Solvent extraction of amino acids into a room temperature ionic liquid with dicyclohexano-18-crown-6

Amino acids Trp, Gly, Ala, Leu are extracted efficiently from aqueous solution at pH 1.5–4.0 (Lys and Arg at pH 1.5–5.5) into the room temperature ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate (BmimPF₆) with dicyclohexano-18-crown-6 (CE). The most hydrophilic amino acids such as Gly are extracted as efficiently as the less hydrophilic (92–96%). The influence of pH, amino acid and crown ether concentration, volume ratio of aqueous and organic phases, and presence of some cations on amino acid recovery were studied. The ratio of amino acid to crown ether in the extracted species is 1:1 for cationic Trp, Leu, Ala, and Gly and to 1:2 for dicationic Arg and Lys. This ionic liquid extraction system was used successfully for the recovery of amino acids from pharmaceutical samples and fermentation broth, and was followed by fluorimetric determination.These results were published in part in Smirnova SV (2002) Ph.D. Thesis, Moscow State University.     

On the sodium and lithium ion affinities of some α-amino acids

The decomposition of 59 different cluster ions (generated by fast atom bombardment) consisting of two different amino acids and a sodium ion was analysed. The only fragment ions of significant abundance could be assigned to sodium ion-bound amino acids. Assuming that the most abundant ion in the fragment ion spectrum corresponds to the amino acid with the highest sodium ion affinity (SIA), the 20 common α-amino acids could be ordered with increasing sodium ion affinity as follows: Gly, Ala, Cys, Val, (Leu, Ile), Ser, Met, Thr, (Phe, Pro), Asp, Tyr, (Glu, Lys), Trp, Asn, Gln, His, Arg. Quantitative determinations were carried out by comparison of the lithium ion affinity (LIA) of Ala with that of dimethylformamide (DMF) in a fragment ion scan of the ion-bound dimer Ala—Li⁺—DMF. LIA(Ala) was calculated from LIA(Ala) = LIA(DMF) – (1/C)ln[I(AlaLi⁺)/I(DMF—Li⁺)], where the constant C was estimated from measurements of proton-bound amine–amino acid clusters. From fragment ion analysis of nine other Li⁺-bound α-amino acid dimers, the following lithium ion affinities were obtained: Gly 51.0, Ala 52.6, Sar 53.5, α-aminobutyric acid 53.7, glycine methyl ester 54.7 and Val 54.8. SIA(Ala) was estimated to be 75% of the lithium ion affinity and from fragment ion analysis of ten Na⁺-bound α-amino acid dimers the following sodium ion affinities were obtained: Gly 37.9, Ala 39.4, α-aminobutyric acid 40.3, Val 41.0, glycine methylster 41.0 and Sar 41.2.     

大亚湾沉积物中氨基酸的垂直分布——沉积物柱样W0中的水解氨基酸

测定了采自大亚湾近岸海域的一个长60cm的沉积物柱样W0中15种水解氨基酸的含量；结果表明，15种水解氨基酸含量均随深度而下降，其中苏氨酸、丝氨酸、甘氨酸、丙氨酸、精氨酸、缬氨酸、苯丙氨酸、亮氨酸、异亮氨酸的含量以及水解氨基酸总量随深度的变化可用指数方程c＝c0e^-kx加以描述；天冬氨酸、谷氨酸、丝氨酸、甘氨酸、丙氨酸和缬氨酸是大亚湾沉积物中最丰富的氨基酸。     

Determination of 13C isotopic enrichment of valine and threonine by GC-C-IRMS after formation of the N(O,S)-ethoxycarbonyl ethyl ester derivatives of the amino acids

We describe a new method of assessing, in a single run, ¹³C isotopic enrichment of both Val and Thr by gas chromatography–combustion–isotope-ratio mass spectrometry (GC–C–IRMS). This method characterised by a rapid one-step derivatisation procedure performed at room temperature to form the N(O,S)-ethoxycarbonyl ethyl ester derivatives, and a polar column for GC. The suitability of this method for Val and Thr in in-vivo samples (mucosal hydrolysate) was demonstrated by studying protein metabolism with two tracers (¹³C-valine or ¹³C-threonine). The intra-day and inter-day repeatability were both assessed either with standards or with in-vivo samples at natural abundance and at low ¹³C isotopic enrichment. For inter-day repeatability CVs were between 0.8 and 1.5% at natural abundance and lower than 5.5% at 0.112 and 0.190 atom% enrichment for Val and Thr, respectively. Overall isotopic precision was studied for eleven standard amino acid derivatives (those of Val, Ala, Leu, Iso, Gly, Pro, Asp, Thr, Ser, Met, and Phe) and was assessed at 0.32‰. The ¹³C isotopic measurement was then extended to the other amino acids (Ala, Val, Leu, Iso, Gly, Pro, Thr, and Phe) at natural abundance for in-vivo samples. The isotopic precision was better than 0.002 atom% per amino acid (for n = 4 rats). This analytical method was finally applied to an animal study to measure Thr utilization in protein synthesis.     

Amino acids of ricin and its polypeptides

Ricin and its corresponding polypeptides (A & B chain) were purified from castor seed. The molecular weight of ricin subunits were 29,000 and 28,000 daltons. The amino acids in ricin determined were Asp45 The22 Ser40 Glu53 Cys4 Gly96 His5 Ile21 Leu33 Lys20 Met4 Phe13 Pro37 Tyr11 Ala45 Val23 Arg20 indicating that ricin contains approximately 516 amino acid residues. The amino acids of the two subunits of ricin A and B chains were Asp23 The12 Ser21 Glu29 Cys2 Gly48 His3 Ile12, Leu17 Lys10 Met2 Phe6 Pro17 Tyr7 Ala35 Val13 Arg13 while in B chain the amino acids were Asp22 The10 Ser19 Glu25 Cys2 Gly47 His1 Ile10, Leu15 Lys11 Met1 Phe7 Pro6 Tyr5 Ala32Val11 Arg10. The total helical content of ricin came around 53.6% which is a new observation.     

Systematic study of the transfer of amino acids across the water/l,2-dichloroethane interface facilitated by dibenzo-18-crown-6

Failitated ion transfer reactions of 20 amino acids with dibenzo-18-crown-6 (DB18C6) at the water/1,2-dichloroethane (W/DCE) interfaces supported at the tips of micro- and nano-pipets were investigated systematically using cyclic voltammetry. It was found that there were only 10 amino acids, that is, Leu, Val, lle, Phe, Trp, Met, Ala, Gly, Cys, Gln (in brief), whose protonated forms as cations can give well-defined facilitated ion transfer voltammograms within the potential window, and the reaction pathway was proven to be consistent with the transfer by interfacial complexation/dissociation (TIC/TID) mechanisms. The association constants of DB 18C6 with different amino acids in the DCE (β°), and the kinetic parameters of reaction were evaluated based on the steady-state voltammetry of micro- or nano-pipets, respectively. The experimental results demonstrated that the selectivity of complexation of protonated amino acid by DB18C6 compared with that of alkali metal cations was low, which can be attributed to the vicinal effect arising from steric hindrance introduced by their side group and the steric bulk effect by lipophilic stabilization. Moreover, the association constants and the standard rate constants for different amino acids showed good correlations with their hydrophobicity (π), except Gly and Met, which inferred that the selectivity of such heterogeneous complex reaction for different amino acids with DB18C6, was not only affected by discrimination in binding these ions to the crown ether macro-cycle, but also significantly modified by the ion transfer Gibbs energy which was closely related to the structure of the transferred ions, protonated amino acids.     

Amino acids in aqueous solution. Effect of molecular structure and temperature on thermodynamics of dissolution

The enthalpies of dissolution of glycine (Gly) and L-α-alanine (Ala) in water at 288.15–318.15 K were measured. The results were compared with the earlier obtained data for L-α-phenylalanine (Phe) and L-α-histidine (His). The standard enthalpies of dissolution (Δ_soln H ₀) and differences (ΔC _p ⁰ ) between the limiting partial molar heat capacity of the amino acids in solution and the heat capacity of the amino acids in the crystalline state were calculated in the temperature interval 273–373 K. Changes in the entropy of dissolution (ΔΔ_soln S ₀) and reduced Gibbs energy [Δ (Δ_soln G ₀/T)] in the temperature interval from 273 to 373 K were determined from the known thermodynamic relationships. The ΔC _p ⁰ value is negative for hydrophilic glycine and positive for other amino acids. The ΔΔ_soln S ⁰ values increase with an increase in the hydrophobicity of the amino acids. The Δ(Δ_soln G ₀/T) values become more negative in the order Ala, Phe, Gly, His. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 711–714, April, 2007.     

The Design of α/β‐Peptides: Study on Three‐Residue Turn Motifs and the Influence of Achiral Glycine on Helix and Turn

Novel three‐residue helix‐turn secondary structures, nucleated by a helix at the N terminus, were generated in peptides that have ‘β‐Caa‐L ‐Ala‐L ‐Ala,’ ‘β‐Caa‐L ‐Ala‐γ‐Caa,’ and ‘β‐Caa‐L ‐Ala‐δ‐Caa’ (in which β‐Caa is C‐linked carbo‐β‐amino acid, γ‐Caa is C‐linked carbo‐γ‐amino acid, and δ‐Caa is C‐linked carbo‐δ‐amino acid) at the C terminus. These turn structures are stabilized by 12‐, 14‐, and 15‐membered (mr) hydrogen bonding between NH(i)/CO(i+2) (i+2 is the last residue in the peptide) along with a 7‐mr hydrogen bond between CO(i)/NH(i+2). In addition, a series of α/β‐peptides were designed and synthesized with alternating glycine (Gly) and (S)‐β‐Caa to study the influence of an achiral α‐residue on the helix and helix‐turn structures. In contrast to previous results, the three ‘β–α–β’ residues at the C terminus (α‐residue being Gly) are stabilized by only a 13‐mr forward hydrogen bond, which resembles an α‐turn. Extensive NMR spectroscopic and molecular dynamics (MD) studies were performed to support these observations. The influence of chirality and side chain is also discussed.     

Spectroscopy of hydrothermal reactions,part 26: Kinetics of decarboxylation of aliphatic amino acids and comparison with the rates of racemization

The kinetics of decarboxylation of six α‐amino acids (glycine, alanine, aminobutyric acid, valine, leucine, and isoleucine) and β‐aminobutyric acid were studied in aqueous solution at 310–330ˆC and 275 bar over the pH₂₅ range 1.5–8.5 by using an in situ FT‐IR spectroscopy flow reactor. Based on the rate of formation of CO₂, the first‐order or pseudo‐first‐order rate constants were obtained along with the Arrhenius parameters. The decarboxylation rates of amino acids follow the order Gly > Leu ≈ Ile ≈ Val > Ala > α‐Aib > β‐Aib. Differences in the concentration between 0.05 and 0.5 m had only a minor effect on the decarboxylation rate. The effect of the position of the amino group on the decarboxylation rate was investigated for α‐, β‐, and γ‐aminobutyric acid and the order was found to be α > β ≫ γ. Although the pH dependence is complex, the decarboxylation rates of α‐amino acids qualitatively have the inverse trend of the racemization rates. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 602–610, 2003     

Calculation of dissociation constants and chemical hardness of some biologically important molecules: A theoretical study

The gas‐phase geometries of neutral, protonated, and deprotonated forms of some biologically important molecules, alanine (Ala), glycine (Gly), phenylalanine (Phe), and tyrosine (Tyr), were optimized using density functional theory at B3LYP/6‐311++G(d) and the ab initio HF/6‐311++G(d) level of theories. The neutral and different stable ionic states of Ala, Gly, Phe, and Tyr have also been solvated in aqueous medium using polarizable continuum model for the determination of solvation free energies in the aqueous solution. The gas‐phase acidity constants of above four molecules have been also calculated at both levels of theories and found that the values calculated at HF/6‐311++G(d) method are in good agreement with experimental results. A thermodynamic cycle was used to determine the solvation free energies for the proton dissociation process in aqueous solution and the corresponding pK_a values of these molecules. The pK_a values calculated at B3LYP/6‐311++G(d) method are well supported by the experimental data with a mean absolute deviation 0.12 pK_a units. Additionally, the chemical hardness and the ionization potential (IP) for these molecules have been also explored at both the level of theories. The Tyr has less value of chemical hardness and IP at both levels of theories compared with other three molecules, Ala, Gly, and Phe. The calculated values of chemical hardness and IP are decreasing gradually with the substitution of the various functional groups in the side chain of the amino acids. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Biomimetic synthesis of esters of natural amino acids

A method for the synthesis of Gly, Ala, Phe, and Thr esters is proposed and considered as being a stage of possible biomimetic synthesis of peptides. The methyl esters of the said amino acids are obtained via intervention of 2‐hydroxypropyl phosphonate. The resulting aminoacyl phosphonates reacts with methanol to produce the amino acid methyl esters, with the release of phosphoric acid. The reaction is carried out at room temperature in water. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:252–255, 2008; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20427     

Enantioselective Solid‐Phase Peptide Synthesis Using Traceless Chiral Coupling Reagents and Racemic Amino Acids

The enantioselective condensing reagent 4,6‐dimethoxy‐1,3,5‐triazine (DMT)/strychnine/BF$\rm{{_{4}^{-}}}$ was obtained by treatment of 2‐chloro‐4,6‐dimethoxy‐1,3,5‐triazine (CDMT) with strychnine tetrafluoroborate. The reagent was useful under typical conditions of solid‐phase peptide synthesis (SPPS) with enantiomerically homogeneous substrates. By SPPS, desired dipeptides were obtained in 84–94% yield using 4 equiv. of racemic Fmoc‐Ala, Fmoc‐Phe, and/or Fmoc‐Tyr for 1 equiv. of Wang resin loaded with Gly, Ala, Leu, Phe, Glu(^tBu), and/or Pro, respectively. For all three Fmoc‐protected amino acids, the configuration of the enantiomer preferred under SPPS conditions was independent of the structure of the acylated component and identical to that established in condensations proceeding in solution. In all cases, the enantiomer ratios L /D (er) were in a similar range, and varied from 9 : 92 to 2 : 98 for alanine, and from 90 : 10 to 100 : 0 for aromatic amino acids. The synthesis of Ac‐L ‐Lys(Ac)‐D ‐Ala‐D ‐Ala‐OH from racemic Fmoc‐Ala gave an L /D ratio of 10 : 90 for the esterification of Wang resin, and 0 : 100 for the formation of peptide bonds.     

配位体交换树脂对中性氨基酸分离性能的研究

采用配位体交换树脂对中性氨基酸(Gly,Ala,Val和Leu)进行了分离,并与一般阳离子交换树脂的分离性能进行了比较,对淋洗剂、柱温等分离条件进行了实验;研究了树脂载体结构、功能基及配位中心离子对分离性能的影响。     

Analysis of amino acids in human vascular endothelial (ECV-304) cells by microchip electrophoresis with fluorescence detection

A rapid and sensitive method was developed for the analysis of amino acids by microchip electrophoresis with Hg-lamp excitation fluorescence detection. Fluorescein-isothiocyanate (FITC) was chosen to estimate the sensitivity of this system, and the detection limit (S/N = 3) with FITC was 1.7 nM, which showed that the system was sensitive as well as simple. Two derivatizing agents, FITC and ortho-phthalaldehyde (OPA) were employed to label amino acids and were compared in the same fluorescence detection system with an Hg lamp as the excitation source. The separation parameters were optimized in detail. Optimum separation of OPA-labeled amino acids was obtained in less than 200 s with 20 mM borate buffer (pH 9.0) containing 20% acetonitrile and 10 mM beta-cyclodextrin. Detection limits for amino acids (alanine (Ala), taurine (Tau), glycine (Gly), glutamic acid (Glu), and aspartic acid (Asp)) of 0.38-1.0 muM were achieved. The method was successfully applied to analysis of amino acids in human vascular endothelial cells (ECV-304). The average amount of amino acids in single ECV-304 cells is estimated to be 5.84 fmol for Ala, 2.78 fmol for Tau, 1.15 fmol for Gly, 3.10 fmol for Glu, and 1.30 fmol for Asp.     

Putative One‐Pot Prebiotic Polypeptides with Ribonucleolytic Activity

KIA7, a peptide with a highly restricted set of amino acids (Lys, Ile, Ala, Gly and Tyr), adopts a specifically folded structure. Some amino acids, including Lys, Ile, Ala, Gly and His, form under the same putative prebiotic conditions, whereas different conditions are needed for producing Tyr, Phe and Trp. Herein, we report the 3D structure and conformational stability of the peptide KIA7H, which is composed of only Lys, Ile, Ala, Gly and His. When the imidazole group is neutral, this 20‐mer peptide adopts a four‐helix bundle with a specifically packed hydrophobic core. Therefore, one‐pot prebiotic proteins with well‐defined structures might have arisen early in chemical evolution. The Trp variant, KIA7W, was also studied. It adopts a 3D structure similar to that of KIA7H and its previously studied Tyr and Phe variants, but is remarkably more stable. When tested for ribonucleolytic activity, KIA7H, KIA7W and even short, unstructured peptides rich in His and Lys, in combination with Mg⁺⁺, Mn⁺⁺ or Ni⁺⁺ (but not Cu⁺⁺, Zn⁺⁺ or EDTA) specifically cleave the single‐stranded region in an RNA stem–loop. This suggests that prebiotic peptide–divalent cation complexes with ribonucleolytic activity might have co‐inhabited the RNA world.     

Separation of Neutral Amino Acids with Ligand Exchange Resins

Four neutral amino acids (Gly, Ala,.Val and Leu) were separated with ligand exchange resins. The separation capacity of the ligand exchange resins is compared with that of common ion exchange resins. The effects of eluent, column temperature, and central metal ions of the support on the separation are studied. The relationship between matrix structure of resins and their separation capacity is analysed.     

Microchip electrophoresis with chemiluminescence detection for assaying ascorbic acid and amino acids in single cells

A method based on microchip electrophoresis (MCE) with chemiluminescence (CL) detection was developed for the determination of ascorbic acid (AA) and amino acids including tryptophan (Trp), glycine (Gly) and alanine (Ala) present in single cells. Cell injection, loading, lysing, electrophoretic separation and CL detection were integrated onto a simple cross microfluidic chip. A single cell was loaded in the cross intersection by electrophoretic means through applying a set of potentials at the reservoirs. The docked cell was lysed rapidly under a direct electric field. The intracellular contents were MCE separated within 130 s. CL detection was based on the enhancing effects of AA and amino acids on the CL reaction of luminol with K₃[Fe(CN)₆]. Rat hepatocytes were prepared and analyzed as the test cellular model. The average intracellular contents of AA, Trp, Gly and Ala in single rat hepatocytes were found to be 38.3, 5.15, 3.78 and 3.84 fmol (n = 12), respectively.     

Effective synthesis of cyclic peptide yunnanin C and analogues via Ser/Thr ligation (STL)-mediated peptide cyclization

Cyclic peptide yunnanin C isolated from the root of Stellaria yunnanensis was efficiently synthesized in which the linear peptide was prepared by Boc-SPPS and the cyclization was realized by serine/threonine ligation (STL)-mediated cyclization. In addition, nine yunnanin C analogues, including mutations of Tyr7Gly, Tyr7Val, Tyr7Pro, Tyr7Phe, Ser1Thr, Pro2Val, Gly5Pro, Phe6Ala and Ile4Ala, were prepared in the same fashion. Here, we demonstrated that STL-mediated peptide cyclization could be an effective approach to construct cyclic peptides. Except that proline at the C-terminus could retard the cyclization process, cyclization of yunnanin C analogues with various C-terminal amino acids proceeded with fast cyclization rate (<4 h) and only trace amount of dimers (<5%) at a working concentration of 5 mM.     

Mechanistic Investigations of Oxidation of Some Dipeptides by Sodium N‐chloro‐p‐toluenesulfonamide in Alkaline Medium:A Kinetic Study

The kinetics of oxidation of five dipeptides (DPP) viz., glycylglycine (Gly-Gly), L-alanyl-L-alanine (Ala-Ala), L-valyl-L-valine (Val-Val), L-leucyl-L-leucine (Leu-Leu) and phenylglycyl-phenylglycine (Phg-Phg) by sodium N-chloro-p-toluenesulfonamide or chloramine-T (CAT) in NaOH medium was studied at 308 K. The reactions follow identical kinetics for all the dipeptides, being first-order dependence each on [CAT]_o, [DPP]_o and fractional-order on [OH^－]. Addition of p-toluenesulfonamide or halide ions (Cl^－ or Br^－) has no significant effect on the rate of reaction. The reaction rate was found to increase with increase in ionic strength of the medium. The solvent isotope effect was studied using D₂O. The activation parameters for the reaction were computed from Arrhenius plots. Equilibrium and decomposition constants were evaluated. The oxidation products of the dipeptides were identified as their corresponding aldehydes. An isokinetic relationship was observed with β＝352 K, indicating that enthalpy factors control the reaction rate. CH₃C₆H₄SO₂NCl^－ of the oxidant has been postulated as the reactive oxidizing species. Under comparable experimental conditions, the rate of oxidation of the dipeptides increases in the order: Phg-Phg＞Ala-Ala＞Val-Val＞Leu-Leu＞Gly-Gly. The kinetics of oxidation of the dipeptides have also been compared with those of their corresponding monomer amino acids. The observed results have been explained by a plausible mechanism and the related rate law has been deduced.     

Assay of amino acids in individual human lymphocytes by capillary zone electrophoresis with electrochemical detection

Amino acids in individual human lymphocytes were determined by capillary zone electrophoresis with electrochemical detection (ED) at a carbon fiber bundle electrode after on-column derivatization with naphthalene-2,3-dicarboxaldehyde (NDA) and CN⁻. In order to inject cells easily, a cell injector was designed. In this method, a single human lymphocyte and then the lysing/derivatizing buffer were electrokinetically injected into the front end of the separation capillary as a chamber to lyse the lymphocyte and derivatize amino acids in the cell. Four amino acids (serine (Ser), alanine (Ala), taurine (Tau), and glycine (Gly)) in single human lymphocytes have been identified. Quantitation has been accomplished through the use of calibration curves.