Characterization of the primary structure of H-protein from Pisum sativum and location of a lipoic acid residue by combined liquid chromatography/mass spectrometry and liquid chromatography/tandem mass spectrometry

The glycine decarboxylase system: a fascinating complex

The mitochondrial glycine decarboxylase multienzyme system, connected to serine hydroxymethyltransferase through a soluble pool of tetrahydrofolate, consists of four different component enzymes, the P-, H-, T- and L-proteins. In a multi-step reaction, it catalyses the rapid destruction of glycine molecules flooding out of the peroxisomes during the course of photorespiration. In green leaves, this multienzyme system is present at tremendously high concentrations within the mitochondrial matrix. The structure, mechanism and biogenesis of glycine decarboxylase are discussed. In the catalytic cycle of glycine decarboxylase, emphasis is given to the lipoate-dependent H-protein that plays a pivotal role, acting as a mobile substrate that commutes successively between the other three proteins. Plant mitochondria possess all the necessary enzymatic equipment for de novo synthesis of tetrahydrofolate and lipoic acid, serving as cofactors for glycine decarboxylase and serine hydroxymethyltransferase functioning.

Identification of unusual (modified and non-encoded) amino acid residues in peptides by combinations of high-performance liquid chromatography and high-performance capillary electrophoresis with matrix-assisted laser desorption ionization time-of-flight mass spectrometry

The techniques for micro-level analysis of some widespread unusual amino acids (phosphorylated and hydroxylated ones) as well as of some genetically non-encoded amino acids were developed for their subsequent identification in the peptide and protein amino acid sequence by narrow-bore column high-performance liquid chromatography (approximately 10 pmol of the sample), high-performance capillary electrophoresis (approximately 1-10 pmol), matrix-assisted laser desorption ionization time-of-flight mass spectrometry (approximately 1-10 pmol), and automatic protein gas phase sequencing (approximately 1-50 pmol).

Biochemical dissection of photorespiration

Progress has been made in the understanding of photorespiration and related proteins (Rubisco, glycolate oxidase and glycine decarboxylase) in the context of recent structural information. Numerous shuttles exist to support transamination, ammonia refixation and the supply or export of reductants generated or consumed (via malate-oxaloacetate shuttles) in the photorespiratory pathway. A porin-like channel that is anion selective represents the major permeability pathway of the peroxisomal membrane.

Folates and one-carbon metabolism in plants and fungi

Folate-dependent pathways of one-carbon metabolism are essential for the synthesis of purines, formylmethionyl-tRNA, thymidylate, serine and methionine. These syntheses use a cellular source of one-carbon substituted, tetrahydrofolate polyglutamate derivatives which are the preferred substrates of most folate-dependent enzymes. In the last decade, there have been major advances in the folate biochemistry of animal, bacterial, fungal and plant systems. These have included the refinement of methods for folate isolation and characterization, basic work on key enzymes of folate biosynthesis and the detailed characterization of proteins that catalyze the generation and utilization of one-carbon substituted folates.

Biomedical and biochemical applications of liquid chromatography-mass spectrometry

This review centres on the application of various LC-MS and LC-MS-MS techniques to the study and solution of practical problems in biomedical research. For this purpose it covers a selection of publications in this area included in the MEDLINE database for the period 1991-mid-1994. As shown herein, LC-MS is increasingly gaining in importance in the biomedical field, especially after the revolution brought about by the introduction of the new liquid-phase atmospheric pressure ionization (API) techniques, such as electrospray (ES) and ionspray. The information in this database shows that thermospray (TS), which clearly dominated LC-MS coupling in the 1980s, is on a downward trend relative to the more modern API techniques which will certainly dominate this application field in the present decade. Studies on drug metabolism, therapeutic drug monitoring and pharmacology have been traditionally carried out by GC-MS. However, LC-MS has lately been replacing classical GC-MS techniques in many of these applications. For instance, LC-ES-MS has greatly facilitated the application of both qualitative and quantitative LC-MS methods to highly polar molecules. This is possible without the need to resort to elaborate sample handling and derivatization procedures for relatively high-molecular-mass compounds such as drug conjugates, biosynthetic and natural peptides and therapeutic proteins obtained by recombinant DNA technology, all of them formerly totally inaccessible to the standard GC-MS or LC-MS methods. With regard to studies on metabolism and biochemical phenomena of endogenous compounds, LC-ES-MS is also becoming very strong in the analysis of structural biopolymers such as peptides, proteins, glycoproteins and glycolipids, and also lower molecular mass compounds such as fatty acids, vitamins, steroids and nucleic acids. For example, structural verification of post-translational modifications in proteins can be efficiently obtained in the time frame of an LC run and suitable MS methods for the location of glycopeptide-containing fractions in proteolytic digests of glycoproteins have been developed. Interesting examples are also shown of the use of LC-MS in clinical studies and the determination of biological markers of disease.

The lipoamide arm in the glycine decarboxylase complex is not freely swinging

Glycine decarboxylase consists of four protein components. Its structural and mechanistic heart is provided by the lipoic acid-containing H-protein which undergoes a cycle of reductive methylamination, methylamine transfer and electron transfer. Lipoic acid attached to a specific lysine side chain is assumed to act as a 'swinging arm' conveying the reactive dithiolane ring from one catalytic centre to another. The X-ray crystal structures of two forms of the H-protein have been determined. The lipoate cofactor is located in the loop of a hairpin configuration but following methylamine transfer it is pivoted to bind into a cleft at the surface of the H-protein. The lipoamide-methylamine arm is, therefore, not free to move in aqueous solvent.

X-ray structure determination at 2.6-A resolution of a lipoate-containing protein: the H-protein of the glycine decarboxylase complex from pea leaves

H-protein, a lipoic acid-containing protein of the glycine decarboxylase (EC 1.4.4.2) complex from pea (Pisum sativum) was crystallized from ammonium sulfate solution at pH 5.2 in space group P3(1)21. The x-ray crystal structure was determined to 2.6-A resolution by multiple isomorphous replacement techniques. The structure was refined to an R value of 23% for reflections between 15- and 2.6-A resolution (F > 2 sigma), including the lipoate moiety and 50 water molecules, for the two protein molecules of the asymmetric unit. The 131-amino acid residues form seven beta-strands arranged into two antiparallel beta-sheets forming a "sandwich" structure. One alpha-helix is observed at the C-terminal end. The lipoate cofactor attached to Lys-63 is located in the loop of a hairpin configuration. The lipoate moiety points toward the residues His-34 and Asp-128 and is situated at the surface of the H-protein. This allows the flexibility of the lipoate arm. This is the first x-ray determination of a lipoic acid-containing protein, and the present results are in agreement with previous theoretical predictions and NMR studies of the catalytic domains of lipoic acid- and biotin-containing proteins.