Mechanism of the Tyrosine Ammonia Lyase Reaction—Tandem Nucleophilic and Electrophilic Enhancement by a Proton Transfer

Quantum mechanics/molecular mechanics calculations in tyrosine ammonia lyase (TAL) ruled out the hypothetical Friedel–Crafts (FC) route for ammonia elimination from L ‐tyrosine due to the high energy of FC intermediates. The calculated pathway from the zwitterionic L ‐tyrosine‐binding state (0.0 kcal mol^?1) to the product‐binding state ((E)‐coumarate+H₂N? MIO; ?24.0 kcal mol^?1; MIO=3,5‐dihydro‐5‐methylidene‐4H‐imidazol‐4‐one) involves an intermediate (IS, ?19.9 kcal mol^?1), which has a covalent bond between the N atom of the substrate and MIO, as well as two transition states (TS1 and TS2). TS1 (14.4 kcal mol^?1) corresponds to a proton transfer from the substrate to the N1 atom of MIO by Tyr300? OH. Thus, a tandem nucleophilic activation of the substrate and electrophilic activation of MIO happens. TS2 (5.2 kcal mol^?1) indicates a concerted C? N bond breaking of the N‐MIO intermediate and deprotonation of the pro‐S β position by Tyr60. Calculations elucidate the role of enzymic bases (Tyr60 and Tyr300) and other catalytically relevant residues (Asn203, Arg303, and Asn333, Asn435), which are fully conserved in the amino acid sequences and in 3D structures of all known MIO‐containing ammonia lyases and 2,3‐aminomutases.     

Mechanistic Investigation of Phenylalanine Ammonia Lyase by Using N‐Methylated Phenylalanines

N‐Methyl‐L ‐phenylalanine ( 5 ), N‐methyl‐4‐nitro‐L ‐phenylalanine ( 6 ), and N,N‐dimethyl‐4‐nitro‐L ‐phenylalanine ( 7 ?H⁺) were investigated as substrates or inhibitors of phenylalanine ammonia lyase from Petroselinum crispum. Whereas the former was a reluctant substrate (K_m =6.6 mM , k_cat =0.22 s^?1), no reverse reaction could be detected by using methylamine and (E)‐cinnamate ( 2 ). The K_m value for ammonia in the reverse reaction by using (E)‐cinnamate ( 2 ) was determined to be 4.4 and 2.6M at pH 8.8 and 10, respectively. The N‐methylated 4‐nitro‐L ‐phenylalanines 6 and 7 showed only strong inhibitory effects (K_i =130 nM and 8 nM , resp.). These and former results are discussed in terms of the mechanism of action of phenyalalanine and histidine ammonia lyases.     

Synthesis of D‐ and L‐Phenylalanine Derivatives by Phenylalanine Ammonia Lyases: A Multienzymatic Cascade Process

The synthesis of substituted D ‐phenylalanines in high yield and excellent optical purity, starting from inexpensive cinnamic acids, has been achieved with a novel one‐pot approach by coupling phenylalanine ammonia lyase (PAL) amination with a chemoenzymatic deracemization (based on stereoselective oxidation and nonselective reduction). A simple high‐throughput solid‐phase screening method has also been developed to identify PALs with higher rates of formation of non‐natural D ‐phenylalanines. The best variants were exploited in the chemoenzymatic cascade, thus increasing the yield and ee value of the D ‐configured product. Furthermore, the system was extended to the preparation of those L ‐phenylalanines which are obtained with a low ee value using PAL amination.     

Simple Synthesis of Ruthenium π Complexes of Aromatic Amino Acids and Small Peptides

The interaction of [Ru(η⁶‐C₁₀H₈)(Cp)]⁺ (Cp=C₅H₅) with aromatic amino acids (L ‐phenylalanine, L ‐tyrosine, L ‐tryptophane, D ‐phenylglycine, and L ‐threo‐3‐phenylserine) under visible‐light irradiation gives the corresponding [Ru(η⁶‐amino acid)(Cp)]⁺ complexes in near‐quantitative yield. The reaction proceeds in air at room temperature in water and tolerates the presence of non‐aromatic amino acids (except those which are sulfur containing), monosaccharides, and nucleotides. The complex [Ru(η⁶‐C₁₀H₈)(Cp)]⁺ was also used for selective labeling of Tyr and Phe residues of small peptides, namely, angiotensin I and II derivatives.     

Investigation on thermoresponsive behavior of biodegradable poly(γ‐glutamic acid)‐graft‐L‐phenylalanine ethyl ester

The thermosensitivity of biodegradable and non‐toxic amphiphilic polymer derived from a naturally occurring polypeptide and a derivative of amino acid was first reported. The amphiphilic polymer consisted of poly(γ‐glutamic acid) (γ‐PGA) as a hydrophilic backbone, and L ‐phenylalanine ethyl ester (L ‐PAE) as a hydrophobic branch. Poly(γ‐glutamic acid)‐graft‐L ‐phenylalanine (γ‐PGA‐graft‐L ‐PAE) with grafting degrees of 7–49% were prepared by varying the content of a water‐soluble carbodiimide (WSC). γ‐PGA‐graft‐L ‐PAE with a grafting degree of 49% exhibited thermoresponsive phase transition behavior in an aqueous solution at around 80°C. The copolymers with grafting degrees in the range of 30–49% showed thermoresponsive properties in NaCl solution. A clouding temperature (T_cloud) could be adjusted by changing the polymer concentration and/or NaCl concentration. The thermoresponsive behavior was reversible. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Further Insight into the Mechanism of the Irreversible Inhibition of Histidine Ammonia‐Lyase by L‐Cysteine and Dioxygen

Histidine ammonia‐lyase (HAL) was irreversibly inhibited by L ‐cysteine at pH 10.5 under aerobic conditions. The inhibited enzyme, still in its intact conformation, showed an absorption maximum at 338 nm. Upon denaturation, followed by pronase digestion, two main chromophoric products 1 and 2 (Figs. 4 and 5, resp.) could be isolated with absorption maxima at 335 and 332 nm, respectively. As determined by MALDI‐TOF mass spectrometry and ¹H‐NMR spectroscopy, in product 1 one of the methylidene H‐atoms of the 3,5‐dihydro‐5‐methylidene‐4H‐imidazol‐4‐one (formerly called 4‐methylideneimidazol‐5‐one; MIO) prosthetic group was substituted by one of the amino groups of L ‐ cystine, while in product 2 the ε‐amino group of L ‐lysine was the analogous substituent. Acid‐catalyzed hydrolysis of product 1 gave compound 3 whose chromophore (λ_max 310 nm) was that of 3,5‐dihydro‐5‐(4‐hydroxymethylidene)‐4H‐imidazol‐4‐one, i.e., of a vinylogous acid. These results support our previous proposal that, in the first step, the L ‐cysteine S‐atom attacks the prosthetic electrophile (Scheme 2). The resulting nucleophilic enolate captures O₂ to form a peroxide. On the basis of the present results, we postulate that the observed products 1 – 3 arise from a vinylogous thioester 4 , which is formed in the conformationally intact inhibited enzyme by an electrocyclic reaction eliminating H₂O₂.     

Amino Acid Ionic Liquids as Chiral Ligands in Ligand‐Exchange Chiral Separations

Recently, amino acid ionic liquids (AAILs) have attracted much research interest. In this paper, we present the first application of AAILs in chiral separation based on the chiral ligand exchange principle. By using 1‐alkyl‐3‐methylimidazolium L ‐proline (L ‐Pro) as a chiral ligand coordinated with copper(II), four pairs of underivatized amino acid enantiomers—dl ‐phenylalanine (dl ‐Phe), dl ‐histidine (dl ‐His), dl ‐tryptophane (dl ‐Trp), and dl ‐tyrosine (dl ‐Tyr)—were successfully separated in two major chiral separation techniques, HPLC and capillary electrophoresis (CE), with higher enantioselectivity than conventionally used amino acid ligands (resolution (R_s)=3.26–10.81 for HPLC; R_s=1.34–4.27 for CE). Interestingly, increasing the alkyl chain length of the AAIL cation remarkably enhanced the enantioselectivity. It was inferred that the alkylmethylimidazolium cations and L ‐Pro form ion pairs on the surface of the stationary phase or on the inner surface of the capillary. The ternary copper complexes with L ‐Pro are consequently attached to the support surface, thus inducing an ion‐exchange type of retention for the dl ‐enantiomers. Therefore, the AAIL cation plays an essential role in the separation. This work demonstrates that AAILs are good alternatives to conventional amino acid ligands for ligand‐exchange‐based chiral separation. It also reveals the tremendous application potential of this new type of task‐specific ILs.     

Pendant structure governed anion sensing property for sulfonamide‐functionalized poly(phenylacetylene)s bearing various α‐amino acids

The colorimetric detection of anionic species has been studied for α‐amino acid‐conjugated poly(phenylacetylene)s, which were prepared by the polymerization of the ethyl esters of N‐(4‐ethynylphenylsulfonyl)‐L ‐alanine, L ‐isoleucine, L ‐valine, L ‐phenylalanine, L ‐aspartic acid, and L ‐glutamic acid using Rh⁺(2,5‐norbornadiene)[(η⁶‐C₆H₅)B^?(C₆H₅)₃] as the catalyst in CHCl₃. The one‐handed helical conformations of all the sulfonamide‐functionalized polymers were characterized by Cotton effects in the circular dichroism spectra. The addition of anions with a relatively high basicity, such as tetra‐n‐butylammonium acetate and fluoride, induced drastic changes in both the optical and chiroptical properties. On the other hand, anions with a relatively low basicity, such as tetra‐n‐butylammonium nitrate, azide, and bromide, had essentially no effects on the helical conformation of all the sulfonamide‐functionalized polymers. The anion signaling property of the sulfonamide‐functionalized polymers possessing α‐amino acid moieties was significantly affected by the installed residual amino acid structures. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 1683–1689, 2010     

1,1′‐Dimethylvanadocene α‐amino acid complexes: synthesis,characterization and antimicrobial behavior toward Escherichia coli B

Eight water‐soluble 1,1′‐dimethylvanadocene amino acid complexes have been prepared via the reaction of (MeCp)₂VCl₂ ( 2 ) with one equivalent of amino acid (aa) in water affording [(MeCp)₂V( aa )]Cl, where aa is glycine ( 3 ), L ‐alanine ( 4 ), L ‐valine ( 5 ), L ‐leucine ( 6 ), L ‐isoleucine ( 7 ), L ‐phenylalanine ( 8 ), L ‐histidine ( 9 ) and L ‐tryptophane ( 10 ). All prepared complexes have been characterized by EPR, IR and Raman spectroscopy, elemental analysis and mass spectrometry. Molecular structures of [(MeCp)₂V(ala)]BPh₄·CH₃OH ( 11 ), [(MeCp)₂V(leu)]PF₆ ( 12 ) and [(MeCp)₂V(ile)]PF₆ ( 13 ) were determined by X‐ray diffraction analysis. Cytotoxic properties of complexes 2–10 were investigated toward Escherichia coli B and compared with analogical unsubstituted vanadocene compounds ( 1, 14–21 ). The results showed that 1,1′‐dimethylvanadocene amino acid complexes have identical or slightly higher antiproliferative activity then their unsubstituted analogs. Copyright © 2006 John Wiley & Sons, Ltd.     

Modeling the retention mechanism for high‐performance liquid chromatography with a chiral ligand mobile phase and enantioseparation of mandelic acid derivatives

The chromatographic retention mechanism describing relationship between retention factor and concentration of Cu²⁺(l ‐phenylalanine)₂ using chiral ligand mobile phase was investigated and eight mandelic acid derivatives were enantioseparated by chiral ligand exchange chromatography. The relationship between retention factor and concentration of the Cu²⁺(l ‐phenylalanine)₂ complex was proven to be in conformity with chromatographic retention mechanism in which chiral discrimination occurred both in mobile and stationary phase. Different copper(II) salts, chiral ligands, organic modifier, pH of aqueous phase, and conventional temperature on retention behavior were optimized. Eight racemates were successfully enantioseparated on a common reversed‐phase column with an optimized mobile phase composed of 6 mmol/L of l ‐phenylalanine or N,N‐dimethyl‐l ‐phenylalanine and 3 mmol/Lof copper(II) acetate or copper(II) sulfate aqueous solution and methanol.     

Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases

Aromatic amino acid ammonia-lyases catalyze the deamination of L-His, L-Phe, and L-Tyr, yielding ammonia plus aryl acids bearing an alpha,beta-unsaturated propenoic acid. We report crystallographic analyses of unliganded Rhodobacter sphaeroides tyrosine ammonia-lyase (RsTAL) and RsTAL bound to p-coumarate and caffeate. His 89 of RsTAL forms a hydrogen bond with the p-hydroxyl moieties of coumarate and caffeate. His 89 is conserved in TALs but replaced in phenylalanine ammonia-lyases (PALs) and histidine ammonia-lyases (HALs). Substitution of His 89 by Phe, a characteristic residue of PALs, yields a mutant with a switch in kinetic preference from L-Tyr to L-Phe. Structures of the H89F mutant in complex with the PAL product, cinnamate, or the PAL-specific inhibitor, 2-aminoindan-2-phosphonate (AIP), support the role of position 89 as a specificity determinant in the family of aromatic amino acid ammonia-lyases and aminomutases responsible for beta-amino acid biosynthesis.     

Cascade Biocatalysis for Sustainable Asymmetric Synthesis: From Biobased l‐Phenylalanine to High‐Value Chiral Chemicals

Sustainable synthesis of useful and valuable chiral fine chemicals from renewable feedstocks is highly desirable but remains challenging. Reported herein is a designed and engineered set of unique non‐natural biocatalytic cascades to achieve the asymmetric synthesis of chiral epoxide, diols, hydroxy acid, and amino acid in high yield and with excellent ee values from the easily available biobased l ‐phenylalanine. Each of the cascades was efficiently performed in one pot by using the cells of a single recombinant strain over‐expressing 4–10 different enzymes. The cascade biocatalysis approach is promising for upgrading biobased bulk chemicals to high‐value chiral chemicals. In addition, combining the non‐natural enzyme cascades with the natural metabolic pathway of the host strain enabled the fermentative production of the chiral fine chemicals from glucose.     

The Polymorphs of L‐Phenylalanine

The solid‐state structure of the amino acid phenylalanine (Phe) offers a potential key to understanding the behavior of a large class of important aromatic compounds. Obtaining good single crystals is, however, notoriously difficult. The structure of the common polymorph of Phe, form I, was first reported by Weissbuch et al. (as D ‐Phe) in 1990, but the correctness of the published C2 unit cell with two disordered molecules in the asymmetric unit was later questioned and other space groups suggested. The identity of form I of L ‐Phe is here established to be P2₁ with Z′=4, based on data from a well‐diffracting single crystal grown from an acetic acid solution of the amino acid. A second new polymorph, form IV, together with the two recently described forms II and III provide unprecedented information on the structural complexity of this essential amino acid. It is furthermore documented that the racemate, dl ‐Phe, does not grow proper single crystals.     

Ester Carbonyl Vibration as a Sensitive Probe of Protein Local Electric Field

The ability to quantify the local electrostatic environment of proteins and protein/peptide assemblies is key to gaining a microscopic understanding of many biological interactions and processes. Herein, we show that the ester carbonyl stretching vibration of two non‐natural amino acids, L ‐aspartic acid 4‐methyl ester and L ‐glutamic acid 5‐methyl ester, is a convenient and sensitive probe in this regard, since its frequency correlates linearly with the local electrostatic field for both hydrogen‐bonding and non‐hydrogen‐bonding environments. We expect that the resultant frequency–electric‐field map will find use in various applications. Furthermore, we show that, when situated in a non‐hydrogen‐bonding environment, this probe can also be used to measure the local dielectric constant (ε). For example, its application to amyloid fibrils formed by Aβ_16–22 revealed that the interior of such β‐sheet assemblies has an ε value of approximately 5.6.     

Synthesis of polypeptides from activated urethane derivatives of α‐amino acids

A series of activated urethane‐type derivatives of α‐amino acids were synthesized and applied to polypeptide synthesis. The urethane used herein, N‐(4‐nitrophenoxycarbonyl)‐α‐amino acids 1 , were synthesized by N‐carbamoylation of γ‐benzyl‐L ‐glutamate, β‐benzyl‐L ‐aspartate, L ‐leucine, L ‐phenylalanine, and L ‐proline, with 4‐nitrophenyl chloroformate. When 1 was dissolved in N,N‐dimethylacetamide (DMAc) and heated at 60 °C, it was smoothly converted into the corresponding polypeptides with releasing 4‐nitrophenol and carbon dioxide. Spectroscopic analyses of the obtained polypeptides revealed that they were comparable with the authentic polypeptides synthesized by the ring‐opening polymerizations of amino acid N‐carboxyanhydrides (NCAs). Besides the successful polycondensations of a series of 1 , their polycondensations of 1a and other 1 were also successfully carried out to obtain the corresponding statistic copolypeptides. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2525–2535, 2008     

Zn( L‐proline)2 as a powerful and reusable organometallic catalyst for the very fast synthesis of 2‐amino‐4H‐benzo[g]chromene derivatives under solvent‐free conditions

An efficient route for the synthesis of 2‐amino‐4H‐benzo[g]chromenes via a three‐component coupling reaction of aldehydes, malononitrile and 2‐hydroxy‐1,4‐naphthaquinone in the presence of Zn( L ‐proline)₂ is reported. High yields, short reaction times, non‐toxicity and recyclability of the catalyst, and easy work‐up are the main merits of this protocol. Copyright © 2015 John Wiley & Sons, Ltd.     

Molecular aggregation in selected crystalline 1:1 complexes of hydrophobic d‐ and l‐amino acids. IV. The l‐phenylalanine series

The amino acid l ‐phenylalanine has been cocrystallized with d ‐2‐aminobutyric acid, C₉H₁₁NO₂·C₄H₉NO₂, d ‐norvaline, C₉H₁₁NO₂·C₅H₁₁NO₂, and d ‐methionine, C₉H₁₁NO₂·C₅H₁₁NO₂S, with linear side chains, as well as with d ‐leucine, C₉H₁₁NO₂·C₆H₁₃NO₂, d ‐isoleucine, C₉H₁₁NO₂·C₆H₁₃NO₂, and d ‐allo‐isoleucine, C₉H₁₁NO₂·C₆H₁₃NO₂, with branched side chains. The structures of these 1:1 complexes fall into two classes based on the observed hydrogen‐bonding pattern. From a comparison with other l :d complexes involving hydrophobic amino acids and regular racemates, it is shown that the structure‐directing properties of phenylalanine closely parallel those of valine and isoleucine but not those of leucine, which shares side‐chain branching at C^γ with phenylalanine and is normally considered to be the most closely related non‐aromatic amino acid.     

Biosynthesis of the N–N‐Bond‐Containing Compound l‐Alanosine

The formation of a N?N bond is a unique biochemical transformation, and nature employs diverse biosynthetic strategies to activate nitrogen for bond formation. Among molecules that contain a N?N bond, biosynthetic routes to diazeniumdiolates remain enigmatic. We here report the biosynthetic pathway for the diazeniumdiolate‐containing amino acid l ‐alanosine. Our work reveals that the two nitrogen atoms in the diazeniumdiolate of l ‐alanosine arise from glutamic acid and aspartic acid, and we clarify the early steps of the biosynthetic pathway by using both in vitro and in vivo approaches. Our work demonstrates a peptidyl‐carrier‐protein‐based mechanism for activation of the precursor l ‐diaminopropionate, and we also show that nitric oxide can participate in non‐enzymatic diazeniumdiolate formation. Furthermore, we demonstrate that the gene alnA, which encodes a fusion protein with an N‐terminal cupin domain and a C‐terminal AraC‐like DNA‐binding domain, is required for alanosine biosynthesis.     

Ring‐opening metathesis polymerization of amino acid‐functionalized norbornene derivatives

Amino acid‐derived novel norbornene derivatives, N,N′‐(endo‐bicyclo[2.2.1] hept‐5‐en‐2,3‐diyldicarbonyl) bis‐L ‐alanine methyl ester (NBA), N,N′‐(endo‐bicyclo[2.2.1]hept‐5‐en‐2,3‐diyldicarbonyl) bis‐L ‐leucine methyl ester (NBL), N,N′‐(endo‐bicyclo[2.2.1]hept‐5‐en‐2,3‐diyldicarbonyl) bis‐L ‐phenylalanine methyl ester (NBF) were synthesized and polymerized using the Grubbs 2nd generation ruthenium (Ru) catalyst. Although NBA, NBL, and NBF did not undergo homopolymerization, they underwent copolymerization with norbornene (NB) to give the copolymers with M_n ranging from 5200 to 38,100. The maximum incorporation ratio of the amino acid‐based unit was 9%, and the cis contents of the main chain were 54–66%. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5337–5343, 2006