Synthesis of asymmetric tetraarylporphyrins and their ytterbium complexes

The synthesis of asymmetric meso-aryl-substituted porphyrins containing three 4-methoxycarbo-nylphenyl groups, and 4-hydroxyphenyl or 4-hydroxy-3-methoxyphenyl radicals or isomeric 3-and 4-pyridyl radicals as a forth substitute, is described. 4-Oxyalkyl derivatives are obtained. The ytterbium complexes of these porphyrins have been synthesized, and their spectral luminescence properties have been studied. A significant difference in the lifetimes of the excited state of ytterbium complexes of the esters and acids of asymmetric porphyrins has been shown.     

Synthesis of asymmetric tetraarylporphyrins and its ytterbium complexes

The synthesis of asymmetric meso-aryl-substituted porphyrins containing three 4-methoxycarbonylphenyl groups, and as a forth substituent 4-hydroxyphenyl or 4-hydroxy-3- methoxyphenyl radicals, or the isomeric 3- and 4-pyridyl substituents is described. O-alkyl derivatives of 4-hydroxyl residue are obtained. The ytterbium complexes ofthese porphyrins were synthesized and studied their luminescence spectral properties were studied. A significant difference in the lifetimes of the excited state ofytterbium complexes of esters and acids of asymmetric porphyrins is demonstrated.     

Spectroscopic and electrochemical studies of novel model compounds for cytochrome c oxidase

Different metalated porphyrin compounds were studied as model complexes for cytochrome c oxidase. All models contain a tyrosine molecule and a copper binding site. Two of the compounds are bearing an axial pyridine ligand that could possibly coordinate with Fe porphyrins. All complexes were studied using NMR and UV-Vis spectroscopies and it was found that the coordination of the axial ligand is possible only in one of the porphyrins. Moreover, the synthesized catalysts were studied as promising enzyme mimics using a rotating disc electrode in the presence of molecular oxygen.     

Guest-dependent conformation of 18-crown-6 tetracarboxylic acid: relation to chiral separation of racemic amino acids

(+)-18-crown-6 tetracarboxylic acid (18C6H(4)) has been used as a chiral selector for various amines and amino acids. To further clarify the structural scaffold of 18C6H(4) for chiral separation, single crystal X-ray analysis of its glycine(+) (1), H3O+ (2), H5O2+ (3), NH4+ (4), and 2CH3NH3+ (5) complexes was performed and the guest-dependent conformation of 18C6H(4) was investigated. The crown ether ring of 18C6H4 in 3, 4, and 5 took a symmetrical C2 or C2-like conformation, whereas that in 1 and 2 took an asymmetric C1 conformation, which is commonly observed in complexes with various optically active amino acids. The overall survey of the present and related complexes suggests that the molecular conformation of 18C6H4 is freely changeable within an allowable range, depending on the molecular shape and interaction mode with the cationic guest. On the basis of the present results, we propose the allowable conformational variation of 18C6H4 and a possible transition pathway from its primary conformation to the conformation suitable for chiral separation of racemic amines and amino acids.     

Solution-phase secondary-ion mass spectrometry of protonated amino acids

Although sulfolane proved unexpectedly to be a poor solvent for solution-phase secondary-ion mass spectrometry of underivatized amino acids in the presence of thallium(I) salts, glycerol was somewhat more effective. Also, the addition of trifluoromethanesulfonic acid proved more effective than addition of the metal in generating molecular ion complexes. A convenient and reliable method for rapidly determining amino acid molecular ions is based on these observations.     

The negatively charged amino acids in the lumenal loop influence the pigment binding and conformation of the major light-harvesting chlorophyll a/b complex of photosystem II

The major chlorophyll (Chl) a/b complexes of photosystem II (LHCIIb), in addition to their primary light-harvesting function, play key roles in the organization of the granal ultrastructure of the thylakoid membranes and in various regulatory processes. These functions depend on the structural stability and flexibility of the complexes. The lumenal side of LHCIIb is exposed to broadly variable pH environments, due to the build-up and decay of the pH gradient during photosynthesis. Therefore, the negatively charged amino acids in the lumenal loop might be of paramount importance for adjusting the structure and functions of LHCIIb. In order to clarify the structural roles of these residues, we investigated the pigment stoichiometries, absorption, linear and circular dichroism spectra of the reconstituted LHCIIb complexes, in which the negatively charged amino acids in the lumenal loop were exchanged to neutral ones (E94G, E107V and D111V). The mutations influenced the pigment binding and the molecular architecture of the complexes. Exchanging E94 to G destabilized the 3(10) helix in the lumenal loop structure and led to an acquired pH sensitivity of the LHCIIb structure. We conclude that these amino acids are important not only for pigment binding in the complexes, but also in stabilizing the conformation of LHCIIb at different pHs.     

Synthesis of prebiotic molecules — Role of some carbonyl compounds in prebiotic chemistry

Methyleneaminoacetonitrile(MAAN) resulting from the interaction of formaldehyde, ammonia and hydrogen cyanide on hydrolysis under mildly alkaline conditions gives a number of amino acids and peptides. Various aldehydes react with glycine to give corresponding hydroxyalkyl amino acids, which on reduction with formic acid are converted to reduced amino acids. Formaldehyde reacts with uracil to give 5-hydroxymethyl uracil which on reduction with formic acid yields thymine. Pyrrole formed by heating serine reacts with aldehydes to form porphyrins. Clays do not seem to influence most of these reactions, except the uracil-formaldehyde — formic acid reaction which results in enhanced yield of thymine.     

New data on abiogenic synthesis of prebiological compounds in volcanic processes

Volcanoes were deduced to be high-productive generators of complex organic compounds. Ash-gas clouds produced by volcanic eruptions can be considered as many-kilometer chemical reactors with a wide range of temperatures and pressures, powerful electric discharges and a large catalytic surface. In the eruption products investigated, nitrogen-containing components of nucleic acids of uracil type, metal complexes of porphyrins and porphyrins in the metal-free form and polycyclic aromatic hydrocarbons have been found. In all, 54 carbon-containing compounds have been identified in the volcanic juvenile ash and in volcanic bombs and 13 groups of carbon-containing compounds whose composition is yet unidentified have been found.     

Molecular design of functional peptides by utilizing unnatural amino acids: toward artificial and photofunctional protein

Unnatural amino acids are effective as building blocks to design functional peptides from the following two points: (1) utilization of rigid unnatural amino acids for the incorporated peptides to control the conformation to appear the function, and (2) incorporation of functional and unnatural amino acids into peptides resulting in appearance of the inherent functions. As a combined strategy, molecular design of artificial metalloproteins utilizing 5'-amino-2,2'-bipyridine-5-carboxilic acid (H-5Bpy-OH) as an unnatural amino acid is proposed. The peptide containing three residues of the unnatural amino acid would fold through coordination to a metal ion. In particular, ruthenium(II) ion would yield a ruthenium tris(bipyridine) derivative as the core complex of the artificial protein, which would appear the similar photochemical functions as that of ruthenium(II) tris(bipyridine) complex. The central complex could form two isomers, fac and mer. For selective synthesis of the mer complex, which is expected as the core complex in the artificial protein, dicyclohexylamide as a bulky group is introduced at the C-terminal of the unnatural amino acid to destabilize the fac complex due to steric hindrance. Furthermore, in order to know the photochemical properties and function of the protein mimics, ruthenium(II) tris(2,2'-bipyridine) complexes bearing amide groups at 5,5' positions have been synthesized as the model complexes. As a result, the direction of amide groups (RNHCO-or RCONH-) in ruthenium complexes is found to significantly affect the emission efficiency: the former reduces the quantum yield and the latter enhances it, respectively. The ruthenium(II) tris(5,5'-diamide-2,2'-bipyridine) complexes are also found to strongly bind with various anions [e.g., halogen ions (Cl-, Br-) and acetate anion] in acetonitrile and to detect these anions through the emission spectral changes under air. The molecular design of artificial protein is expected to develop new fields among peptide, organic, inorganic, and physical chemistry.     

The negatively charged amino acids in the lumenal loop influence the pigment binding and conformation of the major light-harvesting chlorophyll a/b complex of photosystem II

The major chlorophyll (Chl) a/b complexes of photosystem II (LHCIIb), in addition to their primary light-harvesting function, play key roles in the organization of the granal ultrastructure of the thylakoid membranes and in various regulatory processes. These functions depend on the structural stability and flexibility of the complexes. The lumenal side of LHCIIb is exposed to broadly variable pH environments, due to the build-up and decay of the pH gradient during photosynthesis. Therefore, the negatively charged amino acids in the lumenal loop might be of paramount importance for adjusting the structure and functions of LHCIIb. In order to clarify the structural roles of these residues, we investigated the pigment stoichiometries, absorption, linear and circular dichroism spectra of the reconstituted LHCIIb complexes, in which the negatively charged amino acids in the lumenal loop were exchanged to neutral ones (E94G, E107V and D111V). The mutations influenced the pigment binding and the molecular architecture of the complexes. Exchanging E94 to G destabilized the 3₁₀ helix in the lumenal loop structure and led to an acquired pH sensitivity of the LHCIIb structure. We conclude that these amino acids are important not only for pigment binding in the complexes, but also in stabilizing the conformation of LHCIIb at different pHs.     

Photoelectron spectra of complexes of Na and La with N-acetylalanine and N-acetylvaline

X-ray photoelectron spectra of the bioinorganic complexes of Na and La with N-acetylalanine and N-acetylvaline have been measured. It has been found that the spectra of the O 1s core level in the complexes of Na with these amino acids are very different from those in the complexes of La with the same amino acids. The results indicate that in the complexes of La with N-acetylalanine and N-acetylvaline, both the oxygen atoms from the carboxyl group and the oxygen atoms from the carbonyl group of the amino acids will directly coordinate to the La ion, whereas only the oxygen atoms from the carboxyl group of the amino acids can directly coordinate to the Na ion in the complexes of Na with N-acetylalanine and N-acetylvaline.     

Photodynamic and light independent action of 8 to 2 carboxylic free porphyrins on some haem-enzymes

Backgrounds and aims: skin lesions in cutaneous porphyrias appear to be determined by the structural properties of the porphyrins accumulated. To better understand the relationship between the structure and physicochemical properties of porphyrins and their specific effect on protein configuration, the action of a whole range of 8 to 2 carboxylic porphyrins has been studied. Materials and methods: δ-aminolevulinic acid dehydratase (ALA-D) and porphobilinogen deaminase (PBG-D) partially purified from bovine liver, were exposed to 10 μM uroporphyrin (Uro), phyriaporphyrin (Phyria), hexaporphyrin (Hexa), pentaporphyrin (Penta), coproporphyrin (Copro) or protoporphyrin (Proto), either in the dark or under UV light. All experiments were performed in the enzyme solutions after removing the porphyrins. Results: under both illuminating conditions, all porphyrins inactivated the enzymes (20–70% under control values), indicating photodynamic action mediated by oxidative reactions and conformational changes due to direct binding of porphyrins to the protein. Total thiol content in ALA-D was not significantly changed by most porphyrins under UV light, while all porphyrins increase total sulfhydryl groups in PBG-D (23–52% over the control values) indicating changes in the redox status of SH residues. Free amino groups were reduced by all porphyrins in ALA-D (23–56% under controls), instead they were enhanced in PBG-D (23–51% over controls), suggesting protein fragmentation. The formation of molecular aggregates would be the consequence of cross-links between oxidation products, while fragmentation can be attributed to either rupture of disulphur bridges and/or enhancement of free amino groups on the protein enzyme. Conclusions: the effect of the porphyrins on enzyme activity, total SH groups and free amino groups content, was different for ALA-D and PBG-D, even under the same illuminating conditions. On the basis of these results, no correlation between enzyme alterations and the physico-chemical properties of porphyrins could be established.     

Ternary complexes of palladium (II) with levamisole and L-amino acids

The complexes of general formula [(LMS)2Pd(amino acid)]Cl with LMS = levamisole, and amino acid = L-alanine, L-phenylglycine, L-phenylalanine, L-valine, L-methionine, and L-proline, were synthesized by the interaction of [(LMS)2PdCl2] with the sodium salts of L-amino acids. The newly synthesized complexes are characterized by elemental analysis, conductivity, magnetic susceptibility, optical rotation measurements, and UV-Vis, IR and 13C NMR spectral data. Levamisole is coordinated to palladium via the N-7 nitrogen and the amino acids through the amino nitrogen and carboxylate oxygen, except for L-methionine which binds the metal via nitrogen and sulfur atoms. Optically active [(LMS)2Pd(amino acid)]Cl complexes are obtained when L-amino acids or D,L-amino acids are used for the synthesis of these complexes. L-Methionine and L-proline complexes induce new cell forms in Baker's yeast (Saccharomyces cerevisiae) cells.     

C-terminal residues of plant glutamate decarboxylase are required for oligomerization of a high-molecular weight complex and for activation by calcium/calmodulin

Bacterial glutamate decarboxylase (GAD) is a homohexameric enzyme of about 330 kDa. Plant GAD differs from the bacterial enzyme in having a C-terminal extension of 33 amino acids within which resides a calmodulin (CaM)-binding domain. In order to assess the role of the C-terminal extension in the formation of GAD complexes and in activation by Ca2+/CaM, we examined complexes formed with the purified full-length recombinant petunia GAD expressed in E. coli, and with a 9 amino acid C-terminal deletion mutant (GADDeltaC9). Size exclusion chromatography revealed that the full-length GAD formed complexes of about 580 kDa and 300 kDa in the absence of Ca2+/CaM, whereas in the presence of Ca2+/CaM all complexes shifted to approximately 680 kDa. With deletion of 9 amino acids from the C-terminus (KKKKTNRVC(500)), the ability to bind CaM in the presence of Ca2+, and to purify it by CaM-affinity chromatography was retained, but the formation of GAD complexes larger than 340 kDa and enzyme activation by Ca2+/CaM were completely abolished. Hence, responsiveness to Ca2+/CaM is associated with the formation of protein complexes of 680 kDa, and requires some or all of the nine C-terminal amino acid residues. We suggest that evolution of plant GAD from a bacterial ancestral enzyme involved the formation of higher molecular weight complexes required for activation by Ca2+/CaM.     

The porphyrin-sensitized photooxidation of horseradish apoperoxidase.

Horseradish apoperoxidase (apoHRP) was reconstituted with various porphyrin derivatives, e.g., ferric, cupric, manganese, and zinc protoporphyrin IX, metal-free protoporphyrin IX, hematoporphyrin IX and deuteroporphyrin IX. The visible absorption spectra of these porphyrin-apoHRP complexes were examined. The time required for maximum development of the new Soret peak after reconstitution was used to measure the rate of porphyrin-apoHRP reconstitution. All of the four metal-protoporphyrins reconstituted with apoHRP at the same rate as metal-free protoporphyrin IX, whereas, for the metal-free porphyrins, the rates of reconstitution were in the order of deuteroporphyrin IX > hematoporphyrin IX > protoporphyrin IX. The porphyrins on the reconstituted porphyrin-apoHRP complexes were used as localized photosensitizers for photodynamic studies. No amino acid residues were oxidized on illumination of the ferric, cupric and manganese protoporphyrin IX-apoHRP complexes due to the paramagnetic properties of these metal ions. With diamagnetic zinc ion, two histidine and one methionine residues were oxidized which was the same as in the protoporphyrin IX- and hematoporphyrin IX-apoHRP complexes. However, only one histidine was destroyed on illumination of the deuteroporphyrin IX-apoHRP complex. The results confirmed the resistance of horseradish peroxidase to photodynamic action and suggested the involvement of at least one histidine residue in the heme environment of horseradish peroxidase.     

Molecular Basis for Bcl-2 Homology 3 Domain Recognition in the Bcl-2 Protein Family: IDENTIFICATION OF CONSERVED HOT SPOT INTERACTIONS*

The proteins of the Bcl-2 family are important regulators of apoptosis, or programmed cell death. These proteins regulate this fundamental biological process via the formation of heterodimers involving both pro- and anti-apoptotic family members. Disruption of the balance between anti- and pro-apoptotic Bcl-2 proteins is the cause of numerous pathologies. Bcl-xl, an anti-apoptotic protein of this family, is known to form heterodimers with multiple pro-apoptotic proteins, such as Bad, Bim, Bak, and Bid. To elucidate the molecular basis of this recognition process, we used molecular dynamics simulations coupled with the Molecular Mechanics/Poisson-Boltzmann Surface Area approach to identify the amino acids that make significant energetic contributions to the binding free energy of four complexes formed between Bcl-xl and pro-apoptotic Bcl-2 homology 3 peptides. A fifth protein-peptide complex composed of another anti-apoptotic protein, Bcl-w, in complex with the peptide from Bim was also studied. The results identified amino acids of both the anti-apoptotic proteins as well as the Bcl-2 homology 3 (BH3) domains of the pro-apoptotic proteins that make strong, recurrent interactions in the protein complexes. The calculations show that the two anti-apoptotic proteins, Bcl-xl and Bcl-w, share a similar recognition mechanism. Our results provide insight into the molecular basis for the promiscuous nature of this molecular recognition process by members of the Bcl-2 protein family. These amino acids could be targeted in the design of new mimetics that serve as scaffolds for new antitumoral molecules.     

Role of transition metal ferrocyanides (II) in chemical evolution

Due to ease of formation of cyanide under prebiotic conditions, cyanide ion might have formed stable complexes with transition metal ions on the primitive earth. In the course of chemical evolution insoluble metal cyano complexes, which settled at the bottom of primeval sea could have formed peptide and metal amino acid complexes through adsorption processes of amino acids onto these metal cyano complexes.Adsorption of amino acids such as glycine, aspartic acid, and histidine on copper ferrocyanide and zinc ferrocyanide have been studied over a wide pH range of 3.6 – 8.5. Amino acids were adsorbed on the metal ferrocyanide complexes for different time periods. The progress of the adsorption was followed spectro-photometrically using ninhydrin reagent. Histidine was found to show maximum adsorption on both the adsorbents at neutral pH. Zinc ferrocyanide exhibits good sorption behaviour for all the three amino acids used in these investigations.     

High resolution proton magnetic resonance spectroscopy of histones and histone--histone complexes in aqueous solution

Low molecular weight histone complexes of H2A (congruent to dimer), H2B (congruent to tetramer), H3--H4 (congruent to tetramer), H2A--H2B (congruent to dimer), and H2B--H4 (congruent to dimer) have been prepared in 2 M NaCl and neutral pH at 4 degrees C. These materials are free of nonspecific aggregate and are suitable for study by high resolution proton magnetic resonance spectroscopy. Such spectra have been recorded in aqueous solutions under conditions allowing a study of the exchangeable proton resonances of histone complexes for the first time and indicate that the structured regions are rich in hydrophobic amino acids, as well as arginine and some acidic amino acids. Most of the lysine and probably alanine residues remain in a motile, random coil-like state after formation of the complexes. It is suggested that arginine residues may be important in inter- and/or intra-subunit interactions in histone complexes.     

Altered aminoacyl-tRNA synthetase complexes in CHO cell mutants

The Chinese hamster ovary (CHO) aminoacyl-tRNA synthetase mutants Gln-2, His-1, and Lys-101 were analyzed for alterations in respective particulate enzyme forms. The mutant Gln-2 showed a preferential loss of the lower molecular weight enzyme form for glutamine. His-1 showed alterations of the enzyme complexes for several other aminoacyl-tRNA activities but only decreased activity for itself. The mutant Lys-101 only showed an altered Lysyl-tRNA synthetase. These results provide evidence for a model of the intracellular role of the aminoacyl-tRNA synthetase complexes wherein the high molecular weight forms utilize amino acids directly from the extracellular pool while the low molecular weight forms utilize intracellular pools.