Peptide modification by introduction ofα-trifluoromethyl substituted amino acids

Summary Methodology for the synthesis and incorporation of-trifluoromethyl substituted amino acids into N- and C-terminal position of peptides is described. The incorporation of-trifluoromethyl substituted amino acids into strategical positions of peptides enhances proteolytic stability and lipophilicity. Furthermore, it improves transport rates in vivo and permeability through certain body barriers.     

Grouping of amino acids and recognition of protein structurally conserved regions by reduced alphabets of amino acids

Sequence alignment is a common method for finding protein structurally conserved/similar regions. However, sequence alignment is often not accurate if sequence identities between to-be-aligned se- quences are less than 30%. This is because that for these sequences, different residues may play similar structural roles and they are incorrectly aligned during the sequence alignment using substitu- tion matrix consisting of 20 types of residues. Based on the similarity of physicochemical features, residues can be clustered into a few groups. Using such simplified alphabets, the complexity of protein sequences is reduced and at the same time the key information encoded in the sequences remains. As a result, the accuracy of sequence alignment might be improved if the residues are properly clustered. Here, by using a database of aligned protein structures (DAPS), a new clustering method based on the substitution scores is proposed for the grouping of residues, and substitution matrices of residues at different levels of simplification are constructed. The validity of the reduced alphabets is confirmed by relative entropy analysis. The reduced alphabets are applied to recognition of protein structurally conserved/similar regions by sequence alignment. The results indicate that the accuracy or efficiency of sequence alignment can be improved with the optimal reduced alphabet with N around 9.     

Stimulated uptake of amino acids by HeLa cells following ‘preloading’ in high concentrations of amino acids

HeLa cells exposed to 10mM leucine in medium for 30 mins at 37 °C showed greatly increased uptake of tritiated leucine when returned to medium containing 0.1mM levels of labelled amino acid. Further analysis of the phenomenon demonstrates that the steepness of the gradient is essential for rapid uptake to be observed, that no stereo-specificity is involved, and that the peak of uptake is followed by discharge with first order kinetics back to equilibrium. The effect of 14 different amino acids examined individually as 10mM supplements to the labelling medium ranged from slight reduction (lysine, proline) to complete suppression of the ‘stimulated uptake’ (phenylalanine, isoleucine).     

Using click chemistry to access mono- and ditopic β-cyclodextrin hosts substituted by chiral amino acids

A wide range of chiral mono- and ditopic cyclodextrin-based receptors have been synthesized by CuI-catalyzed azide–alkyne cycloaddition starting from mono-6-azido-β-cyclodextrin and chiral amino acids. Of interest, microwaves proved very efficient to access a wide range of ditopic β-cyclodextrin receptors with quantitative yields.     

Stereospecific synthesis of α-methylated amino acids

Summary. Both 2,5-trans and 2,5-cis disubstituted 2-tert-butyl-5-(indol-3-yl)methylimidazolidin-4-ones were synthesised and their enolates were prepared using LDA. While the enolate of the 2,5-trans disubstituted derivative could not be methylated, the enolate of the cis-2,5-disubstituted derivative was successfully methylated with methyl iodide to a product which on hydrolysis gave enantiomerically pure α-methyl-L-tryptophan. Received October 31, 1998, Accepted July 23, 1999     

Critical amino acids in human DNA polymerases η and κ involved in erroneous incorporation of oxidized nucleotides

Oxidized DNA precursors can cause mutagenesis and carcinogenesis when they are incorporated into the genome. Some human Y-family DNA polymerases (Pols) can effectively incorporate 8-oxo-dGTP, an oxidized form of dGTP, into a position opposite a template dA. This inappropriate G:A pairing may lead to transversions of A to C. To gain insight into the mechanisms underlying erroneous nucleotide incorporation, we changed amino acids in human Polη and Polκ proteins that might modulate their specificity for incorporating 8-oxo-dGTP into DNA. We found that Arg61 in Polη was crucial for erroneous nucleotide incorporation. When Arg61 was substituted with lysine (R61K), the ratio of pairing of dA to 8-oxo-dGTP compared to pairing of dC was reduced from 660:1 (wild-type Polη) to 7 : 1 (R61K). Similarly, Tyr112 in Polκ was crucial for erroneous nucleotide incorporation. When Tyr112 was substituted with alanine (Y112A), the ratio of pairing was reduced from 11: 1 (wild-type Polκ) to almost 1: 1 (Y112A). Interestingly, substitution at the corresponding position in Polη, i.e. Phe18 to alanine, did not alter the specificity. These results suggested that amino acids at distinct positions in the active sites of Polη and Polκ might enhance 8-oxo-dGTP to favor the syn conformation, and thus direct its misincorporation into DNA.     

Dietary requirements of “nutritionally non-essential amino acids” by animals and humans

Amino acids are necessary for the survival, growth, development, reproduction and health of all organisms. They were traditionally classified as nutritionally essential or non-essential for mammals, birds and fish based on nitrogen balance or growth. It was assumed that all “non-essential amino acids (NEAA)” were synthesized sufficiently in the body to meet the needs for maximal growth and health. However, there has been no compelling experimental evidence to support this assumption over the past century. NEAA (e.g., glutamine, glutamate, proline, glycine and arginine) play important roles in regulating gene expression, cell signaling, antioxidative responses, neurotransmission, and immunity. Additionally, glutamate, glutamine and aspartate are major metabolic fuels for the small intestine to maintain its digestive function and protect its mucosal integrity. Therefore, based on new research findings, NEAA should be taken into consideration in revising the classical “ideal protein” concept and formulating balanced diets to improve protein accretion, food efficiency, and health in animals and humans.     

New types of biorelevantα-functional carboxylic acids and their application for peptide modification

Summary New methodology for the preparation of L-isoserine and its incorporation into N- and C-terminal position of peptides is described. Furthermore, the new protective group strategy allows regioselective functional group manipulation in multifunctional amino acids like serine and isoserine.     

Solid-phase S-3CR generates N-substituted α-aminonitriles for the synthesis of α-phenyl-α-(1-piperazinyl) substituted amino acids

Summary. Structurally diverse amino acids were prepared as versatile synthons for combinatorial chemistry. Using an optimized solid-phase synthesis by Strecker-three-component-reaction (S-3CR), two different polymer linker constructs carrying piperazine were investigated. (a) Acrylate derived base-labile linker yielded α-aminonitriles with N-alkylated piperazines via Hofmann elimination after quarternisation with an alkyl halide. The crude product purities were in the range of 54–87%. (b) A urethane type linker yielded α-aminonitriles with the free piperazine nitrogen when cleaved with acid and the product purities were 72–93%. The α-aminonitriles were easily converted to novel N^ɛ – Fmoc-protected α-amino acids with α-(1-piperazinyl) and α-phenyl substituents.     

Glycosidase-catalysed synthesis of glycosylated amino acids: synthesis of GalNAcα-Ser and GlcNAcβ-Ser derivatives

A glycosidase from Aspergillus oryzae catalysed the stereospecific formation of various derivatives of the Tn antigen, D-GalNAca1O-L-Ser, employing D-GalNAc-OPhNO - p as glycosyl donor and different N- and C-protected L-Ser derivatives as acceptors. The same glycosidase preparation was also useful for stereospecific preparation of D-GalNAca1O-L-Thr and D-GlcNAc1O-L-Ser derivatives. Yields were in the range 10-50% depending on the type of acceptor. Lipase from porcine pancreas was used for specific hydrolysis, generating a Tn antigen derivative with a free carboxyl group. This facilitates the use of the derivatives in e.g. solid phase synthesis of glycopeptides.     

Stimulation of (Na+K+)-ATPase of rat liver plasma membrane by amino acids

The effect of twelve l-amino acids on the activity of liver plasma membrane (Na⁺K⁺)-ATPase has been tested. Histidine and arginine significantly enhanced the activity. The activtion by histidine showed saturation kinetics with an apparent K_a of about 8 mM, and was evident over a wide range of Na⁺ concentrations. The same amino acid did not significantly affect the Mg²⁺-dependent ATPase activity.     

Pulse radiolysis of aromatic amino acids — State of the art

Summary The pulse radiolysis method as well as the primary processes of water radiolysis and the spectroscopic characteristics of H, OH, HO₂/O₂ ^– and e _aq ^- are briefly presented. Subsequently, kinetic and spectroscopic data of the transients resulting from the resolved multi site attack on aromatic amino acids are discussed. The reactivity of H and e _aq ^- with the same substrates, as well as the effect of oxygen on the major radiolytic processes are reviewed. Finally, the formation of tryptophan radical cation is mentioned shortly. The presented radiation mechanisms are the fundamentals for radiolytic processes occurring in proteins, enzymes and hormones in the living cells.     

d-Amino acids in molecular evolution in space – Absolute asymmetric photolysis and synthesis of amino acids by circularly polarized light

Living organisms on the Earth almost exclusively use l-amino acids for the molecular architecture of proteins. The biological occurrence of d-amino acids is rare, although their functions in various organisms are being gradually understood. A possible explanation for the origin of biomolecular homochirality is the delivery of enantioenriched molecules via extraterrestrial bodies, such as asteroids and comets on early Earth. For the asymmetric formation of amino acids and their precursor molecules in interstellar environments, the interaction with circularly polarized photons is considered to have played a potential role in causing chiral asymmetry. In this review, we summarize recent progress in the investigation of chirality transfer from chiral photons to amino acids involving the two major processes of asymmetric photolysis and asymmetric synthesis. We will discuss analytical data on cometary and meteoritic amino acids and their potential impact delivery to the early Earth. The ongoing and future ambitious space missions, Hayabusa2, OSIRIS-REx, ExoMars 2020, and MMX, are scheduled to provide new insights into the chirality of extraterrestrial organic molecules and their potential relation to the terrestrial homochirality. This article is part of a Special Issue entitled: d-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca.     

A preparation of N-Fmoc-N-methyl-α-amino acids and N-nosyl-N-methyl-α-amino acids

A convenient route for the synthesis of lipophilic N-Fmoc-N-methyl-α-amino acids and N-nosyl-N-methyl-α-amino acids, interesting building blocks to be used for the preparation of N-methylated peptides, is presented. Both nosyl- and Fmoc-protected monomers are accessible, so these compounds can be used in solution as well as in solid phase peptide synthesis. The methodology is based on the use of benzhydryl group to protect temporarily the carboxyl function of N-nosyl-α-amino acids and on the subsequent methylation of the N-nosyl-α-amino acid benzhydryl esters with diazomethane. The benzhydryl esters offer several beneficial features such as simple preparation, stability to methylation and selective deprotection under mild conditions. The overall procedure is highly efficient in that the adopted conditions keep the chiral integrity of amino acid precursors and the process does not require chromatographic purification of the methylated products.     

Asymmetric hydrolysis of α-aminonitriles to optically active amino acids by a nitrilase of Rhodococcus rhodochrous PA-34

Summary Rhodococcus rhodochrous PA-34 isolated from soil as a propionitrile-utilizing microorganism, hydrolysed several -aminonitriles to optically active amino acids. The hydrolysis of -aminonitriles was found to be catalysed by a nitrilase. The characteristics of the purified enzyme revealed that this is a new nitrilase as it has a molecular mass of 45 kDa and acts as a monomer. The optimum pH and temperature for the activity of the purified enzyme were 7.5 and 35° C, respectively. Thiol-specific reagents caused inhibition whereas chelators did not significantly alter the activity of this enzyme. The amino acids produced were of L-form, except for alanine. In the case of leucine production from -aminoisocapronitrile, the enantiomeric ratio of L-leucine to D-leucine was about 60.     

Two γ-Glutamylpeptides of acetylenic amino acids in Tricholomopsis rutilans

Two γ-glutamylpeptides, γ-L-glutamyl-L-2-aminohex-4-ynoic acid and γ-L-glutamyl-L-erythro-2-amino-3-hydroxyhex-4-ynoic acid,