Proteinogenic amino acid

Summary

Proteinogenic amino acids are amino acids that are incorporated biosynthetically into proteins during translation. The word "proteinogenic" means "protein creating". Throughout known life, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard genetic code and an additional 2 (selenocysteine and pyrrolysine) that can be incorporated by special translation mechanisms. In contrast, non-proteinogenic amino acids are amino acids that are either not incorporated into proteins (like GABA, L-DOPA, or triiodothyronine), misincorporated in place of a genetically encoded amino acid, or not produced directly and in isolation by standard cellular machinery (like hydroxyproline). The latter often results from post-translational modification of proteins. Some non-proteinogenic amino acids are incorporated into nonribosomal peptides which are synthesized by non-ribosomal peptide synthetases. Both eukaryotes and prokaryotes can incorporate selenocysteine into their protein

Official source

https://en.wikipedia.org/wiki/Proteinogenic_amino_acid

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An organometallic 4d transition metal complex [CpRhCl2]2, together with commercially available dyes, was used to construct indicator displacement assays (IDAs) for the detection of peptides, amino acids, and nucleotides. The combination of the CpRh complex with the dye azophloxine was found to form a chemosensing ensemble for the sequence-selective detection of histidine- and methionine-containing peptides in water at neutral pH. A strong interaction of the rhodium complex with peptides bearing histidine or methionine residue in the position 1 or 2 allowed to detect these peptides down to a concentration of 0.3 µM. The same organometallic complex and three commercially available dyes were employed to compose an array of IDA chemosensors for the detection of natural amino acids. We found that the variation of the pH can effectively be used to modulate the selectivity of an IDA sensor. An excellent discrimination of 20 amino acids was achieved. The combination of [Cp*RhCl2]2 with the dyes gallocyanine, evans blue, and mordant yellow 10 forms a multicomponent indicator displacement assay (MIDA), which can be used to sense low millimolar concentrations of nucleotides and the pyrophosphate anion in buffered aqueous solution. Moreover, the MIDA allows to simultaneously determine the concentrations of adenosine triphosphate and pyrophosphate/cyclic adenosine monophosphate with a single UV-Vis measurement. In the second part of our work we investigated whether dynamic combinatorial libraries (DCLs) can be used for sensing purposes. We found that the dyes arsenazo I, methylcalcein blue, and glycine cresol red, in combination with the metal salts CuCl2 and NiCl2, form a DCL of differently colored metal-dye complexes. The addition of an analyte able to interact with a member(s) of such a library, results in a re-equilibraion easily detectable by UV-Vis spectroscopy. Using dipeptides as analytes we demonstrated that this way of sensing is very effective – even closely related peptides such as regio- (Ala-Phe vs. Phe-Ala) and stereo- (Phe-Ala vs. D-Phe-Ala) isomers can easily be discriminated. Additionally, we found that the identity of the best sensor depends on the problem to be addressed.

EPFL2007

Results of the mechanistic studies of free-electron based fragmentation methods addressing peptide and protein structure analysis with mass spectrometry (MS), electron capture dissociation (ECD) and electron ionization dissociation (EID), are presented. Series of model peptides, H-RAAAA-X-AAAAK-OH and H-RGGGG-X-GGGGK-OH, were rationally designed and studied to understand the role of a single amino acid residue on ECD process. The results show a direct correlation of ECD product ion abundance (PIA) with amino acid hydrophobicity and radical stability of the central amino acid, X, in model peptides. Moreover, comparison of ECD PIA distributions for polyalanine- and polyglycine -based peptides, despite a substantial structure differences between them, demonstrates a high correlation (R=0.86) as well. Ion activation prior to ECD qualitatively preserves the PIA correlation with hydrophobicity, however redistributes the fragmentation channels. This redistribution can be rationalized in terms of: (i) further dissociation of product ions, due to the excess of ion internal energy; (ii) expansion of precursor ion conformational landscape reducing the conformational specificity in localization of unpaired electron and allowing competition of different reactive groups to induce the backbone cleavage. In particular, the competition between N-terminal R, C-terminal K and central X side chains to participate in formation of aminoketyl radicals was considered to explain the central residue specific formation of z5 and [z6-H] ions; and to explain the shift of branching ratio between c- and z-ions toward the formation of c-ions. Further studies were focused on the studying of free electron – ion interaction cross sections. The difference in low energy electron capture cross sections (CSs) of ECD product ions was found to correlate with ECD PIA pattern being a function of electron irradiation period in ECD. The developed experimental methodology and ECD kinetic model were applied to deduce the dissociation rate constants and electron capture CSs from ECD PIA values. The observed correlation between low energy electron capture CSs and ion mobility (IM) CSs provides interesting material for further studies. Finally, characterization of interaction between high energy (50-100 eV) electrons and protein ions in EID demonstrates that the EID cross sections are proportional (R = 0.98), and of the same order of magnitude, to the values of the IM CSs. The results support the feasibility of employing the EID MS for accurate estimation of the geometrical cross sections of gaseous biomolecular ions as a method of biomolecular structure analysis. To summarize, improved understanding in (i) radical chemistry beyond standard ECD parameters and (ii) electron – ion interactions with respect to the ion structure increases the quantity and quality of information possible to achieve by MS/MS, and, therefore, provides a strong basis for further improvements in peptide and protein structure characterization as well as understanding of energy absorption and relaxation process in biomolecules.

EPFL2012

Rh-catalyzed C-H Bond Heteroarylation with Hypervalent Iodine Reagents and Pd-Catalyzed Tethered Functionalizations of Carbon-Carbon Multiple Bonds.

Ashis Kumar Das

Transition metal-catalyzed C-H activation is a powerful tool for the synthesis of organic building blocks, materials, and natural products. Over the last decade, directing-group-assisted metal-catalyzed C-H functionalization has attracted increasing interest as a means to target specific C-H bonds. Moreover, a large variety of electrophiles has been employed in this kind of processes. In this thesis, we describe a novel C-6 selective C-H heteroarylation of pyridine-2-ones using indoleBX reagents as coupling partners under Rh(I)-catalysis. The reaction worked efficiently also with other analogous heterocyclic substrates and with a quinoline-N-oxide. We were able to obtain 6-(indol-3-yl)pyridinone and 8-(indol-3-yl)quinolone after cleavage of the directing group or rearrangement of the N-oxide moiety. 1,2-Amino alcohols are important structural motifs in organic chemistry that can be observed in natural products, pharmaceutically and biologically active molecules. The palladium-catalyzed difunctionalization of C-C multiple bonds has been broadly investigated as an efficient strategy to access such substructures. This transformation has been reported using either Pd(0)/Pd(II) or Pd(II)/Pd(IV) catalytic cycles, in which the nucleophilic functionalization of a putative Pd(II)-alkyl intermediate is achieved prior to beta-hydride elimination. As a further topic of this thesis, we developed new methods for the synthesis of amino alcohols whereby the Pd-catalyzed difunctionalization of alkynes and alkenes was combined with the tethering approach previously established in our laboratories. We first investigated the Pd-catalyzed enantioselective hydroalkoxylation of propargylic amines. The latter were tethered in situ with a trifluoroacetaldehyde hemiacetal. Best results were obtained with commercially available DACH-Phenyl Trost ligand. Aryl iodides were required as an additive in catalytic amount for successful outcome. A large variety of chiral oxazolidines were obtained in good to excellent yields and ee, followed by a diastereoselective reduction to give protected enantioenriched amino alcohols. A possible mechanism for this transformation relies on a Pd(0)/Pd(II) catalytic cycle involving oxidative addition of aryl iodide with a subsequent oxypalladation/protodemetallation (or reductive elimination) reaction. This is necessary to generate the active complex, not as the start of a cross-coupling event. The use of a commercially available DACH-Ph Trost ligand to produce high enantioselectivity in an unprecedented DYKAT process was critical to success.The Pd-catalyzed amino acetoxylation of cinnamyl alcohols was next taken into consideration towards the synthesis of valuable amino diol derivatives. In this case, preformed substrates were used, where the alcohol moiety was tethered to N-nucleophilic groups. Conditions involving Pd(II)/Pd(IV) catalysis and employing PIDA as a strong oxidant were employed. The use of this hypervalent iodine reagent was key to the success of the transformation. Amino acetoxylated products were obtained in moderate to good yields and dr. The scope of this reaction remains mostly limited to cinnamyl derived substrates. The reaction conditions did not tolerate substituents on the alpha, beta, and gamma positions of the allylic chains. Alkyl chain containing unsaturated alcohols delivered Aza-Wacker-type products.

EPFL2022

EPFL2007

EPFL2012

Rh-catalyzed C-H Bond Heteroarylation with Hypervalent Iodine Reagents and Pd-Catalyzed Tethered Functionalizations of Carbon-Carbon Multiple Bonds.

Ashis Kumar Das

EPFL2022