Trypsin, a high fidelity protease, is the most widely used enzyme for protein digestion in proteomic research. Optimal digestion conditions are well-known and so are the expected cleavage products. However, missed cleavage sites are frequently observed when acidic amino acids, aspartic and glutamic acids, are present near the cleavage site. Also, the sequence motifs with successive lysine and/or arginine residues represent a source of missed cleaved sites. In spite of an adverse role of missed cleaved peptides on proteomic research, the digestion kinetics of these problematic sequences is not well-known. In this work, synthetic peptides with various sequence motifs were used as trypsin substrates. Cleavage products were analyzed with reversed-phase high performance liquid chromatography, and the kinetic constants for selected missed cleavage sites were calculated. Relative digestion speed for lysine and arginine sites is compared, including the digestion motifs flanked with aspartic and glutamic acid. Our findings show that DK and DTR motifs are cleaved by trypsin with 3 orders of magnitude lower speed than the arginine site. These motifs are likely to produce missed cleavage peptides in protein tryptic digests even at prolonged digestion times.
Abstract:Occurrence of D-amino acids in living organisms is a useful indicator of various changes, diseases, or disorders. Determination of amino acid enantiomers, namely the enantiomeric ratio of amino acids or excess of certain D-amino acids, represents a useful tool in the studies of aging processes or biomarkers in disease/disorder diagnosis in humans. The amount of D-amino acids is usually very low. Therefore, suitable sample pretreatment, often derivatization, and highly selective and sensitive separation methods are essential for D-amino acid analysis in this field. Chromatographic techniques offer appropriate choices for solving these tasks. This review covers the advances in methodology and development of improved instrumental chromatographic methods focused on D,L-amino acid separation and determination. New findings in the area of possible D-amino acid biomarkers are also included.
Oligosaccharide-based chiral stationary phases are frequently used for enantioselective separations by different chromatographic techniques, namely gas chromatography, high performance liquid chromatography, supercritical fluid chromatography or capillary electrochromatography. Their multimodal application potential (they are compatible with both polar and/or non-polar mobile phases) makes them suitable chiral selector candidates for separation of a wide variety of structurally diverse compounds. In this paper, separation systems utilizing cyclodextrin- or cyclofructan-based chiral stationary phases in analyses of pharmacologically active compounds are summarized. The review covers the period from 2000 to 2015. This review article can be helpful to analysts searching for an appropriate method for the separation/determination of pharmaceuticals of their interest.
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