D-L amino acid analysis using automated precolumn derivatization with 1-fluoro-2,4-dinitrophenyl-5-alanine amide

Detection and quantification of d-amino acid residues in peptides and proteins using acid hydrolysis

Biomolecular homochirality refers to the assumption that amino acids in all living organisms were believed to be of the l-configuration. However, free d-amino acids are present in a wide variety of organisms and d-amino acid residues are also found in various peptides and proteins, being generated by enzymatic or non-enzymatic isomerization. In mammals, peptides and proteins containing d-amino acids have been linked to various diseases, and they act as novel disease biomarkers. Analytical methods capable of precisely detecting and quantifying d-amino acids in peptides and proteins are therefore important and useful, albeit their difficulty and complexity. Herein, we reviewed conventional analytical methods, especially 0h extrapolating method, and the problems of this method. For the solution of these problems, we furthermore described our recently developed, sensitive method, deuterium-hydrogen exchange method, to detect innate d-amino acid residues in peptides and proteins, and its applications to sample ovalbumin. 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.

Amino acid sequence and D/L-configuration determination methods for D-amino acid-containing peptides in living organisms

D-amino acid-containing peptides with biological activities have been isolated from invertebrates and amphibians, and partial racemization of amino acid residues in mammalian peptides associated with aging and diseases have been discussed. Here, we review the amino acid configuration determination methods in these peptides and recent progress of simultaneous determination method for sequence and configuration of amino acid residues. The applicability of C-terminus sequence analysis and mass spectrometry to configuration determination of amino acids is also discussed.

Qualitative and quantitative aspects of the degradation of several tripeptides derived from the antitumour peptide antagonist [Arg(6), D-Trp(7,9), MePhe(8)] substance P[6-11]

The tripeptides Arg-Trp-Phe, Arg-Trp-Phe-NH2, Phe-Trp-Arg and Phe-Trp-Arg-NH2 were subjected to a degradation study to get a more detailed insight into the degradation processes of the antitumor hexapeptide antagonist [Arg(6), D-Trp(7,9), MePhe(8)] substance P¿6-11¿ which was investigated in earlier research. Degradation kinetics as well as identities of degradation products of the tripeptides emerging in alkaline and acidic media were studied. The amidated forms (Arg-Trp-Phe-NH2, Phe-Trp-Arg-NH2) appear to be less stable than the carboxylic forms (Arg-Trp-Phe, Phe-Trp-Arg). Deamidation of the amide C-terminus, racemization of the Phe and Arg residues, ornithine formation, hydrolysis of the peptide backbone and diketopiperazine formation with elimination of the N-terminal fragments were the major degradative processes. Comparing these reactions with the reactions of antagonist [Arg(6), D-Trp(7,9), MePhe(8)] substance P¿6-11¿ it appeared that racemization of Phe and Arg, hydrolysis of the peptide backbone and diketopiperazine formation did not occur in detectable amounts in the hexapeptide. probably due to lower reaction rates of these reactions compared to the overall degradation rate of antagonist [Arg(6), D-Trp(7,9) MePhe(8)] substance P¿6-11¿.

Characterization and analysis of D-amino acids

The need to screen a large number of natural extracts, with the aim of detecting D-amino acids or isolating and characterizing peptides containing them, has stimulated the development of novel and improved procedures for the analysis of amino acid enantiomeric mixtures, with special attention paid to automation. Different methods for the analysis of D-amino acids are described and discussed.

Hydrolysis and amino acid composition of proteins

Amino acid composition analysis is a classical protein analysis method, which finds a wide application in medical and food science research and is indispensable for protein quantification. It is a complex technique, comprising two steps, hydrolysis of the substrate and chromatographic separation and detection of the residues. A properly performed hydrolysis is a prerequisite of a successful analysis. The most significant developments of the technology in the last decade consist in the (i) reduction of the hydrolysis time by the use of microwave radiation energy; (ii) improvement in the sensitivity of the residue detection, the quantification of the sensitive residues and separation of the enantiomeric forms of the amino acids; (iii) application of amino acid analysis in the large-scale protein identification by database search; and (iv) gradual replacement of the original ion exchange residue separation by reversed-phase high-performance liquid chromatography. Amino acid analysis is currently facing an enormous competition in the determination of the identity of proteins and amino acid homologs by the essentially faster mass spectrometry techniques. The amino acid analysis technology needs further simplification and automation of the hydrolysis, chromatography and detection steps to withstand the pressure exerted by the other technologies.

Analytical techniques used to study the degradation of proteins and peptides: chemical instability

Instability of peptides and proteins can be divided into two forms: chemical and physical instability. Chemical instability is due to modification/alteration of amino acid residues. There are several types of degradation reactions responsible for this instability. Most frequently described reactions are oxidation, reduction, deamidation, hydrolysis, arginine conversion, beta-elimination and racemisation. However, any study of the degradation of a chemical substance lacks reliability when the analytical methodology, that is used is not properly validated. Especially in the investigation, where degradation processes lead to their parent compounds, validation of the analysis is pivotal for the correct interpretation of the results. It is therefore appropriate and useful to assemble an overview of degradation processes in relation to the analytical methods to monitor them. An overview like this can help investigators to make the right choices in their analytical approach of stability problems. The degradation reactions involved in peptide/protein degradation as well as the methods to monitor them are summarized and discussed.

Amino acid sequence and D/L-configuration determination of peptides utilizing liberated N-terminus phenylthiohydantoin amino acids

In this paper, we examined the possibility of using conventional Edman degradation with phenyl isothiocyanate for the simultaneous determination of both the sequence and the D/L-configuration of amino acids in peptides. Boron trifluoride and HCl-methanol (1:10, v/v) were adopted as the cyclization/cleavage and conversion reagents instead of the respective use of anhydrous trifluoroacetic acid (TFA) and 20% aqueous TFA to suppress the amino acid residue racemization. The enantiomeric separation of 18 phenylthiohydantoin amino acids was achieved on two types of chiral stationary phases bonded with beta-cyclodextrin. The proposed Edman procedure was applied to a synthetic beta-amyloid 1-16 with all L-forms as a model peptide, affording the amino acid sequence and configuration determination up to 12 residues.

Structure of fuscopeptins, phytotoxic metabolites of Pseudomonas fuscovaginae

The structure of the fuscopeptins, bioactive lipodepsipeptides produced in culture by the gramineae pathogen Pseudomonas fuscovaginae, has been determined. The combined use of FAB mass spectroscopy NMR spectroscopy and chemical and enzymatic procedures allowed one to define a peptide moiety corresponding to Z-Dhb-D-Pro-L-Leu-D-Ala-D-Ala-D-Ala-D-Ala-D-Val-Gly-D-Ala-D-Val-D-Ala-D- Val-Z-Dhb-Da-Thr-L-Ala-L-Dab-D-Dab-L-Phe with the terminal carboxyl group closing a macrocyclic ring on the hydroxyl group of the allothreonine residue. The N-terminus is in turn acylated by 3-hydroxyoctanoate in fuscopeptin A and 3-hydroxydecanoate in fuscopeptin B. Some preliminary data on the biological activity of fuscopeptins are also reported.