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.     

Alternative structural state of transferrin. The crystallographic analysis of iron-loaded but domain-opened ovotransferrin N-lobe

Transferrins bind Fe3+ very tightly in a closed interdomain cleft by the coordination of four protein ligands (Asp60, Tyr92, Tyr191, and His250 in ovotransferrin N-lobe) and of a synergistic anion, physiologically bidentate CO32-. Upon Fe3+ uptake, transferrins undergo a large scale conformational transition: the apo structure with an opening of the interdomain cleft is transformed into the closed holo structure, implying initial Fe3+ binding in the open form. To solve the Fe3+-loaded, domain-opened structure, an ovotransferrin N-lobe crystal that had been grown as the apo form was soaked with Fe3+-nitrilotriacetate, and its structure was solved at 2.1 A resolution. The Fe3+-soaked form showed almost exactly the same overall open structure as the iron-free apo form. The electron density map unequivocally proved the presence of an iron atom with the coordination by the two protein ligands of Tyr92-OH and Tyr191-OH. Other Fe3+ coordination sites are occupied by a nitrilotriacetate anion, which is stabilized through the hydrogen bonds with the peptide NH groups of Ser122, Ala123, and Gly124 and a side chain group of Thr117. There is, however, no clear interaction between the nitrilotriacetate anion and the synergistic anion binding site, Arg121.     

Potentiometric and spectroscopic studies on Cu(II) complexation to aminophosphonic acid, 1-(3-pyridyl)-1-(n-butylamino)-methanephosphonic acid

The results are reported of a potentiometric and spectroscopic study of the copper(II) complexes of aminophosphonic acid containing a pyridyl side chain. The aminophosphonic acid coordinates similarly to carboxyl amino acids, forming chelate MA and MA₂ species. Stable MAH species with only a phosphonic group coordinated to the metal ion exist at lower pH. The pyridyl side chain was found to be noneffective in the interaction with Cu(II) ion.     

Ternary copper(II) complexes involving 2-(aminomethyl)-benzimidazole and some bio-relevant ligands. Equilibrium studies and kinetics of hydrolysis for glycine methyl ester under complex formation

Formation equilibria of copper(II) complexes of 2-(aminomethyl)-benzimidazole (AMBI) and the ternary complexes Cu(AMBI)L (L = amino acid, amide, dicarboxylic acid or DNA constituents) have been investigated. Ternary complexes of amino acids or amides are formed by a simultaneous mechanism. Amino acids form the complex Cu(AMBI)L, whereas amides form two complex species Cu(AMBI)L and Cu(AMBI)(LH₋₁). The ternary complexes of copper(II) with AMBI and dicarboxylic acids or DNA units are formed by a stepwise mechanism, whereby binding of copper(II) to AMBI is followed by ligation of the dicarboxylic acids or DNA components. The values of Δ log K indicate that the ternary complexes containing aromatic amino acids are significantly more stable than the complexes containing alkyl- and hydroxyalkyl-substituted amino acids. This may be taken as an evidence for a stacking interaction between the aromatic moiety of AMBI and the aromatic side chains of the bio-active ligands. The solid complexes Cu(AMBI)L where L = 1,1-cyclobutanedicarboxylic acid (CBDCA) and malonic acid were separated and identified by elemental analysis and infrared spectroscopy and magnetic moment. The decomposition course and steps for the isolated complexes were analyzed and the kinetic parameters of the non-isothermal decomposition were calculated. The hydrolysis of glycine methyl ester (MeGly) is catalyzed by the Cu(AMBI)²⁺ complex. The kinetic data is fitted assuming that the hydrolysis reaction proceeds in two steps. The first step, involving coordination of the amino acid ester by the amino and carbonyl groups, is followed by rate-determining attack by OH⁻ ion. The second step involves the equilibrium formation of the hydroxo-complex Cu(AMBI)(MeGly)(OH) followed by intramolecular OH⁻ attack.     

The catalytic mechanism of amino acid:tRNA ligases. Synergism and formation of the ternary enzyme-amino acid-ATP complex.

Formation of binary and ternary enzyme-ligand complexes was investigated for amino acid:tRNA ligases specific for L-isoleucine, L-leucine, and L-phenylalanine. Each of the enzymes exhibited synergistic binding when a substrate was substituted by a structurally related compound. The strength of coupling between the sites binding the amino acid and ATP was strongly dependent on the structure of ligands. The phenomenon was observed with the L-leucine and L-phenylalanine-specific enzymes only in the presence of magnesium. Spermine was inhibitory for L-phenylalanine:tRNA ligase. From the variation which structure of the strength of the observed synergism a correlation scheme was derived considering the ammonium group, the carboxylate group and the side chain of the amino acid, and the adenosine and triphosphate moieties of ATP. The strength of coupling between the subsites binding various combinations of these moieties was evaluated. We found that binding of the subgroups of the amino acid exerts an intramolecular synergism. The strength intramolecular synergism was similar to the strength of the intermolecular synergism observed for the simultaneous binding of an amino alcohol and ATP (or MgATP-2-). We have derived a molecular mechanism for the formation of the ternary enzyme-amino acid-ATP (or MgATP-2-) complex taking into account the synergistic phenomena. The complex is considered to involve electrostatic repulsion between the amino acid carboxylate and the ATP triphosphate moieties. When one of the negatively charged groups have been eliminated, the enzymatic rearrangement which facilitates the formation of this complex may be seen as a synergistic coupling.     

Mapping interactions between germinants and Clostridium difficile spores

Germination of Clostridium difficile spores is the first required step in establishing C. difficile-associated disease (CDAD). Taurocholate (a bile salt) and glycine (an amino acid) have been shown to be important germinants of C. difficile spores. In the present study, we tested a series of glycine and taurocholate analogs for the ability to induce or inhibit C. difficile spore germination. Testing of glycine analogs revealed that both the carboxy and amino groups are important epitopes for recognition and that the glycine binding site can accommodate compounds with more widely separated termini. The C. difficile germination machinery also recognizes other hydrophobic amino acids. In general, linear alkyl side chains are better activators of spore germination than their branched analogs. However, L-phenylalanine and L-arginine are also good germinants and are probably recognized by distinct binding sites. Testing of taurocholate analogs revealed that the 12-hydroxyl group of taurocholate is necessary, but not sufficient, to activate spore germination. In contrast, the 6- and 7-hydroxyl groups are required for inhibition of C. difficile spore germination. Similarly, C. difficile spores are able to detect taurocholate analogs with shorter, but not longer, alkyl amino sulfonic acid side chains. Furthermore, the sulfonic acid group can be partially substituted with other acidic groups. Finally, a taurocholate analog with an m-aminobenzenesulfonic acid side chain is a strong inhibitor of C. difficile spore germination. In conclusion, C. difficile spores recognize both amino acids and taurocholate through multiple interactions that are required to bind the germinants and/or activate the germination machinery.     

Screening of metal complex–amino acid side chain interactions by potentiometric titration

Reversible coordination of amino acid side chains to metal complexes is widely used in protein purification (IMAC technique), but available data on affinity and selectivity of such binding processes are limited. We use potentiometric titration of a series of metal complexes with vacant coordination sites in the presence of molecules resembling amino acid side chain functionalities to screen for new affinities. The investigation confirms documented affinities of imidazole to nickel(II) and copper(II) IDA and NTA complexes, and discovers a hitherto unknown binding of zinc(II)- and cadmium(II) cyclen complexes to imidazole.     

Amino acids binding to Zn2+‐cyclen molecular receptor in aqueous solution

Potentiometric titrations and ¹H NMR spectroscopic studies of amino acids binding to the [ZnL]²⁺‐complex where L = cyclen in aqueous solution provide information concerning complexing species identity, their stability, and coordination mode declaration. The amino acids form stable ternary [ZnL(HLⁿ)]²⁺ and [ZnL(Lⁿ)]⁺ complexes. The observations indicate bidentate coordination mode of the deprotonated amino acids, involving both the amine and the carboxylate functions to the [ZnL]²⁺ complex in pH region of about 7.5–9.5. The determined stability constants indicate that [ZnL]²⁺ complex is a very efficient receptor for simple amino acids such as glycine and alanine. Copyright © 2010 John Wiley & Sons, Ltd.     

Interaction of tyrosine-phenol-lyase from Citrobacter intermedius with amino acids and their derivatives: factors determining the effectiveness of binding

The inhibition by L-amino acids and their derivatives of tyrosine phenol-lyase is investigated. Tyramine, alpha-phenylethylamine and tryptamine have no detectable inhibition effect and hence are weakly bonded by an active site. The aromatic amino acid amides are competitive inhibitors but do not manifest an enzymatic isotope exchange of alpha-proton in D2O. Free amino acids however are competitive inhibitors and in the majority of cases exchange alpha-proton. The presence of COOH-group is therefore an important feature which determines the binding efficiency and causes the "active" conformation of the amino acid-PLP complex labelising alpha-proton. In the absence of functional and bulky groups in the amino acid side chain the hydrophobicity is found to be the main factor determining the binding efficiency. For these amino acids a correlation exists between-RTlnKi and side chain hydrophobicity. The amino acids bearing the bulky groups, i. e. valine, leucine and isoleucine have reduced binding efficiency. Lysine and arginine bearing positively charged functional groups possess no inhibition effect. Aspartic and glutamic acids are anomalously strong inhibitors taking into consideration low hydrophobicity of their side chains. One can assume that the electrophilic group able to interact with the terminal COO- -group of aspartic and glutamic acids is located in the active site of tyrosine phenollyase.     

The iron-binding properties of hen ovotransferrin.

1. The distribution of iron between the two iron-binding sites in partially saturated ovotransferrin was studied by labelling with 55Fe and 59Fe and by gel electrophoresis in a urea-containing buffer. 2. When iron is added in the form of chelate complexes at alkaline pH, binding occurs preferentially at the N-terminal binding site. In acid, binding occurs preferentially at the C-terminal site. 3. When simple iron donors (ferric and ferrous salts) are used the metal is distributed at random between the binding sites, as judged by the gel-electrophoresis method. The double-isotope method shows a preference of ferrous salts for the N-terminal site. 4. Quantitative treatment of the results of double-isotope labelling suggests that in the binding of iron to ovotransferrin at alkaline pH co-operative interactions between the sites occur. These interactions are apparently absent in the displacement of copper and in the binding of iron at acid pH.     

Pb(II)-binding capability of aminohydroxamic acids: primary hydroxamic acid derivatives of alpha-amino acids as possible sequestering agents for Pb(II)

Complexes of aminohydroxamic acids, D,L-alpha-alaninehydroxamic acid (alpha-Alaha), sarcosinehydroxamic acid (Sarha), D,L-N-methyl-alpha-alaninehydroxamic acid (N-Me-alpha-Alaha), beta-alaninehydroxamic (beta-Alaha), L-aspartic acid-beta-hydroxamic acid (Asp-beta-ha), L-glutamic acid-gamma-hydroxamic acid (Glu-gamma-ha) and L-histidinehydroxamic acid (Hisha) with lead(II) in aqueous solution were studied by pH-potentiometric, 1H NMR and electrospray ionization mass spectrometric (ESI MS) methods. The results were compared to those of a simple monohydroxamic acid, acetohydroxamic acid and the effects of the amino group, hydroxamate-N, as well as, additional side chain donors on the co-ordination mode and on the stability of the complexes formed were evaluated. It was found that the amino nitrogen atom situating in beta- or in gamma-position (beta-Alaha, Asp-beta-ha, Glu-gamma-ha) does not co-ordinate to Pb(II), only hydroxamate type chelates are formed before the hydrolytic processes. However, the amino-N in alpha-position (alpha-Alaha, Sarha, Hisha) seems to form a stable 5-membered (N,N)-type chelate together with the deprotonated hydroxamate-N above pH 6. On the other hand, the hydroxamate (O,O)-type chelate also exists. Since steric reasons do not allow the coordination of these two chelates of a molecule to the same Pb(II) ion, polynuclear complexes with mixed co-ordination modes are formed with the alpha-derivatives above pH 6. Simple hydroxamate type complexes are formed with N-Me-alpha-Alaha, where the hydroxamate-N is not able to co-ordinate. The co-ordination of the side chain imidazole of Hisha is not measurable, while a weak interaction of the side chain carboxylates of Asp-beta-ha and especially of Glu-gamma-ha can be suggested.     

The identification of protected tyrosine residues in iron-ovotransferrin.

Tetranitromethane reacts with essentially all 21 tyrosine residues of iron-free ovotransferrin. In iron-ovotransferrin, 7 mol of tyrosine/mol of protein are unreactive. Peptides containing the unreactive tyrosine residues were isolated from digests of nitrated iron-ovotransferrin. By comparing the structures of the peptides with the amino acid sequence of ovotransferrin it is found that there are ten protected residues occupying positions 42, 82, 92, 188, 319, 415, 431, 521 and 524 in the polypeptide chain. The problem of identifying the tyrosine residues that form bonds with the metal atoms is discussed.     

Participation of manganese ions complexed with tRNA in the interaction with amino acids and dipeptides.

Carboxyl groups of glycine, beta-alanine, gamma-aminobutyric acid and diglycine interact with Mn2+ coordinated by tRNA, as revealed by 1H and 13C NMR studies. The amino groups of these compounds interact with tRNA phosphate groups. The distances between the coordinated Mn2+ and carboxyl groups and the alpha-protons of glycine were determined. The role of Mn2+ and Mg2+ complexed with nucleic acids in the formation of specific complexes between proteins and nucleic acids is discussed.     

Stereospecificity of alpha-proton exchange reactions catalysed by pyridoxal-5'-phosphate-dependent enzymes

A NMR method for quantifying the catalytic efficiency and stereospecificity of the exchange of the alpha-protons of glycine is described. It is used to determine how the binding of the alpha-carboxylate group of amino acids contributes to the stereospecificity of exchange reactions catalysed by tryptophan synthase, serine hydroxymethyltransferase and a catalytic antibody utilising pyridoxal-5'-phosphate (PLP) as a cofactor. Using larger substrates, it is shown how the size of the amino acid side chain contributes to the stereospecificity of exchange. Mutants of aspartate aminotransferase are used to determine how substrate binding controls the catalytic efficiency and stereospecificity of the exchange of the alpha-protons of aspartate and glutamate. Evidence is presented which shows that with serine hydroxymethyltransferase, L-norleucine is not bound at the same catalytic site as glycine. Finally the catalytic efficiency and stereospecificity of the alpha-proton exchange reactions catalysed by all the PLP-dependent catalysts examined are compared.     

The interaction of glycine, aspartic acid, and lysine by the protonated macrocyclic ligand 6,19-bis(2-hydroxypropyl)-3,6,9,16,19,22-hexaaza-tricyclo-[22.2.2.2(11,14)]triaconta-11,13,24,26,27,29-hexaene

A new hexaaza macrocyclic ligand (L) bearing two 2-hydroxypropyl pendants, 6,19-bis(2-hydroxypropyl)-3,6,9,16,19,22-hexaaza-tricyclo-[22.2.2.2(11,14)]triaconta-11,13,24,26,27,29-hexaene has been synthesized and characterized. The macrocyclic ligand was isolated as a colorless crystal, monoclinic, P2(1)/n, with a=10.757(2), b=14.214(3), c=13.746(3) A, beta=101.40(3) degrees, V=2060.3(7) A3, Z=2, R1=0.0695, and wR2=0.1538 [I>2sigma(I)]. Potentiometric studies of the macrocyclic ligand and three types of amino acids, glycine (equal numbers of carboxylate and amino groups), aspartic acid (more carboxylate groups than amino group), and lysine (more amino groups than carboxylate group) have been performed. The stability constants for the new macrocycle and binary complexes of the amino acid with the macrocyclic ligand are reported. Binary complexes are formed in aqueous solution as a result of hydrogen bonding interaction and electrostatic attraction between the host and the guest. The binding Schemes for the recognition of amino acids are suggested. From the results, it seems that this new macrocyclic ligand is able to bind three different amino acids with selectivity in aqueous solution, and the strength of binding is of the order lysine < glycine < aspartic acid.     

Extraction and carrier-facilitated transport of amino acids using synthetic non-cyclic receptors through bulk liquid membrane

The extraction and carrier-facilitated transport of amino acids (leucine, valine and glycine) was studied through chloroform bulk liquid membrane system using a series of non-cyclic receptors such as diethylene glycol (1), diethylene glycol dimethyl ether (2), diethylene glycol dibutyl ether (3), diethylene glycol dibenzoate (4), triethylene glycol (5) and tetraethylene glycol (6). The amount of amino acid extracted and transported depends mainly upon the structure and the concentration of the receptors and also on the concentration of amino acid. The receptors 1 to 4, having small chain length and flexible end groups, formed stable complexes with amino acids, and the flexibility of receptors in different conformational forms was responsible for their carrier ability, while the receptors 5 and 6, having larger chain length showed poor carrier ability. Hydrophobicity of amino acids also play an important role in the extraction as well as transport process.     

Effects of alterations of the amino-terminal glycine of influenza hemagglutinin fusion peptide on its structure,organization and membrane interactions

Mutations of the glycine residue at the amino terminus of HA2 have been shown to have a large effect on the fusion activity of HA2, the extent of which apparently correlates with the side chain bulkiness of the substituting amino acids. To investigate into the cause of abrogation in fusogenicity and virus-promoted fusion mechanism, we synthesized several peptides in which this glycine was substituted by serine, glutamic acid, or lysine. 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dimyristoyl sn-glycero-3-phosphoglycerol (DMPG) were used as model membranes in the fluorescence, circular dichroism (CD), and FTIR measurements while sodium dodecyl sulfate was used in NMR studies. We found that, for the less active variants, affinity to membrane, degree of solvent dehydration, lipid perturbation, depth of insertion, and helicity were less. Comparison of affinity to membrane bilayer among these analogs revealed that binding of the fusion peptide is determined largely by the hydrophobic effect. Additionally, the orientation is closer to the membrane normal for the wild-type fusion peptide in the helix form while the inactive analogs inserted more parallel to the membrane surface.     

A working hypothesis on the interdependent genesis of nucleotide bases,protein amino acids,and primitive genetic code

In the course of experimental approach to the chemical evolution in the primeval sea, we have found that the main products from formaldehyde and hydroxylamine are glycine, alanine, serine, aspartic acid etc., and the products from glycine and formaldehyde are serine and aspartic acid. Guanine is found in the two-letter genetic codons of all these amino acids.Based upon the finding and taking into consideration the probable synthetic pathways of nucleotide bases and protein amino acids in the course of chemical evolution and a correlation between the two-letter codons and the number of carbon atoms in the carbon skeleton of amino acids, 1 have been led to a working hypothesis on the interdependent genesis of nucleotide bases, protein amino acids, and primitive genetic code as shown in Table I.Protein amino acids can be classified into two groups: Purine Group amino acids and Pyrimidine Group amino acids. Purine bases and Pyrimidine bases are predominant in two-letter codons of amino acids belonging to the former and the latter group respectively.Guanine, adenine, and amino acids of the Purine Group may be regarded as synthesized from C₁ and C₂ compounds and N₁ compounds (including C₁N₁ compunds such as HCN), probably through glycine, in the early stage of chemical evolution.Uracil, cytosine, and amino acids of the Pyrimidine Group may be regarded as synthesized directly or indirectly from three-carbon chain compounds. This synthesis became possible after the accumulation of three-carbon chain compounds and their derivatives in the primeval sea.The Purine Group can be further classified into a Guanine or (Gly+nC₁) Subgroup and an Adenine or (Gly+nC₂) Subgroup or simply nC₂ Subgroup. The Pyrimidine Group can be further classified into a Uracil or C₃C₆C₉ Subgroup and a Cytosine or C₅-chain Subgroup (Table I).It is suggested that the primitive genetic code was established by a specific interaction between amino acids and their respective nucleotide bases. The interaction was dependent upon their concentration in the primeval environments and the binding constants between amino acids and their respective bases.Presented at the International Symposium (Lipmann Symposium) on The Concepts of Chemical Recognition in Biology held in Grignon near Versailles (France) on July 18–20, 1979.     

Effect of alkali ions on the active transport of neutral amino acids into Streptomyces hydrogenans.

The active transport of neutral amino acids into Streptomyces hydrogenans is inhibited by external Na+. There is no indication that in these cells amino acid accumulation is driven by an inward gradient of Na+. The extent of transport inhibition by Na+ depends on the nature of the amino acid. It decreases with increasing chain length of the amino acid molecules i.e. with increasing non-polar properties of the side chain. Kinetic studies show that Na+ competes with the amino acid for a binding site at the amino acid carrier. There is a close relation between the Ki values for Na+ and the number of C atoms of the amino acids. Other cations also inhibit neutral amino acid uptake competitively; the effectiveness decreases in the order Li+ greater than Na+ greater than K+ greater than Rb+ greater than Cs+. Anions do not have a significant effect on the uptake of neutral amino acids. After prolonged incubation of the cells with 150 mM Na+, in addition to the competitive inhibition of transport Na+ induces an increase in membrane permeability for amino acids.     

Synthesis and characterization of metal binding pseudotripeptides.

Metal complexes with peptide or pseudopeptide type ligands can serve as good model compounds for a deeper understanding of enzymatic catalysis, but ligands with a high selectivity for different transition metal cations are hard to find due to the rather flexible nature of peptides. Since such ligands would be the sine qua non condition for the synthesis of heterodinuclear peptide metal complexes with catalytic activity, the search for small, affine and selective metal chelating sequences is of interest. Using four different amino acids (His, Lys, Asp, Glu) a set of 16 pseudotripeptides of the common structure Bz-AS1-Sar-AS2-NH2 has been synthesized, purified and characterized by mass spectrometry and 1H-NMR. Their ability to form metal complexes has been investigated leading to short motifs capable of selectively binding only one or two transition metal cations with high affinity. As expected, the complexation of transition metal cations by pseudotripeptides is strongly dependent not only on the amino acid composition, but also on the sequence with regard to the stability of the resulting complexes, as well as the selectivity of the ligands towards Cu2+, Co2+, Ni2+, Zn2+ and Mn2+.