Starting Amino Acid Research Articles

Identification of N-degrons and N-recognins using peptide pull-downs combined with quantitative mass spectrometry.

Regulated protein degradation controls protein levels of all short-lived proteins to ensure cellular homeostasis and also protects cells from misfolded or other abnormal proteins. The most important players in the degradation system are E3 ubiquitin ligases which recognize exposed sequence motifs, so-called degrons, of target proteins and mark them through the attachment of ubiquitin for degradation. N-terminal (Nt) sequences are extensively used as degrons (N-degrons) and all 20 amino acids are able to feed proteins in 1 of the 5 known N-degron pathways. Studies have mainly focused on characterizing systematically the role of the starting amino acid on protein stability and less on the identification of the E3 ligases involved. Recent data from our lab and literature suggest that there is an extensive interplay of N-recognins and Nt-modifying enzymes like Nt-acetyltransferases (NATs) or N-myristoyltransferases which only starts to be elucidated. It suggests that improperly modified or unexpectedly unmodified proteins become rapidly removed after synthesis ensuring protein maturation and quality control of specific subsets of proteins. Here, we describe a peptide pull-down and down-stream bioinformatics workflow conducted in the MaxQuant and Perseus computational environment to identify N-recognin candidates in an unbiased way using quantitative mass spectrometry (MS)-based proteomics. Our workflow allows the identification of N-recognin candidates for specific N-degrons, to determine their sequence specificity and it can be applied as well more general to identify binding partners of N-terminal modifications. This method paves the way to identify pathways involved in protein quality control and stability acting at the N-terminus.

Hydrothermal synthesis of chiral carbon dots.

Nanocolloidsthat are cumulatively referred to as nanocarbons, attracted significant attention during the last decade because of facile synthesis methods, water solubility, tunable photoluminescence, easy surface modification, and high biocompatibility. Among the latest development in this reserach area are chiral nanocarbons exemplified by chiral carbon dots (CDots). They are expected to have applications in sensing, catalysis, imaging, and nanomedicine. However, the current methods of CDots synthesis show often contradictory chemical/optical properties and structural information that required a systematic study with careful structural evaluation. Here, we investigate and optimize chiroptical activity and photoluminescence of L- and D-CDots obtained by hydrothermal carbonization of L- and D-cysteine, respectively. Nuclear magnetic resonance spectroscopy demonstrates that they are formed via gradual dehydrogenation and condensation reactions of the starting amino acid leading to particles with a wide spectrum of functional groups including aromatic cycles. We found that the chiroptical activity of CDots has an inverse correlation with the synthesis duration and temperature, whereas the photoluminescence intensity has a direct one, which is associated with degree of carbonization. Also, our studies show that the hydrothermal synthesis of cysteine in the presence of boric acid leads to the formation of CDots rather than boron nitride nanoparticles as was previously proposed in several reports. These results can be used to design chiral carbon-based nanoparticles with optimal chemical, chiroptical, and photoluminescent properties.

Convenient Approach to Bicyclic Sultams

AbstractA method for the synthesis of aminomethyl-substituted five-membered sultams has been developed. The aminomethyl sultams were synthesized from the corresponding iodomethyl derivatives by nucleophilic substitution of the iodine atom with sodium azide followed by reduction on Pd/C. This method was further expanded to side-chain-substituted sultams, starting from amino acid esters, to obtain aminomethyl-containing bicycles. The simple practical procedure and available starting amino acid esters, including chiral examples, make various bicyclic sultams readily available.

Biochemical characterization of tyrosine aminotransferase and enhancement of salidroside production by suppressing tyrosine aminotransferase in Rhodiola crenulata

Rhodiola crenulata is a traditional Tibetan medicinal plant mainly distributed in high altitude areas of Tibet. As the main extract of R. crenulata, salidroside has important medicinal activities in enhancing the body’s immunity and resisting microwave radiation by influencing cell metabolism. Tyrosine is the starting amino acid precursor for salidroside biosynthesis. As an aromatic amino acid, tyrosine participates not only in salidroside biosynthesis, but also in other metabolite biosynthesis which might compete against salidroside biosynthetic pathway. In this study, we functionally identified a tyrosine aminotransferase in R. crenulata (RcTAT) that could convert tyrosine into 4-hydroxyphenylpyruvate (4-HPP). The Km and Vmax values of RcTAT for tyrosine were respectively 0.21 mM and 0.17 μmol/min.mg under 9.0 pH and 39 °C. RNAi-mediated suppression of RcTAT expression markedly increased salidroside production in hairy root culture of R. crenulata. In summary, RcTAT is a key gene involved in the metabolic pathway that competes against salidroside biosynthesis, and suppressing its expression is a promising way to elevate salidroside production in planta.

A Bioinformatics Approach for the Prediction of Immunogenic Properties and Structure of the SARS-COV-2 B.1.617.1 Variant Spike Protein.

Background B.1.617.1, a variant of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causing respiratory illness is responsible for the second wave of COVID-19 and associated with a high incidence of infectivity and mortality. To mitigate the B.1.617.1 variant of SARS-CoV-2, deciphering the protein structure and immunological responses by employing bioinformatics tools for data mining and analysis is pivotal. Objectives Here, an in silico approach was employed for deciphering the structure and immune function of the subunit of spike (S) protein of SARS-CoV-2 B.1.617.1 variant. Methods The partial amino acid sequence of SARS-CoV-2 B.1.617.1 variant S protein was analyzed, and its putative secondary and tertiary structure was predicted. Immunogenic analyses including B- and T-cell epitopes, interferon-gamma (IFN-γ) response, chemokine, and protective antigens for SARS-CoV 2 S proteins were predicted using appropriate tools. Results B.1.617.1 variant S protein sequence was found to be highly stable and amphipathic. ABCpred and CTLpred analyses led to the identification of two potential antigenic B cell and T cell epitopes with starting amino acid positions at 60 and 82 (for B cell epitopes) and 54 and 98 (for T cell epitopes) having prediction scores > 0.8. Further, RAMPAGE tool was used for determining the allowed and disallowed regions of the three-dimensional predicted structure of SARS-CoV-2 B.1.617.1 variant S protein. Conclusion Together, the in silico analysis revealed the predicted structure of partial S protein, immunogenic properties, and possible regions for S protein of SARS-CoV-2 and provides a valuable prelude for engineering the targeted vaccine or drug against B.1.617.1 variant of SARS-CoV-2.

Asymmetric synthesis, biological activity and molecular docking studies of some unsaturated α-amino acids, derivatives of glycine, allylglycine and propargylglycine

New enantiomerically enriched unsaturated tailor-made amino acids have been obtained. As a starting amino acid synthon for the asymmetric synthesis of tailor-made unsaturated amino acids, Ni(II) square-planar complexes of Schiff’s bases of propargylglycine, allylglycine and glycine with chiral auxiliary (S)-2-N-(N’-benzylprolyl)-aminobenzophenone ((S)-BPB) were used. The Cα-alkylation of propargylglycine, allylglycine and glycine moieties resulted in the asymmetric synthesis of novel (S)-α-propargylglycine, (S)-α-allylglycine and glycine derivatives containing an aromatic group in the side chain (de 80–95,5%). After purification and cleavage of the metal complexes, the amino acids were isolated in high enantiomeric purity (ee >99%). Of the obtained seven tailor-made amino acids four showed inhibitory activity to collagenase G. The amino acid with an acetylene bond in the side chain (IC50 = 1.29 ± 0.02 mM) had the best result. Molecular docking showed that the amino acids with activity to collagenase G contained hydrogen and π-π bonds with the enzyme.

The Ambidextrous Pictet–Spengler Reaction: Access to the (+)- or (–)-Enantiomers of the Bioactive C-19 Methyl-Substituted Sarpagine/Macroline/Ajmaline Alkaloids from Either d- or l-Tryptophan

Depicted in the following is the proof of concept, which is important to illustrate the full potential of the ambidextrous Pictet–Spengler (P-S) reaction. Previously, both d-tryptophan and l-tryptophan were employed to synthesize the key intermediates toward the natural enantiomers of C-19 methyl-substituted alkaloids. Now the enantiomeric series of the same key intermediates could also be synthesized from both d- or l-tryptophan in high yield and optical purity via this P-S/Dieckmann protocol. One can make either the natural or the unnatural alkaloids from either of the chiral starting amino acid esters, stereo- and enantiospecifically for biological screening.

Conformational analyses for hydrated oligopeptides by quantum chemical calculation (QCC): effects of intra-molecular hydrogen bonds

The structures and energies of anhydrate and hydrate (hydrate rate: h of 1) states of l-alanine (LA), glycine (G), l-proline (LP), and N-methyl glycine (MG) pentamers were calculated by quantum chemical calculation using B3LYP/6-31G(d,p), for four kinds of conformers (β-extended: φ/ψ = t−/t+, PPII: g−/t+, PPII-like: g−/g+, and α-helix: g−/g−). In LA and G, which have imino proton (NH), three conformation types of β-extended, PPII-like, and α-helix were obtained, and water molecules were mainly inserted between intra-molecular hydrogen bond of CO···HN in PPII-like and α-helix and attached to CO group in β-extended. In LA and G, PPII-like conformers were the most stable in the anhydrate and hydrate states, and the result for LA was different from some experimental and theoretical results reported by other works reporting that the main stable conformation of alanine oligopeptide was PPII. On the other hand, in LP and MG, which have no imino proton, two conformers (PPII and PPII-like) and three conformers (PPII, PPII-like, and α-helix) were obtained, respectively. PPII conformers were the most stable in the anhydrate and hydrate states, and the result for LP supported the reported experimental results that the main conformation of proline oligomer was PPII. It was found that the formation pattern and stability of conformation of oligopeptide were strongly dominated by the presence/absence of intra-molecular hydrogen bonding of CO···HN or the presence/absence of NH2 group in the starting amino acid.

Mitocryptides from Human Mitochondrial DNA-Encoded Proteins Activate Neutrophil Formyl Peptide Receptors: Receptor Preference and Signaling Properties.

Phagocytic neutrophils express formyl peptide receptors (FPRs; FPR1 and FPR2) that distinctly recognize peptides starting with an N-formylated methionine (fMet). This is a hallmark of bacterial metabolism; similar to prokaryotes, the starting amino acid in synthesis of mitochondrial DNA-encoded proteins is an fMet. Mitochondrial cryptic peptides (mitocryptides; MCTs) with an N-terminal fMet could be identified by our innate immune system; however, in contrast to our knowledge about bacterial metabolites, very little is known about the recognition profiles of MCTs. In this study, we determined the neutrophil-recognition profiles and functional output of putative MCTs originating from the N termini of the 13 human mitochondrial DNA-encoded proteins. Six of the thirteen MCTs potently activated neutrophils with distinct FPR-recognition profiles: MCTs from ND3 and ND6 have a receptor preference for FPR1; MCTs from the proteins ND4, ND5, and cytochrome b prefer FPR2; and MCT-COX1 is a dual FPR1/FPR2 agonist. MCTs derived from ND2 and ND4L are very weak neutrophil activators, whereas MCTs from ND1, ATP6, ATP8, COX2, and COX3, do not exert agonistic or antagonistic FPR effects. In addition, the activating MCTs heterologously desensitized IL-8R but primed the response to the platelet-activating factor receptor agonist. More importantly, our data suggest that MCTs have biased signaling properties in favor of activation of the superoxide-generating NADPH oxidase or recruitment of β-arrestin. In summary, we identify several novel FPR-activating peptides with sequences present in the N termini of mitochondrial DNA-encoded proteins, and our data elucidate the molecular basis of neutrophil activation by MCTs.

Chiral ethylene-bridged flavinium salts: the stereoselectivity of flavin-10a-hydroperoxide formation and the effect of substitution on the photochemical properties

A series of chiral non-racemic N1,N10-ethylene bridged flavinium salts 4 was prepared using enantiomerically pure 2-substituted 2-aminoethanols (R = isopropyl, phenyl, benzyl, 4-methoxybenzyl, 4-benzyloxybenzyl) derived from amino acids as the sole source of chirality. The flavinium salts were shown to form 10a-hydroperoxy- and 10a-methoxy-adducts with moderate to high diastereoselectivity depending on the ethylene bridge substituent originating from the starting amino acid. High diastereoselectivities (dr values from 80:20 to >95:5) were observed for flavinium salts bearing benzyl substituents attached to the ethylene bridge. The benzyl group preferred the face-to-face (syn) orientation relative to the flavinium unit; thereby effectively preventing nucleophilic attack from one side. This conformation was found to be the most stable according to the DFT calculations. Consequently, the presence of benzyl groups causes intermolecular fluorescence quenching resulting in a significant decrease in the fluorescence quantum yield from 11% for 4a bearing an isopropyl substituent to 0.3% for 4c containing a benzyl group and to a value lower than 0.1% for the benzyloxybenzyl derivative 4e.

Nutritional strategy of early amino acid administration in very low birth weight infants.

Relative to a fetus of the same gestational age, very low birth weight (VLBW) infants are more likely to be underfed and to undergo growth restriction during their early hospital stay. The current trend towards "early and aggressive" nutritional strategies in VLBW infants aims to overcome the early nutritional deficiency and thereby boost postnatal catch-up growth, simultaneously improving long-term neurodevelopmental outcomes. Although the minimum starting amino acid (AA) dose to prevent negative nitrogen balance is well established, the upper limit and the rate of increase of early AA doses are controversial. Most randomized controlled trials show that early and high-dose (target, 3.5 to 4.9 g/kg/day) AA regimens, with or without high nonprotein calories, do not improve long-term growth and neurodevelopment. High-dose AA supplementation may lead to early metabolic disturbances and excessive or disproportionate plasma AA levels, particularly in infants of very low gestational age. Further large studies are needed to clarify the optimal strategy for early administration of parenteral AA doses in VLBW infants.

ChemInform Abstract: Substrate Control in Enantioselective and Diastereoselective Aldol Reaction by Memory of Chirality: A Rapid Access to Enantiopure β‐Hydroxy Quaternary α‐Amino Acids.

AbstractAn asymmetric aldol reaction memorizing the underlying chirality of the starting amino acid is reported for the first time.

A One-Pot Procedure for the Preparation ofN-9-Fluorenylmethyloxycarbonyl-α-amino Diazoketones from α-Amino Acids

The study describes a new "one-pot" route to the synthesis of N-9-fluorenylmethyloxycarbonyl (Fmoc) α-amino diazoketones. The procedure was tested on a series of commercially available free or side-chain protected α-amino acids employed as precursors. The conversion into the title compounds was achieved by masking and activating the α-amino acids with a single reagent, namely, 9-fluorenylmethyl chloroformate (Fmoc-Cl). The resulting N-protected mixed anhydrides were reacted with diazomethane to lead to the α-amino diazoketones, which were isolated by flash column chromatography in very good to excellent overall yields. The versatility of the procedure was verified on lipophilic α-amino acids and further demonstrated by the preparation of N-Fmoc-α-amino diazoketones also from α-amino acids containing side-chain masking groups, which are orthogonal to the Fmoc one. The results confirmed that tert-butyloxycarbonyl (Boc), tert-butyl ((t)Bu), and 2,2,4,6,7-pentamethyldihydrobenzofuran-5-sulfonyl (Pbf), three acid-labile protecting groups mostly adopted in the solution and solid-phase peptide synthesis, are compatible to the adopted reaction conditions. In all cases, the formation of the corresponding C-methyl ester of the starting amino acid was not observed. Moreover, the proposed method respects the chirality of the starting α-amino acids. No racemization occurred when the procedure was applied to the synthesis of the respective N-Fmoc-protected α-amino diazoketones from L-isoleucine and L-threonine and to the preparation of a diastereomeric pair of N-Fmoc-protected dipeptidyl diazoketones.

Synthesis of indolizidines from optically pure α‐amino acids via stereocontrolled rhodium‐catalyzed hydroformylation of N‐allylpyrroles

Indolizidine alkaloids have attracted considerable attention because of their vast array of structural diversity and varied biological activity. This article relates the results that we obtained in the field of the total synthesis of indolizidines from α-amino acids, based on the rhodium-catalyzed hydroformylation of N-allylpyrroles intermediates. The formed pyrrolylbutanals undergo an intramolecular cyclodehydration to 5,6-dihydroindolizines, which are fully hydrogenated to indolizidines. All reaction sequences are stereocontrolled: indeed, the chiral center in the starting amino acid is transferred into 5,6-dihydroindolizine moiety with complete stereochemical integrity and the new stereogenic center at C9 carbon atom in the final indolizidines is generated in only one configuration.

An evaluation of the critical parameters for abiotic peptide synthesis in submarine hydrothermal systems.

It has been proposed that oligopeptides may be formed in submarine hydrothermal systems (SHSs). Oligopeptides have been synthesized previously under simulated SHS conditions which are likely geochemically implausible. We have herein investigated the oligomerization of glycine under SHS-like conditions with respect to the limitations imposed by starting amino acid concentration, heating time, and temperature. When 10(-1) M glycine solutions were heated at 250 degrees C for < 20 min glycine oligomers up to tetramers and diketopiperazine (DKP) were detectable. At 200 degrees C, less oligomerization was noted. Peptides beyond glycylglycine (gly2) and DKP were not detected below 150 degrees C. At 10(-2) M initial glycine concentration and below, only gly2, DKP, and gly3 were detected, and then only above 200 degrees C at < 20 min reaction time. Gly3 was undetectable at longer reaction times. The major parameters limiting peptide synthesis in SHSs appear to be concentration, time, and temperature. Given the expected low concentrations of amino acids, the long residence times and range of temperatures in SHSs, it is unlikely that SHS environments were robust sources of even simple peptides. Possible unexplored solutions to the problems presented here are also discussed.

Chlorine dioxide reaction with selected amino acids in water

Chlorine dioxide is a hypochlorite alternative disinfectant agent. In this context, we have determined the products formed in the reaction of ClO 2 with selected amino acids as model compounds that can be present in natural waters. The reaction of tryptophane, histidine and tyrosine (10 ppm each) with ClO 2 were studied at molar ratios ranging from 0.25 to 4 in the presence or absence of oxygen. It was found that in the absence of oxygen adding substoichiometric amounts of ClO 2 creates products that are structurally similar to the starting amino acids. Through a series of cascade reactions the initial product distribution gradually evolves toward simple, small carbon chain products that are far from the starting amino acid. The reaction product distribution revealed that chlorine dioxide can attack the electron-rich aromatic moieties as well as the nitrogen atom lone electron pair. Our study is relevant to gain knowledge on the reaction mechanism of ClO 2 with ubiquitous amino acids present in natural waters.

Is the early and aggressive administration of protein to very low birth weight infants safe and efficacious?

Most conventionally managed very low birth weight infants experience postnatal growth restriction. There is some evidence that this postnatal growth restriction may have long-lasting effects, and contribute to short stature and poor neurodevelopmental outcomes. There is also evidence suggesting that early protein intake may improve growth in these very low birth weight infants. Therefore, to optimize protein intake early in the infant's neonatal course seems a logical goal. Randomized controlled trials provide evidence of short-term safety and efficacy for starting amino acid infusion as soon as possible after birth at 2.5-3.0 g/kg/day in very low birth weight infants; however, there are no long-term data to support the safety or efficacy of this practice. There is some evidence from recent studies of improved growth by providing 4.0 g/kg/day of amino acid early in the neonatal period while keeping the nitrogen to energy ratio above 1:100 and continuing with this protein intake during the infants stay in the hospital. At the present time long-term safety of this strategy is also not known. Appropriately designed large-scale randomized controlled trials are needed to determine the long-term safety and efficacy of early and aggressive administration of protein to very low birth weight infants.

A methylenic group binds guanidinoacetic acid to glycine and serine in two novel copper(II) complexes: Synthesis, X-ray structure and spectroscopic characterization

New condensed amino acids were observed in two Cu(II) complexes, both involving guanidinoacetic acid (GAA). The copper(II) complexes, 1 and 2, were synthesized and characterized by X-ray crystallography and infrared spectroscopy. Vibrational assignments were performed with the aid of density functional theory (DFT) calculations. Both complexes present an elongation of the carbon chain of the starting amino acid, GAA. One methylenic group binds GAA to the other amino acid, which can be glycine or serine. Complex 1 presents a new condensed synthetic amino acid, glycine-3- N-methylguanidino acetic acid (Gly-mGAA) that is the result/product of the reaction between GAA and glycine, with an addition of one carbon in the chain. In complex 2, a similar ligand to Gly-mGAA was observed, but in this case it is a product of the reaction between GAA and serine, that is, serine-3- N-methylguanidino acetic acid (Ser-mGAA). Gly-mGAA and Ser-mGAA coordinate to Cu(II) through two nitrogen atoms and two oxygen atoms. In addition, we attempt to propose the mechanism for formation of Ser-mGAA and Gly-mGAA in two steps. The first one involves a deamidination reaction between two GAA species, producing the intermediate N, N′-guanidinodiacetic acid. The second step involves a decarboxylation process between GAA and Ser or Gly.

Chiral Photocages Based on Phthalimide Photochemistry

A new class of photoremovable protecting groups, based on a photoinduced decarboxylation reaction coupled with the elimination of the caged molecule, is described for 2-phthalimido-3-hydroxy-propionate derivatives. When derived from enantiopure N-phthaloyl- serine or threonine, the chirality of the starting amino acid is transmitted to the protected (caged) molecule. These photocages possess good properties for their use in biological systems, and the introduction of chirality opens new possibilities for the study of diastereoselective photochemistry and stereodifferentiation processes involving the release of the caged molecule.

The enduracidin biosynthetic gene cluster from Streptomyces fungicidicus

The biosynthetic gene cluster for the 17 aa peptide antibiotic enduracidin has been cloned and sequenced from Streptomyces fungicidicus ATCC 21013. The 84 kb gene cluster contains 25 ORFs and is located within a 116 kb genetic locus that was fully sequenced. Targeted disruption of non-ribosomal peptide synthetase (NRPS) genes in the cluster abolished enduracidin production and confirmed function. The cluster includes four genes, endA-D, encoding two-, seven-, eight- and one-module NRPSs, respectively, and includes unique modules for the incorporation of citrulline and enduracididine. The NRPS organization generally follows the collinearity principle, and starts with a condensation domain (C domain) similar to those found in other lipopeptide systems for the coupling of an acyl group to the starting amino acid. The sixth module of EndB, corresponding to Thr(8), is missing an adenylation domain (A domain) and this module is presumed to be loaded in trans by the single module protein EndD. The most striking feature of the NRPS organization is the lack of epimerization domains (E domains) in light of the fact that the product has seven d-amino acid residues. Sequence analysis reveals that C domains following modules corresponding to d-amino acids belong to a unique subset of C domains able to catalyse both epimerization and condensation reactions. Other genes directing lipid modification and activation, and formation of the non-proteinogenic amino acids 4-hydroxyphenylglycine and enduracididine are readily identified, as are genes possibly involved in regulation of antibiotic biosynthesis and export. These findings provide the basis to further genetically manipulate and improve lipodepsipeptide antibiotics via combinatorial and chemical methods.