Solid state radiolysis of sulphur-containing amino acids: cysteine,cystine and methionine

The sulphur-containing proteinaceous amino acids l-cysteine, l-cystine and l-methionine were irradiated in the solid state to a dose of 3.2 MGy. This dose corresponds to that delivered by radionuclide decay in a timescale of 1.05 × 10⁹ years to the organic matter buried at a depth >20 m in comets and asteroids. The purity of the sulphur-containing amino acids was studied by differential scanning calorimetry (DSC) before and after the solid state radiolysis and the preservation of the chirality after the radiolysis was studied by chirooptical methods (optical rotatory dispersion, ORD) and by FT-IR spectroscopy. Although the high radiation dose of 3.2 MGy delivered, all the amino acids studied show a high radiation resistance. The best radiation resistance was offered by l-cysteine. The radiolysis of l-cysteine leads to the formation of l-cystine. The radiation resistance of l-methionine is not at the level of l-cysteine but also l-methionine is able to survive the dose of 3.2 MGy. Furthermore in all cases examined the preservation of chirality after radiolysis was clearly observed by the ORD spectroscopy although a certain level of radioracemization was measured in all cases. The radioracemization is minimal in the case of l-cysteine and is more pronounced in the case of l-methionine. In conclusion, the study shows that the sulphur-containing amino acids can survive for 1.05 × 10⁹ years and, after extrapolation of the data, even to the age of the Solar System i.e. to 4.6 × 10⁹ years.     

Mass spectrometric analysis of selected radiolyzed amino acids in an astrochemical context

A selection of amino acids, namely arginine, proline and tyrosine previously irradiated to 3.2 mega-Gray in the solid state and analyzed by differential scanning calorimetry (DSC) and optical rotatory dispersion (ORD) were analyzed in the present work by mass spectrometry with the purpose to identify the radiolysis products and validate the results obtained previously with DSC and ORD. The radiolysis of amino acids is a top-down approach of a research program designed to assess the radiolysis resistance of these molecules for 4.6 × 10⁹ years once buried in primitive bodies of the Solar System.     

Interaction of urea with amino acids: implications for urea-induced protein denaturation

The molecular mechanism of urea-induced protein denaturation is not yet fully understood. Mainly two opposing mechanisms are controversially discussed, according to which either hydrophobic, or polar interactions are the dominant driving force. To resolve this question, we have investigated the interactions between urea and all 20 amino acids by comprehensive molecular dynamics simulations of 22 tripeptides. Calculation of atomic contact frequencies between the amino acids and solvent molecules revealed a clear profile of solvation preferences by either water or urea. Almost all amino acids showed preference for contacts with urea molecules, whereas charged and polar amino acids were found to have slight preferences for contact with water molecules. Particularly strong preference for contacts to urea were seen for aromatic and apolar side-chains, as well as for the protein backbone of all amino acids. Further, protein-urea hydrogen bonds were found to be significantly weaker than protein-water or water-water hydrogen bonds. Our results suggest that hydrophobic interactions are the dominant driving force, while hydrogen bonds between urea and the protein backbone contribute markedly to the overall energetics by avoiding unfavorable unsatisfied hydrogen bond sites on the backbone. In summary, we suggest a combined mechanism that unifies the two current and seemingly opposing views.     

Pulse radiolysis of pyridinecarboxylic acids in aqueous solution

The reactivity of OH, e^-_aq and H radicals towards aqueous carboxypyridines: picolinic acid (2-pyridinecarboxylic acid), PA; isonicotinic acid (4-pyridinecarboxylic acid), i-NA; 2,6-pyridinedicarboxylic acid, 2,6-PDCA; and 3,5-pyridinedicarboxylic acid, 3,5-PDCA was investigated in the pH-range 1–13.8. The absorption spectra of the OH-adducts, H-adducts and pyridinyl radicals are given as well as the formation and decay kinetics. In acid (but not in alkaline) solution, the reaction of H-atoms leads to the formation of two distinct products, namely H-adduct and pyridinyl radicals. The yields of pyridinyl radical are: 20% for PA, 75% for i-NA, 60% for 2,6-PDCA and 25% for 3,5-PDCA (a yield of 50% has been found earlier for nicotinic acid, NA).     

氨基酸残基延展态可及表面积的预测

氨基酸残基的延展态可及表面积(ASA)对预测蛋白质结构和功能起着至关重要的作用.采用偏最小二乘法和多元回归法成功构建了具有较高准确率的预测氨基酸延展态ASA的模型.所得模型具有良好的预测性和可重复性,在模型中,训练集的最优Rt2r可以达到0.998 3,而测试集的Rt2e最优可以达到0.999 2.     

Pulse radiolysis studies of short-lived species in solid amino acids as precursors of radicals and detected by ESR

The aim of the study was to bring closer solid state radiation chemistry and ESR spectroscopy by looking for precursors of free radicals which give ESR signals. It has been performed using time-resolved spectrophotometry (pulse radiolysis of the solid state) and diffuse reflection spectrophotometry. Alanine has been especially considered as the most investigated amino acid, important for radiation dosimetry. Absorption of the transient (Λ maximum at 460 nm) is identified as the species during deamination. The stable absorption spectrum with the Λ maximum at 345 nm is due to the same radical as the one detected by ESR. Other amino acids: valine, threonine, glutamine and arginine show similar behaviour: microsecond spectrum of the intermediate appears always at longer wavelenghts. The transient spectrum changes into stable absorption in UV of a lower wavelenght. Along with the optical spectrum, the ESR spectrum appears, of similar stability. Also, other features indicate that the same radical is responsible for both the electronic and ESR spectrum. Some amino acids, like methionine give intensive transient absorption in the microsecond range but no ESR signal, after completion of consecutive fast reactions. In that case any optical absorption is due to the stable product of radiolysis, i.e. compounds with paired electrons only.     

Methylthiohydantoin amino acids: chromatographic separation and comparison to phenylthiohydantoin amino acids

Most phenylthiohydantoin (PTH) amino acids and most methylthiohydantoin (MTH) amino acids may be separated from one another by thin-layer chromatography (TLC) using the same sequential development technique with the same two solvents. Similarly, a single solvent system may be used in high-performance liquid chromatography (HPLC) to separate most PTH-amino acids and most MTH-amino acids. When both TLC and HPLC separations are performed on a sample, all MTH-and PTH-amino acids can be uniquely identified. Since many solid-phase protein sequencing techniques generate both MTH-and PTH-amino acids, these analytical systems simplify identification of the amino acid derivatives. Although the chromatographic properties of MTH-and PTH-amino acids are similar, they are not identical (contrary to a previous report).     

Empirical and ab initio calculations of thermochemical parameters of amino acids: IV. Non-Typical amino acids: Hydroxyamino acids, thioamino acids, and heterocyclic amino(imino) acids

Using a set of computational methods we calculated the basic thermochemical characteristics of the fifteen non-typical L-??-amino acids of hydroxyaminocarboxylic and thioaminomonocarboxylic series, and of some heterocyclic amino(imino)carboxylic acids.     

Abc amino acids: design, synthesis, and properties of new photoelastic amino acids

Photoisomerizable amino acids provide a direct avenue to the experimental manipulation of bioactive polypeptides, potentially allowing real-time, remote control of biological systems and enabling useful applications in nanobiotechnology. Herein, we report a new class of photoisomerizable amino acids intended to cause pronounced expansion and contraction in the polypeptide backbone, i.e., to be photoelastic. These compounds, termed Abc amino acids, employ a photoisomerizable azobiphenyl chromophore to control the relative disposition of aminomethyl and carboxyl substituents. Molecular modeling of nine Abc isomers led to the identification of one with particularly attractive properties, including the ability to induce contractions up to 13 A in the backbone upon trans --> cis photoisomerization. This isomer, designated mpAbc, has substituents at meta and para positions on the inner (azo-linked) and outer rings, respectively. An efficient synthesis of Fmoc-protected mpAbc was executed in which the biaryl components were formed via Suzuki couplings and the azo linkage was formed via amine/nitroso condensation; protected forms of three other Abc isomers were prepared similarly. An undecapeptide incorporating mpAbc was synthesized by conventional solid-phase methods and displayed characteristic azobenzene photochemical behavior with optimal conversion to the cis isomer at 360 nm and a thermal cis --> trans half-life of 100 min at 80 degrees C.     

Effects of thermal history on solid state and melting behavior of amino acids

Dielectric Thermal Analysis (DETA) of drugs, proteins and amino acids reveals a strongly linear conductivity increase prior to and peaking at the melt, associated with dielectric viscoelastic properties of the material. Premelt onset and peak are shown to depend on thermal history. Comparisons of neat amino acid samples to samples heated to 150 °C; dried in a desiccator; or heated above their melting point and cooled show significant premelt and melt shifts. Melts are also correlated with phase transitions observed by Differential Scanning Calorimetry (DSC). Activation energies attributed to charging in the premelt for amino acids were typically 250 J/mole.     

Concurrent esterification and N-acetylation of amino acids with orthoesters: A useful reaction with interesting mechanistic implications

The concurrent esterification and N-acetylation of amino acids has been studied with triethyl orthoacetate (TEOA) and triethyl orthoformate (TEOF). In a surprising finding, only 1 equiv of TEOA in refluxing toluene was necessary to convert l-proline and l-phenylalanine into the corresponding N-acetyl ethyl esters in good yield. The same transformation using TEOF was not effective. Stereochemical outcome and stoichiometric studies as well as structural variation of the amino acids in this reaction provided unexpected mechanistic insight.     

Gas chromatography of amino acids: Use of a fused-silica capillary column in the determination of plasma amino acids

A capillary chromatographic procedure using a fused silica column is described which can be used to quantitatively determine amino acids in plasma following the pre-chromatographic “clean-up” described in a recent paper [1]. In substituting this procedure for that involving a packed column, advantage has been taken of the greater resolving power to separate amino acids from background component peaks. In order to extend this advantage and provide a sound basis for quantitative analysis, the technique of cold on-column injection was employed. As a result, good precision of standard analysis was obtained with relative standard deviation (RSD) values for all amino acids of less than 4%. Application of the entire procedure to plasma samples yields RSD values of better than 10% for all amino acids with recoveries ranging from 72% to 104%. Simultaneous determination of plasma amino acid levels by gas chromatography (GC) using capillary columns and by classical ion exchange (CIE) showed reasonable agreement. Statistical evaluation showed no significant difference between twelve amino acids. Values for the remaining two, namely, phenylalanine and histidine are significantly different (p < 0.005). Comparison of the values obtained from GC capillary and packed columns reveals no significant difference between fourteen amino acids. Significant differences exist between results for phenylalanine and tyrosine (p < 0.001). It is concluded that there is good agreement between data obtained by GC capillary and CIE techniques and that differences between results for phenylalanine and histidine are method related.     

Radiolytic degradation of 4-nitrophenol in aqueous solutions: Pulse and steady state radiolysis study

The radiation induced degradation of 4-nitrophenol (4-NP) has been studied by gamma irradiation, while the reactivity and spectral features of the short lived transients formed by reaction with primary transient radicals at different pHs has been investigated by pulse radiolysis technique. In steady state radiolysis a dose of 4.4 k Gy is able to degrade 98% of 1×10⁻⁴ mol dm⁻³ 4-NP. 4-NP has pK_a at 7.1, above which it is present in the anionic form. At pH 5.2, ^•OH and N₃^• radicals were found to react with 4-NP with rate constants of 4.1×10⁹ dm³ mol⁻¹ s⁻¹ and 2.8×10⁸ dm³ mol⁻¹ s⁻¹, respectively. Differences in the absorption spectra of species formed in the reactions of 4-NP with ^•OH and N₃^• radicals suggested that ^•OH radicals add to the aromatic ring of 4-NP along with electron transfer reaction, whereas N₃^• radicals undergo only electron transfer reaction. At pH 9.2, rate constants for the reaction of ^•OH radicals with 4-NP was found to be higher by a factor of 2 compared to that at pH 5.2. This has been assigned to the deprotonation of 4-NP at pH 9.2.     

Positron annihilation in amino acids

Positron lifetime measurements were performed on eight different amino acids, τ₁, τ₂ and I₂ values were observed at around 0.35 nsec, 0.7–1.2 nsec and 20–30%, respectively. The long-lived component seems to be produced by positronium states trapped in the crystalline lattice or by positronium atoms bound to molecules.     

Coordination chemistry of phosphanyl amino acids: solid state and solution structures of neutral and cationic rhodium complexes

Copper phosphide or arsenide complexes, [Cu(EPh(2))(neo)] (E = P, As, neo = 2,9-dimethyl-1,10-phenanthroline; trivial name: neocuprine) react selectively with the N-protected brominated serine derivatives, 2-(S)-(alkoxycarbonylamino)-3-bromomethylpropionates ((ROCO)SerBr, : R = PhCH(2), : tBu, : Me) to give the corresponding phosphanylated or arsanylated amino acids, (ROCO)SerPhos (: Phos = PPh(2)) and (Z)SerArs (Ars = AsPh(2), Z = PhCH(2)OCO). The dipeptide (Z)AlaSerPhos was likewise prepared. The phosphanes , and the arsane reacted cleanly with [Rh(2)(micro-Cl)(2)(cod)(2)] to give the rhodium(I) complexes [RhCl(cod)((Z)SerPhos)] , [RhCl(cod)((Boc)SerPhos)] (Boc = tBuOCO), [RhCl(cod)((Z)AlaSerPhos)] , and [RhCl(cod)((Z)SerArs)] which were characterized by X-ray diffraction studies. A common structural feature is an intramolecular (N)H[dot dot dot]Cl(Rh)-hydrogen bridge which according to NMR investigations remains intact in solution. The abstraction of chloride from the coordination sphere of Rh(I) in or has a profound structural impact. While in and , the ligands bind in a monodentate fashion, via the phosphorus atom only, they serve as bidentate ligands via the phosphorus centre and the peptidic C=O group in [Rh(cod)(kappa(2)-(Z)SerPhos)]PF(6) and [Rh(cod)(kappa(2)-(Z)AlaSerPhos)]PF(6). This causes also the amino acid residue structures to change from alpha-helix type in and to a beta-sheet type in both. Addition of chloride to and fully re-establishes the structures of both. The complexes [RhCl(cod)((Z)SerPhos)] and [RhCl(cod)((Boc)SerPhos)] show good activities in homogeneously catalyzed hydrogenations of olefins while the dipeptide complex is less active. Phosphane addition to greatly diminishes the catalytic activity. The cationic complex [Rh(cod)(kappa(2)-(Z)AlaSerPhos)]PF(6) shows low activity which, however, is greatly increased by addition of one equivalent of phosphane.