18875-39-3Relevant articles and documents
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Borders,D.B. et al.
, p. 3123 - 3133 (1970)
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New insights into the palladium-mediated selective hydrolysis of the His18-Thr19 peptide bond in cytochrome c: 1H NMR and density functional theory investigation for model compounds
Sun, Xiao-Juan,Zhang, Lin,Zhang, Yu,Yang, Gao-Sheng,Guo, Zi-Jian,Zhu, Long-Gen
, p. 818 - 822 (2003)
The peptides, CH3CO-Met-His-GlyH, CH3CO-CysMe-His-GlyH, CH3CO-CysMe-His-Gly-OEt and its imidazole derivatives, Nτ-benzyl, Nτ-tosyl, N-benzyl-Nπ-phenacyl, have been synthesized and used as model compounds for the mechanistic study of the selective cleavage of cytochrome c promoted by Pd(II) complexes. The peptide bond cleavage of these substrates by cis-[Pd(en)(solvent)2]2+ (solvent: D2O or CD3OD) was monitored by 1H NMR spectroscopy. The results showed that the methionine-containing tripeptide differs from the S-methylcysteine-containing tripeptides in the mode of coordination to Pd(II). The former coordinates to Pd(II) through a sulfur atom, an amide nitrogen of methionine and an Nπ atom of imidazole, forming a polycyclic chelate, and is resistant to hydrolysis. The latter, as a model compound for cleavage of the His18-Thr19 bond in cytochrome c with Pd(II) complexes, coordinates to Pd(II) via a sulfur atom, an amide nitrogen and a carbonyl oxygen of histidine to form a polycyclic chelate in which the His-Gly peptide bond is cleaved. Kinetic studies showed that protonation of the Nπ atom of imidazole in the S-methylcysteine-containing tripeptides is one of the key factors in controlling the cleavage of the His-Gly bond. In order to obtain theoretical guidance on the cleavage reaction, the geometries of a representative Nπ protonated tripeptide cation of CH3CO-CysMe-His-GlyNMe and its Pd(II) complex with and without ancillary water molecules are optimized at the B3LYP density functional theory level using 3-21G, 6-31G(d) and LanL2DZ basis sets. Based on the experimental and theoretical results obtained from the model compounds, a mechanism is proposed for the first time to explain the nature of selective cleavage of the His18-Thr19 bond in cytochrome c promoted by Pd(II) complexes. Coordination of Pd(II) to the carbonyl oxygen of histidine and hydrogen bond formed between the C=O and ancillary dimer water weaken and polarize the C=O double bond of histidine, giving rise to cleavage of the peptide bond.
Kinetics and mechanism of base hydrolysis of a-aminoacid esters catalysed by [pd(1,3-diamino-2-hydroxypropane)(H2O)2]2+ complex
Al-Qalaf,Al Bassam,Shoukry
, p. 1706 - 1708 (2013)
Amino acid esters (L) react with [Pd(DHP(H2O)2] 2+ , (DHP = 1,3-diamino-2-hydroxopropane) giving mixed ligand [Pd(DHP)L]2+ The kinetics of hydrolysis of [Pd(DHP)L]2+ have been studied by pH-stat technique and rate constants were obtained. Rate acceleration observed for glycine methyl ester is high. The effect with methionine methyl ester and histidine methyl ester are much less marked, as the mixed-ligand complexes with these ligands do not involve alkoxycarbonyl donors. Possible mechanisms for these reactions are considered. Activation parameters have been determined for glycine methyl ester.
Abiotic asparagine formation from simple amino acids by contact glow discharge electrolysis
Munegumi, Toratane,Shimoyama, Akira,Harada, Kaoru
, p. 393 - 394 (1997)
Asparagine, one of the most important amino acids for prebiotic peptide formation in aqueous media, was formed using Contact Glow Discharge Electrolysis (CGDE) against aqueous solutions containing simple amino acids and carboxylic acid amides.
Glycine enolates: The effect of formation of iminium ions to simple ketones on α-amino carbon acidity and a comparison with pyridoxal iminium ions
Crugeiras, Juan,Rios, Ana,Riveiros, Enrique,Amyes, Tina L.,Richard, John P.
, p. 2041 - 2050 (2008)
Equilibrium constants in D2O were determined by 1H NMR analyses for formation of imines/iminium ions from addition of glycine methyl ester to acetone and from addition of glycine to phenylglyoxylate. First-order rate constants, also determined by 1H NMR, are reported for deuterium exchange between solvent D2O and the α-amino carbon of glycine methyl ester and glycine in the presence of increasing concentrations of ketone and Bronsted bases. These rate and equilibrium data were used to calculate second-order rate constants for deprotonation by DO- and by Bronsted bases of the α-imino carbon of the ketone adducts. Formation of the iminium ion between acetone and glycine methyl ester and between phenylglyoxylate and glycine is estimated to cause 7 unit and 15 unit decreases, respectively, in the pKa's of 21 and 29 for deprotonation of the parent carbon acids. The effect of formation of iminium ions to phenylglyoxylate and to 5′-deoxypyridoxal (DPL) [Toth, K.; Richard, J. P. J. Am. Chem. Soc. 2007, 129, 3013-3021] on the carbon acidity of glycine is similar. However, DPL is a much better catalyst than phenylglyoxylate of deprotonation of glycine, because of the exceptionally large thermodynamic driving force for conversion of the amino acid and DPL to the reactive iminium ion.
Hasselstrom et al.
, p. 350 (1957)
Mechanism of pH-dependent photolysis of aliphatic amino acids and enantiomeric enrichment of racemic leucine by circularly polarized light.
Nishino,Kosaka,Hembury,Shitomi,Onuki,Inoue
, p. 921 - 924 (2001)
It has been proposed that the origin of biological homochirality may be the result of irradiation of a racemic sample of amino acids by circularly polarized light (CPL). To determine the mechanism of enantiomeric enrichment, the irradiation of aliphatic amino acids by CPL was undertaken. An enantiomerically enriched sample (e.g., L isomer enrichment from r-CPL) was found to result from the preferential excitation/decomposition of one enantiomer over another via a Norrish Type II mechanism (leucine, valine, and isoleucine), with the enantiomeric excess dependent on the degree of protonation of the amino/carboxylic acid moiety.
Metzler et al.
, p. 2786 (1953)
The structure of the proline utilization a proline dehydrogenase domain inactivated by N-propargylglycine provides insight into conformational changes induced by substrate binding and flavin reduction
Srivastava, Dhiraj,Zhu, Weidong,Johnson Jr., William H.,Whitman, Christian P.,Becker, Donald F.,Tanner, John J.
, p. 560 - 569 (2010)
Proline utilization A (PutA) from Escherichia coli is a flavoprotein that has mutually exclusive roles as a transcriptional repressor of the put regulon and a membrane-associated enzyme that catalyzes the oxidation of proline to glutamate. Previous studies have shown that the binding of proline in the proline dehydrogenase (PRODH) active site and subsequent reduction of the FAD trigger global conformational changes that enhance PutA-membrane affinity. These events cause PutA to switch from its repressor to its enzymatic role, but the mechanism by which this signal is propagated from the active site to the distal membrane-binding domain is largely unknown. Here, it is shown that N-propargylglycine irreversibly inactivates PutA by covalently linking the flavin N(5) atom to the ε-amino of Lys329. Furthermore, inactivation locks PutA into a conformation that may mimic the proline-reduced, membrane-associated form. The 2.15A resolution structure of the inactivated PRODH domain suggests that the initial events involved in broadcasting the reduced flavin state to the distal membrane-binding domain include major reorganization of the flavin ribityl chain, severe (35°) butterfly bending of the isoalloxazine ring, and disruption of an electrostatic network involving the flavin N(5) atom, Arg431, and Asp370. The structure also provides information about conformational changes associated with substrate binding. This analysis suggests that the active site is incompletely assembled in the absence of the substrate, and the binding of proline draws together conserved residues in helix 8 and the β1-αl loop to complete the active site. 2009 American Chemical Society.
Zn(ii) complex for selective and rapid scission of protein backbone
Yashiro, Morio,Kawakami, Yukiko,Taya, Jun-Ichi,Arai, Suguru,Fujii, Yuki
, p. 1544 - 1546 (2009)
A ZnII complex with an aldehyde group hydrolyzed porcine pancreatic elastase under mild conditions, pH 8.0, 50 °C, by the Schiff base formation between the ZnII complex and the NH2 group in the protein, suggesting that a ZnII compound can be active toward peptide hydrolysis when it strongly binds to the substrate.
Degradation of the Amadori compound N-(1-deoxy-d-fructos-1-yl)glycine in aqueous model systems
Davidek, Tomas,Clety, Nathalie,Aubin, Sandra,Blank, Imre
, p. 5472 - 5479 (2002)
The fate of the Amadori compound N-(1-deoxy-D-fructos-1-yl)glycine (DFG) was studied in aqueous model systems as a function of time and pH. The samples were reacted at 90 °C for up to 7 h while maintaining the pH constant at 5, 6, 7, or 8. Special attenti
Structures and reactivity of synthetic zinc(II) complexes resembling the active sites and reaction intermediates of aminopeptidases
Rivas, Juan C. Mareque,Salvagni, Emiliano,Parsons, Simon
, p. 460 - 461 (2004)
Herein we report the first crystallographic characterization and hydrolysis of a synthetic zinc(II) complex that resembles the active site and reaction intermediates proposed for aminopeptidases.
Spicamycin, a new differentiation inducer of mouse myeloid leukemia cells (M1) and human promyelocytic leukemia cells (HL- 60)
Hayakawa,Nakagawa,Kawai,et al.
, p. 2685 - 2691 (1985)
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Welter et al.
, p. 1385 (1978)
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Studies on the synthesis and stability of α-ketoacyl peptides
Sajapin, Johann,Hellwig, Michael
, p. 1425 - 1438 (2020)
Oxidative stress, an excess of reactive oxygen species (ROS), may lead to oxidative post-translational modifications of proteins resulting in the cleavage of the peptide backbone, known as α-amidation, and formation of fragments such as peptide amides and α-ketoacyl peptides (α-KaP). In this study, we first compared different approaches for the synthesis of different model α-KaP and then investigated their stability compared to the corresponding unmodified peptides. The stability of peptides was studied at room temperature or at temperatures relevant for food processing (100?°C for cooking and 150?°C as a simulation of roasting) in water, in 1% (m/v) acetic acid or as the dry substance (to simulate the thermal treatment of dehydration processes) by HPLC analysis. Oxidation of peptides by 2,5-di-tert-butyl-1,4-benzoquinone (DTBBQ) proved to be the most suited method for synthesis of α-KaPs. The acyl side chain of the carbonyl-terminal α-keto acid has a crucial impact on the stability of α-KaPs. This carbonyl group has a catalytic effect on the hydrolysis of the neighboring peptide bond, leading to the release of α-keto acids. Unmodified peptides were significantly more stable than the corresponding α-KaPs. The possibility of further degradation reactions was shown by the formation of Schiff bases from glyoxylic or pyruvic acids with glycine and proven through detection of transamination products and Strecker aldehydes of α-keto acids by HPLC–MS/MS. We propose here a mechanism for the decomposition of α-ketoacyl peptides.
Reactivity of Dimeric Tetrazirconium(IV) Wells-Dawson Polyoxometalate toward Dipeptide Hydrolysis Studied by a Combined Experimental and Density Functional Theory Approach
Ly, Hong Giang T.,Mihaylov, Tzvetan,Absillis, Gregory,Pierloot, Kristine,Parac-Vogt, Tatjana N.
, p. 11477 - 11492 (2015)
Detailed kinetic studies on the hydrolysis of glycylglycine (Gly-Gly) in the presence of the dimeric tetrazirconium(IV)-substituted Wells-Dawson-type polyoxometalate Na14[Zr4(P2W16O59)2(μ3-O)2(OH)2(H2O)4]·57H2O (1) were performed by a combination of 1H, 13C, and 31P NMR spectroscopies. The catalyst was shown to be stable under a broad range of reaction conditions. The effect of pD on the hydrolysis of Gly-Gly showed a bell-shaped profile with the fastest hydrolysis observed at pD 7.4. The observed rate constant for the hydrolysis of Gly-Gly at pD 7.4 and 60 °C was 4.67 × 10-7 s-1, representing a significant acceleration as compared to the uncatalyzed reaction. 13C NMR data were indicative for coordination of Gly-Gly to 1 via its amide oxygen and amine nitrogen atoms, resulting in a hydrolytically active complex. Importantly, the effective hydrolysis of a series of Gly-X dipeptides with different X side chain amino acids in the presence of 1 was achieved, and the observed rate constant was shown to be dependent on the volume, chemical nature, and charge of the X amino acid side chain. To give a mechanistic explanation of the observed catalytic hydrolysis of Gly-Gly, a detailed quantum-chemical study was performed. The theoretical results confirmed the nature of the experimentally suggested binding mode in the hydrolytically active complex formed between Gly-Gly and 1. To elucidate the role of 1 in the hydrolytic process, both the uncatalyzed and the polyoxometalate-catalyzed reactions were examined. In the rate-determining step of the uncatalyzed Gly-Gly hydrolysis, a carboxylic oxygen atom abstracts a proton from a solvent water molecule and the nascent OH nucleophile attacks the peptide carbon atom. Analogous general-base activity of the free carboxylic group was found to take place also in the case of polyoxometalate-catalyzed hydrolysis as the main catalytic effect originates from the -C=·Zr(IV) binding.
Molecular insight from DFT computations and kinetic measurements into the steric factors influencing peptide bond hydrolysis catalyzed by a dimeric Zr(IV)-substituted keggin type polyoxometalate
Mihaylov, Tzvetan T.,Ly, Hong Giang T.,Pierloot, Kristine,Parac-Vogt, Tatjana N.
, p. 9316 - 9328 (2016)
Peptide bond hydrolysis of several peptides with a Gly-X sequence (X = Gly, Ala, Val, Leu, Ile, Phe) catalyzed by a dimeric Zr(IV)- substituted Keggin type polyoxometalate (POM),(Et2NH2)8[{α-PW11O39Zr- (μ-OH)(H2O)}2]·7H2O (1), was studied by means of kinetic experiments and 1H NMR spectroscopy. The observed rate of peptide bond hydrolysis was found to decrease with increase of the side chain bulkiness, from 4.44 × 10-7 s-1 for Gly-Gly to 0.81 × 10-7 s-1 for Gly-Ile. A thorough DFT investigation was performed to elucidate (a) the nature of the hydrolytically active species in solution, (b) the mechanism of peptide bond hydrolysis, and (c) the influence of the aliphatic residues on the rate of hydrolysis. Formation of substrate-catalyst complexes of the dimeric POM 1 was predicted as thermodynamically unlikely. Instead, the substrates prefer to bind to the monomerization product of 1, [α-PW11O39Zr(OH)(H2O)]4- (2), which is also present in solution. In the hydrolytically active complex two dipeptide ligands are coordinated to the Zr(IV) center of 2. The first ligand is bidentate-bound through its amino nitrogen and amide oxygen atoms, while the second ligand is monodentate-bound through a carboxylic oxygen atom. The mechanism of hydrolysis involves nucleophilic attack by a solvent water molecule on the amide carbon atom of the bidentate-bound ligand. In this process the uncoordinated carboxylic group of the same ligand acts as a general base to abstract a proton from the attacking water molecule. The decrease of the hydrolysis rate with an increase in the side chain bulkiness is mostly due to the increased ligand conformational strain in the rate-limiting transition state, which elevates the reaction activation energy. The conformational strain increases first upon substitution of Hα in Gly-Gly with the aliphatic α substituent and second with the β branching of the α substituent.
Chemical evolution of simple amino acids to asparagine under discharge onto the primitive hydrosphere: Simulation experiments using contact glow discharge
Munegumi, Toratane
, p. 1208 - 1215 (2014)
Asparagine is an important amino acid for abiotic polypeptide synthesis. In simulation experiments, it was obtained in 3.0% yield (based on the amount of consumed alanine) from alanine (100 mM) and formamide (200 mM) by contact glow discharge (Harada discharge) onto aqueous solutions. The present results suggest that asparagine could be abiotically synthesized from simple amino acids under possible primitive earth conditions.
Purification and characterization of biliverdin-binding protein from larval hemolymph of the swallowtail butterfly, Papilio xuthus L.
Yamanaka,Ito,Koga,Sato,Ochiai,Endo
, p. 1978 - 1981 (2000)
The biliverdin-binding protein from the larval hemolymph of the swallowtail butterfly, Papilio xuthus L., was purified and characterized. The crude biliverdin-binding protein, obtained by ammonium sulfate fractionation, was purified in two steps, the firs
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Boutwell,Kuick
, p. 4166 (1930)
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Deactivation behavior and aggregation mechanism of supported Au nanoparticles in the oxidation of monoethanolamine to glycine
Li, Zengxi,Meng, Xiangzhan,Wang, Hui,Yan, Ruiyi,Zhang, Yongqiang
, (2020)
Deactivation behaviors of gold catalysts in the liquid-phase oxidation of monoethanolamine to glycine were revealed. Properties of the catalysts including Au loading, the valence distribution, and particle size of Au nanoparticles before and after batch reactions were investigated by BET, ICP, XRD, XPS, and TEM. It was found that the main reason for the catalytic deactivation was aggregation of Au nanoparticles. The Au aggregation mechanism of oxidative dissolution-reductive deposition in the reaction was proposed and this mechanism could help to understand the common aggregation of Au nanoparticles in the liquid-phase oxidation of alcohols.
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Skraup,Heckel
, p. 1351 (1905)
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Kinetic study of the reaction of acetoacetate with glycine and sodium nitroprusside.
Laios,Pardue
, p. 1903 - 1909 (1993)
This paper describes an extensive kinetic study of the reactions involved in the determination of acetoacetate in body fluids. It is concluded that acetoacetate reacts with glycine to produce an imine intermediate that tautomerizes to an enamine. It is also concluded that nitroprusside reacts with the imine intermediate to produce an unstable product with an absorption maximum near 540 nm. This product decays slowly to produce a stable product with an absorption maximum near 393 nm. A proposed reaction pathway is used to develop kinetic equations, rate constants, equilibrium constants, and molar absorptivity of the unstable product that permit quantitative prediction of the kinetic behavior for a wide range of reactant concentrations.
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Billman,Parker
, p. 761 (1943)
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Galat
, p. 707 (1947)
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Enhanced carboxypeptidase efficacies and differentiation of peptide epimers
Sung, Yu-Sheng,Putman, Joshua,Du, Siqi,Armstrong, Daniel W.
, (2022/01/29)
Carboxypeptidases enzymatically cleave the peptide bond of C-terminal amino acids. In humans, it is involved in enzymatic synthesis and maturation of proteins and peptides. Carboxypeptidases A and Y have difficulty hydrolyzing the peptide bond of dipeptides and some other amino acid sequences. Early investigations into different N-blocking groups concluded that larger moieties increased substrate susceptibility to peptide bond hydrolysis with carboxypeptidases. This study conclusively demonstrates that 6-aminoquinoline-N-hydroxysuccimidyl carbamate (AQC) as an N-blocking group greatly enhances substrate hydrolysis with carboxypeptidase. AQC addition to the N-terminus of amino acids and peptides also improves chromatographic peak shapes and sensitivities via mass spectrometry detection. These enzymes have been used for amino acid sequence determination prior to the advent of modern proteomics. However, most modern proteomic methods assume that all peptides are comprised of L-amino acids and therefore cannot distinguish L-from D-amino acids within the peptide sequence. The majority of existing methods that allow for chiral differentiation either require synthetic standards or incur racemization in the process. This study highlights the resistance of D-amino acids within peptides to enzymatic hydrolysis by Carboxypeptidase Y. This stereoselectivity may be advantageous when screening for low abundance peptide stereoisomers.
Recreating the natural evolutionary trend in key microdomains provides an effective strategy for engineering of a thermomicrobial N-demethylase
Gu, Zhenghua,Guo, Zitao,Shao, Jun,Shen, Chen,Shi, Yi,Tang, Mengwei,Xin, Yu,Zhang, Liang
, (2022/03/09)
N-demethylases have been reported to remove the methyl groups on primary or secondary amines, which could further affect the properties and functions of biomacromolecules or chemical compounds; however, the substrate scope and the robustness of N-demethylases have not been systematically investigated. Here we report the recreation of natural evolution in key microdomains of the Thermomicrobium roseum sarcosine oxidase (TrSOX), an N-demethylase with marked stability (melting temperature over 100 C) and enantioselectivity, for enhanced substrate scope and catalytic efficiency on -C-N-bonds. We obtained the structure of TrSOX by crystallization and X-ray diffraction (XRD) for the initial framework. The natural evolution in the nonconserved residues of key microdomains—including the catalytic loop, coenzyme pocket, substrate pocket, and entrance site—was then identified using ancestral sequence reconstruction (ASR), and the substitutions that accrued during natural evolution were recreated by site-directed mutagenesis. The single and double substitution variants catalyzed the N-demethylation of N-methyl-L-amino acids up to 1800- and 6000-fold faster than the wild type, respectively. Additionally, these single substitution variants catalyzed the terminal N-demethylation of non-amino-acid compounds and the oxidation of the main chain -C-N- bond to a -C=N- bond in the nitrogen-containing heterocycle. Notably, these variants retained the enantioselectivity and stability of the initial framework. We conclude that the variants of TrSOX are of great potential use in N-methyl enantiomer resolution, main-chain Schiff base synthesis, and alkaloid modification or degradation.
Enhancing the Catalytic Activity of MOF-808 Towards Peptide Bond Hydrolysis through Synthetic Modulations
Parac-Vogt, Tatjana N.,Simms, Charlotte,de Azambuja, Francisco
supporting information, p. 17230 - 17239 (2021/12/02)
The performance of MOFs in catalysis is largely derived from structural features, and much work has focused on introducing structural changes such as defects or ligand functionalisation to boost the reactivity of the MOF. However, the effects of different parameters chosen for the synthesis on the catalytic reactivity of the resulting MOF remains poorly understood. Here, we evaluate the role of metal precursor on the reactivity of Zr-based MOF-808 towards hydrolysis of the peptide bond in the glycylglycine model substrate. In addition, the effect of synthesis temperature and duration has been investigated. Surprisingly, the metal precursor was found to have a large influence on the reactivity of the MOF, surpassing the effect of particle size or number of defects. Additionally, we show that by careful selection of the Zr-salt precursor and temperature used in MOF syntheses, equally active MOF catalysts could be obtained after a 20 minute synthesis compared to 24 h synthesis.
