated cyt c variants are consistent with this sequence, but the differences between Met and His dissociation rates are attenuated because the former process is limited by the heme crevice opening. Analyses of activation parameters and comparisons to those for the Lys-to-Met ligand switch in the alkaline transition suggest that ligand dissociation is entropically driven in all the variants and accompanied by Lys protonation at neutral pH. The described thiolate redox-linked switches have offered a wealth of new information about interactions of different protein-derived ligands with the heme iron in cyt c model proteins, and we anticipate that the strategy of employing these switches could benefit studies of other redox metalloproteins and model complexes.

Chirogenesis in Zinc Porphyrins: Theoretical Evaluation of Electronic Transitions, Controlling Structural Factors and Axial Ligation

In the present work, sixteen different zinc porphyrins (possessing different meso substituents) with and without a chiral guest were modelled using DFT and TD-DFT approaches in order to understand the influence of various controlling factors on electronic circular dichroism (ECD) spectra. Two major aspects are influenced by these factors: excitation energy of the electronic transitions and their intensity. In the case of excitation energy, the influence increases in the following order: orientation of the peripheral substituents Collapse

Key Words

• circular dichroism
• density functional calculations
• porphyrins
• supramolecular chemistry
• transition metals

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MESH Headings Collapse

Grants

• PUTJD749 Estonian Research Council
• PRG399 Estonian Research Council
• 828779 European Union's H2020-FETOPEN
• Estonian Research Council

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Affiliation(s)

Irina Osadchuk Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia ICGMUniv MontpellierCNRS, ENSCMMontpellierFrance
Riina Aav Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia
Victor Borovkov Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia
Eric Clot ICGMUniv MontpellierCNRS, ENSCMMontpellierFrance

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PorphyStruct: A Digital Tool for the Quantitative Assignment of Non-Planar Distortion Modes in Four-Membered Porphyrinoids

PorphyStruct, a new digital tool for the analysis of non‐planar distortion modes of different porphyrinoids, and its application to corrole structures is reported. The program makes use of the normal‐coordinate structure decomposition technique (NSD) and employs sets of normal modes equivalent to those established for porphyrins in order to describe the out‐of‐plane dislocation pattern of perimeter atoms from corroles, norcorroles, porphycenes and other porphyrinoids quantitatively and in analogy to the established terminology. A comparative study of 17 porphyrin structures shows very similar results to the original NSD analysis and no systematic error. Application to corroles is successful and reveals the necessity to implement an extended basis of normal modes for a large share of experimental structures. The results frequently show the concomitant occurence of several modes but remain interpretable. For group XI metal corroles the phenomenon of supersaddling was unravelled, allowing for more in‐depths discussions of structure‐function correlations.

Structural effects of meso-halogenation on porphyrins

The use of halogens in the crystal engineering of supramolecular porphyrin assemblies has been a topic of strong interest over the past decades. With this in mind we have characterized a series of direct meso-halogenated porphyrins using single crystal X-ray crystallography. This is accompanied by a detailed conformational analysis of all deposited meso-halogenated porphyrins in the CSD. In this study we have used the Hirshfeld fingerprint plots together with normal-coordinate structural decomposition and determined crystal structures to elucidate the conformation, present intermolecular interactions, and compare respective contacts within the crystalline architectures. Additionally, we have used density functional theory calculations to determine the structure of several halogenated porphyrins. This contrasts conformational analysis with existing X-ray structures and gives a method to characterize samples that are difficult to crystallize. By using the methods outlined above we were able to deduce the impact a meso halogen has on a porphyrin, for example, meso-halogenation is dependent on the type of alternate substituents present when forming supramolecular assemblies. Furthermore, we have designed a method to predict the conformation of halogenated porphyrins, without need of crystallization, using DFT calculations with a high degree of accuracy.

Interplays of electron and nuclear motions along CO dissociation trajectory in myoglobin revealed by ultrafast X-rays and quantum dynamics calculations

Ultrafast structural dynamics with different spatial and temporal scales were investigated during photodissociation of carbon monoxide (CO) from iron(II)-heme in bovine myoglobin during the first 3 ps following laser excitation. We used simultaneous X-ray transient absorption (XTA) spectroscopy and X-ray transient solution scattering (XSS) at an X-ray free electron laser source with a time resolution of 80 fs. Kinetic traces at different characteristic X-ray energies were collected to give a global picture of the multistep pathway in the photodissociation of CO from heme. In order to extract the reaction coordinates along different directions of the CO departure, XTA data were collected with parallel and perpendicular relative polarizations of the laser pump and X-ray probe pulse to isolate the contributions of electronic spin state transition, bond breaking, and heme macrocycle nuclear relaxation. The time evolution of the iron K-edge X-ray absorption near edge structure (XANES) features along the two major photochemical reaction coordinates, i.e., the iron(II)-CO bond elongation and the heme macrocycle doming relaxation were modeled by time-dependent density functional theory calculations. Combined results from the experiments and computations reveal insight into interplays between the nuclear and electronic structural dynamics along the CO photodissociation trajectory. Time-resolved small-angle X-ray scattering data during the same process are also simultaneously collected, which show that the local CO dissociation causes a protein quake propagating on different spatial and temporal scales. These studies are important for understanding gas transport and protein deligation processes and shed light on the interplay of active site conformational changes and large-scale protein reorganization.

Purification of the key enzyme complexes of the anammox pathway from DEMON sludge

Anaerobic Ammonium Oxidation ("anammox") is a bacterial process in which nitrite and ammonium are converted into nitrogen gas and water, yielding energy for the cell. Anammox is an important branch of the global biological nitrogen cycle, being responsible for up to 50% of the yearly nitrogen removal from the oceans. Strikingly, the anammox process uniquely relies on the extremely reactive and toxic compound hydrazine as a free intermediate. Given its global importance and biochemical novelty, there is considerable interest in the enzymes at the heart of the anammox pathway. Unfortunately, obtaining these enzymes in sufficiently large amounts for biochemical and structural studies is problematic, given the slow growth of pure cultures of anammox bacteria when high cell densities are required. However, the anammox process is being applied in wastewater treatment to remove nitrogenous waste in processes like DEamMONification (DEMON). In plants using such processes, which rely on a combination of aerobic ammonia-oxidizers and anammox organisms, kilogram amounts of anammox bacteria-containing sludge are readily available. Here, we report a protein isolation protocol starting from anammox cells present in DEMON sludge from a wastewater treatment plan that readily yields pure preparations of key anammox proteins in the tens of milligrams, including hydrazine synthase HZS and hydrazine dehydrogenase (HDH), as well as hydroxylamine oxidoreductase (HAO). HDH and HAO were active and of sufficient quality for biochemical studies and for HAO, the crystal structure could be determined. The method presented here provides a viable way to obtain materials for the study of proteins not only from the central anammox metabolism but also for the study of other exciting aspects of anammox bacteria, such as for example, their unusual ladderane lipids.

Gas-Phase Transformation of Fluorinated Benzoporphyrins to Porphyrin-Embedded Conical Nanocarbons

Geodesic nitrogen-containing graphene fragments are interesting candidates for various material applications, but the available synthetic protocols, which need to overcome intrinsic strain energy during the formation of the bowl-shaped skeletons, are often incompatible with heteroatom-embedded structures. Through this mass spectrometry-based gas-phase study, we show by means of collision-induced dissociation experiments and supported by density functional theory calculations, the first evidence for the formation of a porphyrin-embedded conical nanocarbon. The influences of metalation and functionalization of the used tetrabenzoporphyrins have been investigated, which revealed different cyclization efficiencies, different ionization possibilities, and a variation of the dissociation pathway. Our results suggest a stepwise process for HF elimination from the fjord region, which supports a selective pathway towards bent nitrogen-containing graphene fragments.

Spin cascade and doming in ferric hemes: Femtosecond X-ray absorption and X-ray emission studies

The structure-function relationship is at the heart of biology, and major protein deformations are correlated to specific functions. For ferrous heme proteins, doming is associated with the respiratory function in hemoglobin and myoglobins. Cytochrome c (Cyt c) has evolved to become an important electron-transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe Kα and Kβ X-ray emission spectroscopy (XES) with Fe K-edge X-ray absorption near-edge structure (XANES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the iron ion, causing the ferric heme to undergo doming, which we identify. We also argue that this pattern is common to a wide diversity of ferric heme proteins, raising the question of the biological relevance of doming in such proteins.

Weak Interactions and Conformational Changes in Core-Protonated A2- and Ax-Type Porphyrin Dications

Individual chemical motifs are known to introduce structural distortions to the porphyrin macrocycle, be it in the core or at the periphery of the macrocycle. The interplay when introducing two or more of these known structural motifs has been scarcely explored and is not necessarily simply additive; these structural distortions have a chance to compound or negate to introduce new structural types. To this end, a series of compounds with complementary peripheral (5,15-disubstitution) and core (acidification) substitution patterns were investigated. The single-crystal X-ray structures of 18 5,15-diphenylporphyrin, 5,15-diphenylporphyrindi-ium diacid, and related compounds are reported, including the first example of a 5,15-dialkylporphyrindi-ium. Normal-coordinate structural decomposition (NSD) analysis is used for a detailed analysis of the conformation of the porphyrin subunit within the crystal structures. An elongation of porphyrin macrocycles along the C₅,C₁₅- axis (B_2g symmetry) is observed in all of the free base porphyrins and porphyrin dications; distance across the core is around 0.3 Å in the free base and diacid compounds, and more than doubled in 5,15-dipentylporphyrin and 5,15-dipentylporphyrindi-ium diacid. While the free base porphyrins are largely planar, a large out-of-plane distortion can be observed in 5,15-diphenylporphyrin diacids, with the expected “projective saddle” shape characteristic for such systems. The combination of these two distortions (B_2u and B_2g) from regular porphyrin structure results in a macrocycle best characterized in the chiral point-group D₂. A rare structural type of a cis-hydrogen bond chelate is observed for 5,15-dipentylporphyrindi-ium diacid, which adopts an achiral C_2v symmetry. Crystallographic data indicate that the protonated porphyrin core forms hydrogen bonding chelates (N-H⋯X⋯H-N) to counter-anions. Weaker interactions, such as induced intramolecular C-H⋯O interactions from the porphyrin periphery are described, with distances characteristic of charge-assisted interactions. This paper offers a conceptual framework for accessing porphyrin macrocycles with designable distortion and symmetry, useful for the selective perturbation of electronic states and a design-for-application approach to solid state porphyrin materials.

Investigations of Low-Symmetrical Tetraaryltetrabenzoporphyrins Produced by Mixed Condensation Reactions

Within the past decade, tetraaryltetrabenzoporphyrins (TATBPs) have gained rising attention due to their potential in various fields of materials science and medicinal chemistry. However, this class of compounds still lacks in structural diversity, especially in the case of low-symmetrical compounds. Herein, mixed condensations were utilized to generate TATBPs with different substituents either in the meso-positions or the periphery of the macrocycle with total yields of 55-58%. The separation of crude mixtures was achieved by feasible chromatographic purification. The influence of symmetry on the electronic properties of TATBPs was studied by optical spectroscopy, electrochemistry, and X-ray diffraction.

Short-Chained Anthracene Strapped Porphyrins and their Endoperoxides

The syntheses of short-chained anthracene-strapped porphyrins and their Zn(II)complexes are reported. The key synthetic step is a [2+2] condensation between a dipyrromethane and an anthracene bisaldehyde, 2,2'-((anthracene-9,10-diylbis(methylene))bis(oxy))dibenzaldehyde. Following exposure to white light, self-sensitized singlet oxygen and the anthracene moieties underwent [4+2] cycloaddition reactions to yield the corresponding endoperoxides. 1H NMR studies demonstrate that the endoperoxide readily formed in [D]chloroform and decayed at 85 °C. X-ray crystallography and absorption spectroscopy were used to confirm macrocyclic distortion in the parent strapped porphyrins and endoperoxides. Additionally, X-ray crystallography indicated that endoperoxide formation occurred exclusively on the outside face of the anthracene moiety.

Iron transitions during activation of allosteric heme proteins in cell signaling

Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.

A Comprehensive Study on Tetraaryltetrabenzoporphyrins

Tetraaryltetrabenzoporphyrins (TATBPs) show, due to their optoelectronic properties, rising potential as dyes in various fields of physical and biomedical sciences. However, unlike in the case of porphyrins, the potential structural diversity of TATBPs has been explored only to little extent, owed mainly to synthetic hurdles. Herein, we prepared a comprehensive library of 30 TATBPs and investigated their fundamental properties. We elucidated structural properties by X-ray crystallography and found explanations for physical properties such as solubility. Fundamental electronic aspects were studied by optical spectroscopy as well as by electrochemistry and brought in context to the stability of the molecules. Finally, we were able to develop a universal synthetic protocol, utilizing a readily established isoindole synthon, which gives TATBPs in high yields, regardless of the nature of the used arylaldehyde and without meticulous chromatographic purifications steps. This work serves as point of orientation for scientists, that aim to utilize these molecules in materials, nanotechnological, and biomedical applications.

Distinctive structural properties of THB11, a pentacoordinate Chlamydomonas reinhardtii truncated hemoglobin with N- and C-terminal extensions

Hemoglobins (Hbs) utilize heme b as a cofactor and are found in all kingdoms of life. The current knowledge reveals an enormous variability of Hb primary sequences, resulting in topological, biochemical and physiological individuality. As Hbs appear to modulate their reactivities through specific combinations of structural features, predicting the characteristics of a given Hb is still hardly possible. The unicellular green alga Chlamydomonas reinhardtii contains 12 genes encoding diverse Hbs of the truncated lineage, several of which possess extended N- or C-termini of unknown function. Studies on some of the Chlamydomonas Hbs revealed yet unpredictable structural and biochemical variations, which, along with a different expression of their genes, suggest diverse physiological roles. Chlamydomonas thus represents a promising system to analyze the diversification of Hb structure, biochemistry and physiology. Here, we report the crystal structure, resolved to 1.75 Å, of the heme-binding domain of cyanomet THB11 (Cre16.g662750), one of the pentacoordinate algal Hbs, which offer a free Fe-coordination site in the reduced state. The overall fold of THB11 is conserved, but individual features such as a kink in helix E, a tilted heme plane and a clustering of methionine residues at a putative tunnel exit appear to be unique. Both N- and C-termini promote the formation of oligomer mixtures, and the absence of the C terminus results in reduced nitrite reduction rates. This work widens the structural and biochemical knowledge on the 2/2Hb family and suggests that the N- and C-terminal extensions of the Chlamydomonas 2/2Hbs modulate their reactivity by intermolecular interactions.

Ruffling and doming: Structural and redox studies on meso-aryl and β-alkyl chromyl(V)corroles

Chromyl(V) complexes of eleven different meso-aryl- and [Formula: see text]-alkylcorrole ligands have been prepared and characterized by analytical, spectroscopical, electrochemical and structural means. All seven new complexes show the expected optical spectra of chromyl(V) corroles with the Soret band situated slightly above (meso-arylcorroles) or below ([Formula: see text]-alkylcorrole) 400 nm, and with an isotropic room temperature EPR signal for the [Formula: see text] ion Cr(V) at about [Formula: see text]. Cyclic voltammetry evidences two or three quasi-reversible one-electron redox steps, which are characterized as two ligand-centered processes and one metal-centered process based on spectroelectrochemical measurements and a Hammett analysis. Chemical reduction to a chromyl(IV) corrolate was successfully performed using NaHg and NEt3. Citric acid, however, produces a different reduction product, for which an isocorrole structure is proposed. Six chromyl(V) corroles could be analysed by seven single crystal diffraction analyses. The obtained molecular data prove the presence of remarkably similar CrN4O coordination units independent of the corrole substitution pattern, and of macrocyclic conformations which can be understood as comprised mainly of a doming mode, a more or less pronounced saddling mode, and one out of two different and dominating ruffling modes.

Investigating the Impact of Conformational Molecular Engineering on the Crystal Packing of Cavity Forming Porphyrins

Herein we report the synthesis of 5,10,15,20-tetraaryl-(X)-substituted-2,3,7,8,12,13,17,18-octaethylporphyrins (OETArXPs) and a structural investigation of their solid-state properties via small molecule X-ray diffraction. A series of halogen (fluorine to iodine), nitrogenous (azido, cyano), alkyl (TMS-acetylene and acetylene), and chained (benzyloxy) porphyrins were chosen as the initial target molecules. Following this, a selection of tetravalent metal complexes [Cu(II), Ni(II), and Pd(II)] based on these porphyrins were synthesized to allow for an investigation of the effects of metal complexes on the structural properties of these highly substituted porphyrins. The size of the halogen atom affects the potential of intermolecular interactions and the resulting crystal packing in these 4-halo-OETArXP complexes. The fluorine series have an equal preference for alkyl or aryl groups (ortho-hydrogen), the chlorine series favor interactions between the alkyl groups, and the bromine appears to favor the aryl (ortho- and meta-hydrogens). This results in an extensive cupping pattern in the unit cell. For the 2,6-halo-OETArXP it was established that the change in position alters the types of the intermolecular contacts toward face-to-edge or face-to-face interactions and alters the packing patterns observed. Within the 4-benzyloxy-OETArXP series the meso-substituent favors interacting with the core of the porphyrin macrocycle. The 4-cyano-OETArXP is a suitable hydrogen-bond acceptor and results in an interesting Z-shape network. Additionally, it was highlighted that solvent effects play a much larger role in crystal packing than intermolecular/intramolecular interaction or metal(II) center substitution. This is accompanied by a study using both the azide- and acetylene-OETArXPs as a base molecule to allow for a quick one-step reaction for the generation of a variety of functionalized compounds. Using a copper(I)-catalyzed azide-alkyne cycloaddition reaction, we were able to append hydrogen bonding functionalities to the OETArXPs framework in high yields. The crystal packing images included in this work shows the potential to create selective and functional receptor sites based on free base porphyrins. However, insofar as analytical measurements indicate, the design of such a free base porphyrin through crystal engineering has not yet been realized. The variety of porphyrin packing arrangements herein indicates the need for further studies.

Naturally Occurring A51V Variant of Human Cytochrome c Destabilizes the Native State and Enhances Peroxidase Activity

The A51V variant of human cytochrome c is linked to thrombocytopenia 4 (THC4), a condition that causes decreased blood platelet counts. A 1.82 Å structure of the A51V variant shows only minor changes in tertiary structure relative to the wild-type (WT) protein. Guanidine hydrochloride denaturation demonstrates that the global stability of the A51V variant is 1.3 kcal/mol less than that of the WT protein. The midpoint pH, pH_1/2, of the alkaline transition of the A51V variant is 1 unit less than that of the WT protein. Stopped-flow pH jump experiments show that the A51V substitution affects the triggering ionization for one of two kinetically distinguishable alkaline conformers and enhances the accessibility of a high-spin heme transient. The pH_1/2 for acid unfolding of the A51V variant is 0.7 units higher than for that of the WT protein. Consistent with the greater accessibility of non-native conformers for the A51V variant, the k_cat values for its peroxidase activity increase by 6- to 15-fold in the pH range of 5-8 versus those of the WT protein. These data along with previously reported data for the other THC4-linked variants, G41S and Y48H, underscore the role of Ω-loop C (residues 40-57) in modulating the peroxidase activity of cytochrome c early in apoptosis.

Assessment of the intramolecular magnetic interactions in the highly saddled iron(iii) porphyrin π-radical cations: the change from planar to saddle conformations

The intramolecular magnetic interactions in one-electron oxidized iron(iii) porphyrin π-radical cations, [Fe(OETPP˙)Cl][SbCl6] (1), [Fe(OMTPP˙)Cl][SbCl6] (2) and [Fe(TPP˙)Cl][SbCl6] (3), have been compared by means of X-ray crystallography, SQUID magnetometry, cyclic voltammetry, UV-Vis spectroelectrochemical analysis, NMR spectroscopy analysis and unrestricted DFT calculations. Unlike a generally recognized antiferromagnetic coupling dxy↑dxz↑dyz↑dz2↑dx2-y2↑P˙+(a2u)↓ (S = 2) state via a weak bonding interaction as in (3), we have disclosed that a strong bonding interaction among iron dx2-y2 and porphyrin a2u orbitals forms in (1) into a highly delocalized Ψπ = [P˙+(a2u) + FeIII(dx2-y2, dz2)] orbital that is able to accommodate two spin-paired electrons to form the Ψπ2dxy1dxz1dyz1, dz21 (S = 2) ground state. Concurrently, the spin polarization effect is exerted on the paired spins in the Ψπ orbital by magnetic induction from the remaining unpaired electrons in the iron d orbitals. The interpretation mentioned above is further verified by the diamagnetic nature of the saddled copper(ii) porphyrin π-cation radical, CuII(OETPP˙)(ClO4) (S = 0), where the strong bonding interaction leads to the Ψπ2dxy2dxz2dyz2dz22 (S = 0) ground state but no spin polarization exists. Thus, the magnetic nature of the iron(iii) porphyrin π-radical cation is tuneable by saddling the ring planarity.

Single hydroxo-bridged group 13 metalloporphyrin dimers: Solution studies and solid-state structures

The syntheses of indium, gallium and aluminum porphyrin dimers with a single hydroxo-bridge, [Formula: see text][M(Porph)]2(OH)[Formula: see text], are described. Emphasis is given to indium and gallium derivatives. The X-ray structures for [Formula: see text] [Ga(OEP)]2(OH)[Formula: see text] ClO4 and [Formula: see text] [In(OEP)]2(OH)[Formula: see text] ClO4 (two forms) are presented. The dimeric molecules can be synthesized by the acid-treatment of the corresponding hydroxo-ligated monomeric complexes [M(OEP)(OH)] and [M(TPP)(OH)]. The nature of the starting material (the hydroxo-ligated monomer) was first suggested by IR spectroscopy and further proved by proton-deuterium exchange followed by 1H NMR spectroscopy. The structure of a monomeric indium hydroxide complex, [In(OEP)(OH)], is also presented. The synthesis of the dimer for all metals can be monitored by UV-vis spectroscopy, which clearly demonstrates that a blue-shift of the Soret band accompanies formation of the dimer from the monomer. A strong [Formula: see text]–[Formula: see text]interaction between the two porphyrin rings of these [Formula: see text]-hydroxo-bridged dimers is confirmed both by solution state studies (1H NMR and UV-vis spectroscopy) and the X-ray structures of [Formula: see text] [M(OEP)]2(OH)[Formula: see text] ClO4 (M = In, Ga). In addition, exposure of methylene chloride solutions of these bridged complexes to white light afforded the corresponding chloro derivatives, [M(Porph)Cl]. The stereochemistry of a range of [Formula: see text]-hydroxo dimers is discussed and DFT simulations at the HSEH1PBE/SDD level of theory provide suitable structural models and further electronic structure insights on selected [Ga(Porph)(OH)] and [Formula: see text] [Ga(Porph)]2(OH)[Formula: see text][Formula: see text] derivatives.

A 60-heme reductase complex from an anammox bacterium shows an extended electron transfer pathway

The hydroxylamine oxidoreductase/hydrazine dehydrogenase (HAO/HDH) protein family constitutes an important group of octaheme cytochromes c (OCCs). The majority of these proteins form homotrimers, with their subunits being covalently attached to each other via a rare cross-link between the catalytic heme moiety and a conserved tyrosine residue in an adjacent subunit. This covalent cross-link has been proposed to modulate the active-site heme towards oxidative catalysis by distorting the heme plane. In this study, the crystal structure of a stable complex of an HAO homologue (KsHAOr) with its diheme cytochrome c redox partner (KsDH) from the anammox bacterium Kuenenia stuttgartiensis was determined. KsHAOr lacks the tyrosine cross-link and is therefore tuned to reductive catalysis. The molecular model of the KsHAOr–KsDH complex at 2.6 Å resolution shows a heterododecameric (α6β6) assembly, which was also shown to be the oligomeric state in solution by analytical ultracentrifugation and multi-angle static light scattering. The 60-heme-containing protein complex reveals a unique extended electron transfer pathway and provides deeper insights into catalysis and electron transfer in reductive OCCs.

pH-Induced Switch between Different Modes of Cytochrome c Binding to Cardiolipin-Containing Liposomes

Fluorescence, visible circular dichroism (CD), absorption, and resonance Raman spectroscopy techniques were combined to explore structural changes of ferricytochrome c upon its binding to cardiolipin-containing liposomes (20% 1,1',1,2'-tetraoleyolcardiolipin and 1,2-deoleyol-sn-glycero-3-phosphocholine) at acidic pH (6.5). According to the earlier work of Kawai [J. Biol. Chem.2005, 280, 34709-347171],cytochrome c binding at this pH is governed by interactions between the phosphate head groups of cardiolipin and amino acid side chains of the so-called L-site, which contains the charged residues K22, K25, K27, and potentially H26 and H33. We found that L-site binding causes a conformational transition that involves a change of the protein's ligation and spin state. In this paper, we report spectroscopic responses to an increasing number of cardiolipin-containing liposomes at pH 6.5 in the absence and presence of NaCl. The latter was found to mostly inhibit protein binding already with 50 mM concentration. The inhibition effect can be quantitatively reproduced by applying the electrostatic theory of Heimburg [Biophys. J.1995, 68, 536-546]. A comparison with corresponding spectroscopic response data obtained at pH 7.4 reveals major differences in that the latter indicates hydrophobic binding, followed by an electrostatically driven conformational change. Visible CD data suggest that structural changes in the heme pocket of liposome-bound ferricytochrome c resemble to some extent those in the denatured protein in urea at neutral and acidic pH. The measured noncoincidence between absorption and CD Soret band of cytochrome c in the presence of a large access of cardiolipin is caused by the electric field at the membrane surface. The very fact that its contribution to the internal electric field in the heme pocket is detectable by spectroscopic means suggests some penetration of the protein into membrane surface.

Structure and conformation of photosynthetic pigments and related compounds. 15. Conformational analysis of chlorophyll derivatives – implications for hydroporphyrinsin vivo

Controlling the function of chlorophylls depends in part on their 3D conformation. The NSD program presents a powerful tool to identify the distortion modes in phytochlorins.

Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled Sensors

In order to respond to external stimuli, bacteria have evolved sensor proteins linking external signals to intracellular outputs that can then regulate downstream pathways and phenotypes. Globin coupled sensor proteins (GCSs) serve to link environmental O₂ levels to cellular processes by coupling a heme-containing sensor globin domain to a catalytic output domain. However, the mechanism by which O₂ binding activates these proteins is currently unknown. To provide insights into the signaling mechanism, two distinct dimeric complexes of the isolated globin domain of the GCS from Bordetella pertussis ( BpeGlobin) were solved via X-ray crystallography in which differences in ligand-bound states were observed. Both monomers of one dimer contain Fe(II)-O₂ states, while the other dimer consists of the Fe(III)-H₂O and Fe(II)-O₂ states. These data provide the first molecular insights into the heme pocket conformation of the active Fe(II)-O₂ form of these enzymes. In addition, heme distortion modes and heme-protein interactions were found to correlate with the ligation state of the globin, suggesting that these conformational changes play a role in O₂-dependent signaling. Fourier transform infrared spectroscopy (FTIR) of the full-length GCS from B. pertussis ( BpeGReg) and the closely related GCS from Pectobacterium carotovorum ssp. carotovorum ( PccGCS) confirmed the importance of an ordered water within the heme pocket and two distal residues (Tyr43 and Ser68) as hydrogen-bond donors. Taken together, this work provides mechanistic insights into BpeGReg O₂ sensing and the signaling mechanisms of diguanylate cyclase-containing GCS proteins.

Influence of heme c attachment on heme conformation and potential

Heme c is characterized by its covalent attachment to a polypeptide. The attachment is typically to a CXXCH motif in which the two Cys form thioether bonds with the heme, "X" can be any amino acid other than Cys, and the His serves as a heme axial ligand. Some cytochromes c, however, contain heme attachment motifs with three or four intervening residues in a CX₃CH or CX₄CH motif. Here, the impacts of these variations in the heme attachment motif on heme ruffling and electronic structure are investigated by spectroscopically characterizing CX₃CH and CX₄CH variants of Hydrogenobacter thermophilus cytochrome c₅₅₂. In addition, a novel CXCH variant is studied. ¹H and ¹³C NMR, EPR, and resonance Raman spectra of the protein variants are analyzed to deduce the extent of ruffling using previously reported relationships between these spectral data and heme ruffling. In addition, the reduction potentials of these protein variants are measured using protein film voltammetry. The CXCH and CX₄CH variants are found to have enhanced heme ruffling and lower reduction potentials. Implications of these results for the use of these noncanonical motifs in nature, and for the engineering of novel heme peptide structures, are discussed.

Lysine as a heme iron ligand: A property common to three truncated hemoglobins from Chlamydomonas reinhardtii

BACKGROUND

The nuclear genome of Chlamydomonas reinhardtii encodes a dozen hemoglobins of the truncated lineage. Four of these, named THB1-4, contain a single ~130-residue globin unit. THB1, which is cytoplasmic and capable of nitric oxide dioxygenation activity, uses a histidine and a lysine as axial ligands to the heme iron. In the present report, we compared THB2, THB3, and THB4 to THB1 to gain structural and functional insights into algal globins.

METHODS

We inspected properties of the globin domains prepared by recombinant means through site-directed mutagenesis, electronic absorption, CD, and NMR spectroscopies, and X-ray crystallography.

RESULTS

Recombinant THB3, which lacks the proximal histidine but has a distal histidine, binds heme weakly. NMR data demonstrate that the recombinant domains of THB2 and THB4 coordinate the ferrous heme iron with the proximal histidine and a lysine from the distal helix. An X-ray structure of ferric THB4 confirms lysine coordination. THB1, THB2, and THB4 have reduction potentials between -65 and -100 mV, are capable of nitric oxide dioxygenation, are reduced at different rates by the diaphorase domain of C. reinhardtii nitrate reductase, and show different response to peroxide treatment.

CONCLUSIONS

Three single-domain C. reinhardtii hemoglobins use lysine as a distal heme ligand in both Fe(III) and Fe(II) oxidation states. This common feature is likely related to enzymatic activity in the management of reactive oxygen species.

GENERAL SIGNIFICANCE

Primary structure analysis of hemoglobins has limited power in the prediction of heme ligation. Experimental determination reveals variations in this essential property across the superfamily.

Surface Engineering of Gold Nanorods for Cytochrome c Bioconjugation: An Effective Strategy To Preserve the Protein Structure

The surface of gold nanorods (Au NRs) has been appropriately engineered to achieve a suitable interface for bioconjugation with horse heart cytochrome c (HCc). HCc, an extensively studied and well-characterized protein, represents an ideal model for nanoparticle (NP)-protein conjugation studies because of its small size, high stability, and commercial availability. Here, the native state of the protein has been demonstrated for the first time, by means of Raman spectroscopy, to be retained upon conjugation with the anisotropic Au nanostructures, thus validating the proposed protocol as specifically suited to mostly preserve the plasmonic properties of the NRs and to retain the structure of the protein. The successful creation of such bioconjugates with the retention of the protein structure and function along with the preservation of the NP properties represents a challenging but essential task, as it provides the only way to access functional hybrid systems with potential applications in biotechnology, medicine, and catalysis. In this perspective, the organic capping surrounding the Au NRs plays a key role, as it represents the functional interface for the conjugation step. Cetyltrimethylammonium bromide-coated Au NRs, prepared by using a seed-mediated synthetic route, have been wrapped with polyacrylic acid (PAA) by means of electrostatic interactions following a layer-by-layer approach. The resulting water-dispersible negatively charged AuNRs@PAA NPs have then been electrostatically bound to the positively charged HCc. The bioconjugation procedure has been thoroughly monitored by the combined analysis of UV-vis absorption, resonance Raman and Fourier transform infrared spectroscopies, transmission electron microscopy microscopy, and ζ-potential, which verified the successful conjugation of the protein to the nanorods.

The Eponymous Cofactors in Cytochrome P460s from Ammonia-Oxidizing Bacteria Are Iron Porphyrinoids Whose Macrocycles Are Dibasic

The enzymes hydroxylamine oxidoreductase and cytochrome (cyt) P460 contain related unconventional "heme P460" cofactors. These cofactors are unusual in their inclusion of nonstandard cross-links between amino acid side chains and the heme macrocycle. Mutagenesis studies performed on the Nitrosomonas europaea cyt P460 that remove its lysine-heme cross-link show that the cross-link is key to defining the spectroscopic properties and kinetic competence of the enzyme. However, exactly how this cross-link confers these features remains unclear. Here we report the 1.45 Å crystal structure of cyt P460 from Nitrosomonas sp. AL212 and conclude that the cross-link does not lead to a change in hybridization of the heme carbon participating in the cross-link but rather enforces structural distortions to the macrocycle away from planarity. Time-dependent density functional theory coupled to experimental structural and spectroscopic analysis suggest that this geometric distortion is sufficient to define the spectroscopic properties of the heme P460 cofactor and provide clues toward establishing a relationship between heme P460 electronic structure and function.

Sensing of diclofenac by a porphyrin-based artificial receptor

The synthesis of a porphyrin chemosensor is here reported as well as its sensing activity in detecting the emerging pollutant diclofenac with an overall 1 : 1 binding constant of about 10⁵ M⁻¹.

Heterocorrole Conformations: Little Saddling, Much Ruffling

10-Heterocorrole complexes with oxygen, sulfur, and selenium at position 10 of the macrocycle and with the divalent ions of nickel, copper, and palladium were prepared and investigated. The focus was set on the size adaptation and matching mechanisms of cavity size versus ionic radius in corrole-type macrocycles. A full set of single-crystal X-ray analytical data revealed that in all but one case the N₄ binding site of the ring-contracted tetrapyrrole was larger than necessary to bind the metal ion without deformation. In-plane size adaptation through M-N bond-length elongation by 2.5-3.2 % was effective, as well as pronounced out-of-plane ruffling of the macrocycle for those compounds with a more severe size mismatch. Such ruffling had been excluded for corroles previously, but is apparently the most efficient mechanism to adapt to small central ions.

Self-Assembled DNA/Peptide-Based Nanoparticle Exhibiting Synergistic Enzymatic Activity

Designing enzyme-mimicking active sites in artificial systems is key to achieving catalytic efficiencies rivaling those of natural enzymes and can provide valuable insight in the understanding of the natural evolution of enzymes. Here, we report the design of a catalytic hemin-containing nanoparticle with self-assembled guanine-rich nucleic acid/histidine-rich peptide components that mimics the active site and peroxidative activity of hemoproteins. The chemical complementarities between the folded nucleic acid and peptide enable the spatial arrangement of essential elements in the active site and effective activation of hemin. As a result, remarkable synergistic effects of nucleic acid and peptide on the catalytic performances were observed. The turnover number of peroxide reached the order of that of natural peroxidase, and the catalytic efficiency is comparable to that of myoglobin. These results have implications in the precise design of supramolecular enzyme mimetics, particularly those with hierarchical active sites. The assemblies we describe here may also resemble an intermediate in the evolution of contemporary enzymes from the catalytic RNA of primitive cells.