Exploring the Association of Electron-Donating Corroles with Phthalocyanines as Electron Acceptors.

Electron-donating corroles (Cor) were integrated with electron-accepting phthalocyanines (Pc) to afford two different non-covalent Cor ⋅ Pc systems. At the forefront was the coordination between a 10-meso-pyridine Cor and a ZnPc. The complexation was corroborated in a combination of NMR, absorption, and fluorescence assays, and revealed association with binding constants as high as 106  m-1 . Steady-state and time-resolved spectroscopies evidenced that regardless of exciting Cor or Pc, the charge-separated state evolved efficiently in both cases, followed by a slow charge-recombination to reinstate the ground state. The introduction of non-covalent linkages between Cor and Pc induces sizeable differences in the context of light harvesting and transfer of charges when compared with covalently linked Cor-Pc conjugates.

A Leopard Cannot Change Its Spots: Unexpected Products from the Vilsmeier Reaction on 5,10,15-Tritolylcorrole.

The reaction of 5,10,15-tritolylcorrole with 3-dimethylaminoacrolein (3-DMA) and POCl3 gives a further example of the rebel reactivity of this contracted macrocycle. While no evidence was obtained for the formation of the expected ß-acrolein corrole, the inner core substituted N21,N22-3-formylpropylcorrole and the 10-acrolein isocorrole were the reaction products. By increasing the temperature or the amount of the Vilsmeier reagent, the 10-isocorrole became the unique reaction product. The formation of the isocorrole by electrophilic attack of the Vilsmeier reagent to the 10-position of the corrole is unprecedented in the porphyrinoids field and it could pave the way for a novel route to the preparation of stable isocorroles.

A novel method using nuclear magnetic resonance for plasma protein binding assessment in drug discovery programs.

A new methodology based on Nuclear Magnetic Resonance (NMR) was developed to determine plasma protein binding (PPB) of drug candidates in drug discovery programs. A strong correlation was found between the attenuation of NMR signals of diverse drugs in the presence of different plasma concentrations and their fraction bound (fb) reported in the literature. Based on these results, a protocol for a rapid calculation of fb of small molecules was established. The advantage of using plasma instead of purified recombinant proteins and the possibility of pool analysis to increase throughput were also evaluated. This novel methodology proved to be very versatile, cost-effective, fast and suitable for automation. As a plus, it contemporarily provides a quality check and solubility of the compound.

A Highly Emissive Water-Soluble Phosphorus Corrole.

The synthesis, spectroscopic, and optical properties of the water-soluble phosphorus complex of a 2-sulfonato-10-(4-sulfonatophenyl)-5,15-dimesitylcorrole have been investigated. The compound was prepared by adopting a novel strategy for the corrole sulfonation, leading to the regioselective isomer in an almost quantitative yield. The phosphorus coordination has a key role in determining the corrole substitution pattern, limiting the formation of poly-substituted species, which affected the reaction of the corrole free base. The resulting complex shows excellent optical properties in terms of emission quantum yield, also in polar protic solvents, including water. 31 P NMR spectroscopy in CD3 OD indicates that the P sulfonate complex has been isolated in a hexacoordinated geometry with two different ligands (L1=-OH, L2=-OCH3 ), and it is prone to axial ligand exchange with methanol, with no evidence of intermediate pentacoordinated species. The morphological characterization of thin layers of the P corrole deposited onto an Au(111) surface showed that the addition of an intermediate layer of reduced graphene oxide allows for a better control of corrole aggregation, inducing also transformation of the Au(111) reconstructed surface.

Structural and functional characterization of a cold-adapted stand-alone TPM domain reveals a relationship between dynamics and phosphatase activity.

The TPM domain constitutes a family of recently characterized protein domains that are present in most living organisms. Although some progress has been made in understanding the cellular role of TPM-containing proteins, the relationship between structure and function is not clear yet. We have recently solved the solution and crystal structure of one TPM domain (BA42) from the Antarctic bacterium Bizionia argentinensis. In this work, we demonstrate that BA42 has phosphoric-monoester hydrolase activity. The activity of BA42 is strictly dependent on the binding of divalent metals and retains nearly 70% of the maximum at 4 °C, a typical characteristic of cold-adapted enzymes. From HSQC, 15 N relaxation measurements, and molecular dynamics studies, we determine that the flexibility of the crossing loops was associated to the protein activity. Thermal unfolding experiments showed that the local increment in flexibility of Mg2+ -bound BA42, when compared with Ca2+ -bound BA42, is associated to a decrease in global protein stability. Finally, through mutagenesis experiments, we unambiguously demonstrate that the region comprising the metal-binding site participates in the catalytic mechanism. The results shown here contribute to the understanding of the relationship between structure and function of this new family of TPM domains providing important cues on the regulatory role of Mg2+ and Ca2+ and the molecular mechanism underlying enzyme activity at low temperatures.

5,10,15-Triferrocenylcorrole Complexes.

Complexes of 5,10,15-triferrocenylcorrole were synthesized from the crude free-base corrole product obtained by the reaction of ferrocenyl aldehyde and pyrrole. Direct formation of the complex in this manner leads to an increase of the reaction yield by protecting the corrole ring toward oxidative decomposition. The procedure was successful and gave the expected product in the case of the copper and triphenylphosphinecobalt complexes, but an unexpected result was obtained in the case of the nickel derivative, where metal insertion led to a ring opening of the macrocycle at the 5 position, giving as a final product a linear tetrapyrrole nickel complex bearing two ferrocenyl groups. The purified 5,10,15-triferrocenylcorrole complexes have been fully characterized by a combination of spectroscopic methods, electrochemistry, spectroelectrochemistry, and density functional theory calculations. Copper derivatives of 10-monoferrocenyl- and 5,15-diferrocenylcorrole were prepared to investigate how the number and position of the ferrocenyl groups influenced the spectroscopic and electrochemical properties of the resulting complexes. A complete assignment of resonances in the (1)H and (13)C NMR spectra was performed for the cobalt and nickel complexes, and detailed electrochemical characterization was carried out to provide additional insight into the degree of communication between the meso-ferrocenyl groups on the conjugated macrocycle and the central metal ion of the ferrocenylcorrole derivatives.

Solution and crystal structure of BA42, a protein from the Antarctic bacterium Bizionia argentinensis comprised of a stand-alone TPM domain.

The structure of the BA42 protein belonging to the Antarctic flavobacterium Bizionia argentinensis was determined by nuclear magnetic resonance and X-ray crystallography. This is the first structure of a member of the PF04536 family comprised of a stand-alone TPM domain. The structure reveals a new topological variant of the four ß-strands constituting the central ß-sheet of the αßα architecture and a double metal binding site stabilizing a pair of crossing loops, not observed in previous structures of proteins belonging to this family. BA42 shows differences in structure and dynamics in the presence or absence of bound metals. The affinity for divalent metal ions is close to that observed in proteins that modulate their activity as a function of metal concentration, anticipating a possible role for BA42.

New example of hemiporphycene formation from the corrole ring expansion.

The reaction of 5,10,15-tris(4-tert-butylphenyl)corrole with 2,3-bis(bromomethyl)-5,6-dicyanopyrazine provides a new example of corrole ring expansion to a hemiporphycene derivative. The ring expansion is regioselective, with insertion of the pyrazine derivative at the 5-position of the corrole ring, affording the corresponding 5-hemiporphycene. Different macrocyclic products accompany formation of the 5-hemiporphycene, depending on the reaction experimental conditions. Br-substitued 5-hemiporphycenes and the 2-Br substituted corrole were obtained in 1,2,4-trichlorobenzene, while in refluxing toluene traces of an inner core substituted corrole were observed together with a significant amount of the unreacted corrole. These results provide an important indication of the reaction pathway. The coordination behavior of the 5-hemiporphycene, together with detailed electrochemical characterization of the free-base and some metal complexes, provides evidence for the reactivity of the peripheral pyrazino group.

Phenyl derivative of iron 5,10,15-tritolylcorrole.

The phenyl-iron complex of 5,10,15-tritolylcorrole was prepared by reaction of the starting chloro-iron complex with phenylmagnesium bromide in dichloromethane. The organometallic complex was fully characterized by a combination of spectroscopic methods, X-ray crystallography, and density functional theory (DFT) calculations. All of these techniques support the description of the electronic structure of this phenyl-iron derivative as a low-spin iron(IV) coordinated to a closed-shell corrolate trianion and to a phenyl monoanion. Complete assignments of the (1)H and (13)C NMR spectra of the phenyl-iron derivative and the starting chloro-iron complex were performed on the basis of the NMR spectra of the regioselectively ß-substituted bromo derivatives and the DFT calculations.

The corrole and ferrocene marriage: 5,10,15-triferrocenylcorrolato Cu.

Two synthetic routes have been defined for the preparation of a 5,10,15-triferrocenylcorrole Cu derivative. This complex has been characterized and the preliminary electrochemical investigation shows a strong interaction among the corrole and meso ferrocenyl substituents. The results obtained suggest that peculiar properties are gained by combining the eccentric characteristics of ferrocenyl substitution with the corrole macrocycle.

¹H, ¹5N, and ¹³C chemical shift assignments of the C-Ala domain of the alanyl-tRNA synthetase of the psychrophilic bacterium Bizionia argentinensis sp. nov.

A gene encoding a protein classified as alanyl-tRNA synthetase (AlaRS) was found in the genome of the psychrophilic bacteria Bizionia argentinensis. The enzyme is constituted by three domains with an evolutionarily conserved modular arrangement: the N-terminal aminoacylation domain, the editing domain and the C-terminal domain (C-Ala). Herein we report the near complete NMR resonance assignment of the 122 amino acid C-Ala domain from B. argentinensis. The chemical shift data, reported for the first time for a C-Ala domain, constitute the basis for NMR structural studies aimed at elucidating the cold-adaptation mechanism of AlaRS.

Synthesis and characterization of functionalized meso-triaryltetrabenzocorroles.

5,10,15-Triaryltetrabenzocorroles functionalized with different electron-withdrawing groups on the ß,ß'-fused rings have been prepared by a cross-coupling Heck procedure between octabrominated copper corrole and a terminal alkene bearing electron-withdrawing moieties. The spectroscopic characterization of these complexes showed red-shifted UV-vis absorption bands characterized by a significant band broadening. The same feature was observed in the case of NMR spectra, where low-resolution groups of signals were observed. This behavior derives from a strong tendency of these macrocycles to aggregate in solution, as has been demonstrated by an (1)H NMR study performed on one of these tetrabenzocorroles. The influence of the substituents on the fused benzene ring on the properties of the tetrabenzocorroles was investigated by electrochemistry and spectroelectrochemistry, and comparisons were made between properties of the newly synthesized compounds and those of the tetrabenzocorroles reported earlier in the literature.

The ß-scaffold of the LOV domain of the Brucella light-activated histidine kinase is a key element for signal transduction.

Light-oxygen-voltage (LOV) domains are blue-light-activated signaling modules present in a wide range of sensory proteins. Among them, the histidine kinases are the largest group in prokaryotes (LOV-HK). Light modulates the virulence of the pathogenic bacteria Brucella abortus through LOV-HK. One of the striking characteristic of Brucella LOV-HK is the fact that the protein remains activated upon light sensing, without recovering the basal state in the darkness. In contrast, the light state of the isolated LOV domain slowly returns to the dark state. To gain insight into the light activation mechanism, we have characterized by X-ray crystallography and solution NMR spectroscopy the structure of the LOV domain of LOV-HK in the dark state and explored its light-induced conformational changes. The LOV domain adopts the α/ß PAS (PER-ARNT-SIM) domain fold and binds the FMN cofactor within a conserved pocket. The domain dimerizes through the hydrophobic ß-scaffold in an antiparallel way. Our results point to the ß-scaffold as a key element in the light activation, validating a conserved structural basis for light-to-signal propagation in LOV proteins.

1H, 15N and 13C chemical shift assignments of the BA42 protein of the psychrophilic bacteria Bizionia argentinensis sp. nov.

BA42 is a protein belonging to the psychrophilic bacteria Bizionia argentinensis sp. nov. Bioinformatics analysis showed that it presents significant sequence identity with a Pfam A family, DUF 477, found both in eukarya and eubacteria but of unknown function in all these organisms. Here, we report the NMR spectra assignment of this 145 amino acid protein. These data will allow performing NMR structural studies with the aim of using the three-dimensional structure as relevant information in order to determine the function of this family of proteins.

Draft genome sequence of Bizionia argentinensis, isolated from Antarctic surface water.

A psychrotolerant marine bacterial strain, designated JUB59(T), was isolated from Antarctic surface seawater and classified as a new species of the genus Bizionia. Here, we present the first draft genome sequence for this genus, which suggests interesting features such as UV resistance, hydrolytic exoenzymes, and nitrogen metabolism.

The structure of the elicitor Cerato-platanin (CP), the first member of the CP fungal protein family, reveals a double ψß-barrel fold and carbohydrate binding.

Cerato-platanin (CP) is a secretion protein produced by the fungal pathogen Ceratocystis platani, the causal agent of the plane canker disease and the first member of the CP family. CP is considered a pathogen-associated molecular pattern because it induces various defense responses in the host, including production of phytoalexins and cell death. Although much is known about the properties of CP and related proteins as elicitors of plant defense mechanisms, its biochemical activity and host target(s) remain elusive. Here, we present the three-dimensional structure of CP. The protein, which exhibits a remarkable pH and thermal stability, has a double ψß-barrel fold quite similar to those found in expansins, endoglucanases, and the plant defense protein barwin. Interestingly, although CP lacks lytic activity against a variety of carbohydrates, it binds oligosaccharides. We identified the CP region responsible for binding as a shallow surface located at one side of the ß-barrel. Chemical shift perturbation of the protein amide protons, induced by oligo-N-acetylglucosamines of various size, showed that all the residues involved in oligosaccharide binding are conserved among the members of the CP family. Overall, the results suggest that CP might be involved in polysaccharide recognition and that the double ψß-barrel fold is widespread in distantly related organisms, where it is often involved in host-microbe interactions.

Structural characterization of the Hepatitis C Virus NS3 protease from genotype 3a: the basis of the genotype 1b vs. 3a inhibitor potency shift.

The first structural characterization of the genotype 3a Hepatitis C Virus NS3 protease is reported, providing insight into the differential susceptibility of 1b and 3a proteases to certain inhibitors. Interaction of the 3a NS3 protease with a P2-P4 macrocyclic and a linear phenethylamide inhibitor was investigated. In addition, the effect of the NS4A cofactor binding on the conformation of the protease was analyzed. Complexation of NS3 with the phenethylamide inhibitor significantly stabilizes the protease but binding does not involve residues 168 and 123, two key amino acids underlying the different inhibition of genotype 1b vs. 3a proteases by P2-P4 macrocycles. Therefore, we studied the dynamic behavior of these two residues in the phenethylamide complex, serving as a model of the situation in the apo 3a protein, in order to explore the structural basis of the inhibition potency shift between the proteases of the genotypes 1b and 3a.

A new member of the ribbon-helix-helix transcription factor superfamily from the plant pathogen Xanthomonas axonopodis pv.citri.

XACb0070 is an uncharacterized protein coded by the two large plasmids isolated from Xanthomonas axonopodis pv. citri, the agent of citrus canker and responsible for important economical losses in citrus world production. XACb0070 presents sequence homology only with other hypothetical proteins belonging to plant pathogens, none of which have their structure determined. The NMR-derived solution structure reveals this protein is a homodimer in which each monomer presents two domains with different structural and dynamic properties: a folded N-terminal domain with beta alpha alpha topology which mediates dimerization and a long disordered C-terminal tail. The folded domain shows high structural similarity to the ribbon-helix-helix transcriptional repressors, a family of DNA-binding proteins of conserved 3D fold but low sequence homology: indeed XACb0070 binds DNA. Primary sequence and fold comparison of XACb0070 with other proteins of the ribbon-helix-helix family together with examination of the genes in the vicinity of xacb0070 suggest the protein might be the component of a toxin-antitoxin system.

Indirect DNA readout on the protein side: coupling between histidine protonation, global structural cooperativity, dynamics, and DNA binding of the human papillomavirus type 16 E2C domain.

DNA sequence recognition by the homodimeric C-terminal domain of the human papillomavirus type 16 E2 protein (E2C) is known to involve both direct readout and DNA-dependent indirect readout mechanisms, while protein-dependent indirect readout has been deduced but not directly observed. We have investigated coupling between specific DNA binding and the dynamics of the unusual E2C fold, using pH as an external variable. Nuclear magnetic resonance and isothermal titration calorimetry show that pH titration of His318 in the complex interface and His288 in the core of the domain is coupled to both binding and the dynamics of the beta-barrel core of E2C, with a tradeoff between dimer stability and function. Specific DNA binding is, in turn, coupled to the slow dynamics and amide hydrogen exchange in the entire beta-barrel, reaching residues far apart from the DNA recognition elements but not affecting the two helices of each monomer. The changes are largest in the dimerization interface, suggesting that the E2C beta-barrel acts as a hinge that regulates the relative position of the DNA recognition helices. In conclusion, the cooperative dynamics of the human papillomavirus type 16 E2C beta-barrel is coupled to sequence recognition in a protein-dependent indirect readout mechanism. The patterns of residue substitution in genital papillomaviruses support the importance of the protonation states of His288 and His318 and suggest that protein-dependent indirect readout and histidine pH titration may regulate DNA binding in the cell.

ATP acts as a regulatory effector in modulating structural transitions of cytochrome c: implications for apoptotic activity.

The binding of lipids (free fatty acids as well as acidic phospholipids) to cytochrome c (cyt c) induces conformational changes and partial unfolding of the protein, strongly influencing cyt c oxidase/peroxidase activity. ATP is unique among the nucleotides in being able to turn non-native states of cyt c back to the native conformation. The peroxidase activity acquired by lipid-bound cyt c turns out to be very critical in the early stages of apoptosis. Nucleotide specificity is observed for apoptosome formation and caspase activation, the cleavage occurring only in the presence of dATP or ATP. In this study, we demonstrate the connection between peroxidase activity and oleic acid-induced conformational transitions of cyt c and show how ATP is capable of modulating such interplay. By NMR measurement, we have demonstrated that ATP interacts with a site (S1) formed by K88, R91, and E62 and such interaction was weakened by mutation of E62, suggesting the selective role in the interaction played by the base moiety. Interestingly, the interactions of ATP and GTP with cyt c are significantly different at low nucleotide concentrations, with GTP being less effective in perturbing the S1 site and in eliciting apoptotic activity. To gain insights into the structural features of cyt c required for its pro-apoptotic activity and to demonstrate a regulatory role for ATP (compared to the effect of GTP), we have performed experiments on cell lysates by using cyt c proteins mutated on amino acid residues that, as suggested by NMR measurements, belong to S1. Thus, we provide evidence that ATP acts as an allosteric effector, regulating structural transitions among different conformations and different oxidation states of cyt c, which are endowed with apoptotic activity or not. On this basis, we suggest a previously unrecognized role for ATP binding to cyt c at low millimolar concentrations in the cytosol, beyond the known regulatory role during the oxidative phosphorylation in mitochondria.