Philipp Christen

The Molecular Evolution of Pyridoxal‐5′‐Phosphate‐Dependent Enzymes

The pyridoxal-5-phosphate-dependent enzymes (B6 enzymes) that act on amino acid substrates are of multiple evolutionary origin. The numerous common mechanistic features of B6 enzymes thus are not historical traits passed on from a common ancestor enzyme but rather reflect evolutionary or chemical necessities. Family profile analysis of amino acid sequences supported by comparison of the available three-dimensional (3-D) crystal structures indicates that the B6 enzymes known to date belong to four independent evolutionary lineages of homologous (or more precisely paralogous) proteins, of which the alpha family is by far the largest. The alpha family (with aspartate aminotransferase as the prototype enzyme) includes enzymes that catalyze, with several exceptions, transformations of amino acids in which the covalency changes are limited to the same carbon atom that carries the amino group forming the imine linkage with the coenzyme (i.e., Calpha in most cases). Enzymes of the beta family (tryptophan synthase beta as the prototype enzyme) mainly catalyze replacement and elimination reactions at Cbeta. The D-alanine aminotransferase family and the alanine racemase family are the two other independent lineages, both with relatively few member enzymes. The primordial pyridoxal-5-phosphate-dependent enzymes apparently were regio-specific catalysts that first diverged into reaction-specific enzymes and then specialized for substrate specificity. Aminotransferases as well as amino acid decarboxylases are found in two different evolutionary lineages. Comparison of sequences from eukaryotic, archebacterial, and eubacterial species indicates that the functional specialization of most B6 enzymes has occurred already in the universal ancestor cell. The cofactor pyridoxal-5-phosphate must have emerged very early in biological evolution; conceivably, organic cofactors and metal ions were the first biological catalysts. In attempts to stimulate particular steps of molecular evolution, oligonucleotide-directed mutagenesis of active-site residues and directed molecular evolution have been applied to change both the substrate and reaction specificity of existent B6 enzymes. Pyridoxal-5-phosphate-dependent catalytic antibodies were elicited with a screening protocol that applied functional selection criteria as they might have been operative in the evolution of protein-assisted pyridoxal catalysis.

Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics

The assimilation of one-carbon (C1) compounds, such as methanol, by serine cycle methylotrophs requires the continuous regeneration of glyoxylate. Instead of the glyoxylate cycle, this process is achieved by a not yet established pathway where CoA thioesters are known to play a key role. We applied state-of-the-art metabolomics and 13C metabolomics strategies to demonstrate how glyoxylate is generated during methylotrophic growth in the isocitrate lyase-negative methylotroph Methylobacterium extorquens AM1. High-resolution mass spectrometry showed the presence of CoA thioesters specific to the recently proposed ethylmalonyl-CoA pathway. The operation of this pathway was demonstrated by short-term 13C-labeling experiments, which allowed determination of the sequence of reactions from the order of label incorporation into the different CoA derivatives. Analysis of 13C positional enrichment in glycine by NMR was consistent with the predicted labeling pattern as a result of the operation of the ethylmalonyl-CoA pathway and the unique operation of the latter for glyoxylate generation during growth on methanol. The results also revealed that 2 molecules of glyoxylate were regenerated in this process. This work provides a complete pathway for methanol assimilation in the model methylotroph M. extorquens AM1 and represents an important step toward the determination of the overall topology of its metabolic network. The operation of the ethylmalonyl-CoA pathway in M. extorquens AM1 has major implications for the physiology of these methylotrophs and their role in nature, and it also provides a common ground for C1 and C2 compound assimilation in isocitrate lyase-negative bacteria.

Heavy metal ions are potent inhibitors of protein folding

Environmental and occupational exposure to heavy metals such as cadmium, mercury and lead results in severe health hazards including prenatal and developmental defects. The deleterious effects of heavy metal ions have hitherto been attributed to their interactions with specific, particularly susceptible native proteins. Here, we report an as yet undescribed mode of heavy metal toxicity. Cd2+, Hg2+ and Pb2+ proved to inhibit very efficiently the spontaneous refolding of chemically denatured proteins by forming high-affinity multidentate complexes with thiol and other functional groups (IC(50) in the nanomolar range). With similar efficacy, the heavy metal ions inhibited the chaperone-assisted refolding of chemically denatured and heat-denatured proteins. Thus, the toxic effects of heavy metal ions may result as well from their interaction with the more readily accessible functional groups of proteins in nascent and other non-native form. The toxic scope of heavy metals seems to be substantially larger than assumed so far.

Heavy Metals and Metalloids As a Cause for Protein Misfolding and Aggregation

While the toxicity of metals and metalloids, like arsenic, cadmium, mercury, lead and chromium, is undisputed, the underlying molecular mechanisms are not entirely clear. General consensus holds that proteins are the prime targets; heavy metals interfere with the physiological activity of specific, particularly susceptible proteins, either by forming a complex with functional side chain groups or by displacing essential metal ions in metalloproteins. Recent studies have revealed an additional mode of metal action targeted at proteins in a non-native state; certain heavy metals and metalloids have been found to inhibit the in vitro refolding of chemically denatured proteins, to interfere with protein folding in vivo and to cause aggregation of nascent proteins in living cells. Apparently, unfolded proteins with motile backbone and side chains are considerably more prone to engage in stable, pluridentate metal complexes than native proteins with their well-defined 3D structure. By interfering with the folding process, heavy metal ions and metalloids profoundly affect protein homeostasis and cell viability. This review describes how heavy metals impede protein folding and promote protein aggregation, how cells regulate quality control systems to protect themselves from metal toxicity and how metals might contribute to protein misfolding disorders.

Arsenite interferes with protein folding and triggers formation of protein aggregates in yeast.

Summary Several metals and metalloids profoundly affect biological systems, but their impact on the proteome and mechanisms of toxicity are not fully understood. Here, we demonstrate that arsenite causes protein aggregation in Saccharomyces cerevisiae. Various molecular chaperones were found to be associated with arsenite-induced aggregates indicating that this metalloid promotes protein misfolding. Using in vivo and in vitro assays, we show that proteins in the process of synthesis/folding are particularly sensitive to arsenite-induced aggregation, that arsenite interferes with protein folding by acting on unfolded polypeptides, and that arsenite directly inhibits chaperone activity. Thus, folding inhibition contributes to arsenite toxicity in two ways: by aggregate formation and by chaperone inhibition. Importantly, arsenite-induced protein aggregates can act as seeds committing other, labile proteins to misfold and aggregate. Our findings describe a novel mechanism of toxicity that may explain the suggested role of this metalloid in the etiology and pathogenesis of protein folding disorders associated with arsenic poisoning.

Induction of antibodies against murine full-length prion protein in wild-type mice

The causative and infectious agent of the transmissible spongiform encephalopathies, e.g. bovine spongiform encephalopathy in cattle or variant Creutzfeldt-Jakob disease in humans, is a pathogenic form of the scrapie prion protein (PrP(Sc)) generated by a conformational rearrangement in the normal cellular prion protein (PrP(C)). Anti-PrP antibodies have been shown to exert a protective effect against infection with PrP(Sc). However, the generation of anti-PrP antibodies has proven quite difficult in wild-type animals, PrP being a notoriously poor immunogen. We developed a vaccine against PrP by mixing recombinant murine PrP 23-231 with DnaK, an Hsp70 homolog in Escherichia coli, and cross-linking the two proteins by means of glutaraldehyde. After three injections of the vaccine into BALB/c mice at 6, 8 and 9 weeks of age, a low-titer immune response was detected with ELISA in all animals. The specificity of the antibodies for PrP was confirmed with Western blotting. The straightforward procedure might render active immunization against prion infection feasible.

Isolation, crystallization and preliminary crystallographic data of aspartate aminotransferase from chicken heart mitochondria☆

Abstract The mitochondrial isoenzyme of aspartate aminotransferase (E.C. 2.6.1.1) has been isolated from chicken heart in an electrophoretically and immunologically homogeneous form. Large, well-diffracting single crystals of this enzyme, a dimeric molecule with a molecular weight of 90,000, have been grown by vapour phase diffusion against polyethylene glycol solutions. The crystals belong to space group P1. The unit cell, with the dimensions a = 55.6 A , 6 = 58.7 A , c = 76.0 A , α = 85.3 °, β = 109.2 °, γ = 115.6 °, contains a single dimer. The diffraction pattern extends to at least 2.1 A resolution.

Neurotoxicity of prion peptide 106-126 not confirmed.

Prion‐related diseases are accompanied by neurodegeneration, astroglial proliferation and formation of proteinase K‐resistant aggregates of the scrapie isoform of the prion protein (PrPSc). The synthetic PrP fragment 106‐126 was reported to be neurotoxic towards cultured rat hippocampal neurons (Forloni, G., Angeretti, N., Chiesa, R., Monzani, E., Salmona, M., Bugiani, O. and Tagliavini, F. (1993) Nature 362, 543–546) and mouse cortical cells (Brown, D.R., Herms, J. and Kretzschmar, H.A. (1994) Neuroreport 5, 2057–2060). However, we found the viability of these and other neuronal cell types not to be impaired in the presence of PrP106‐126 under widely varied sets of conditions. Aged preparations of the peptide as well as synthetic deamidated and isomerized derivatives that correspond to the aging products of the peptide proved also to lack neurotoxicity. Apparently, PrP106‐126 cannot serve as a model for the interaction of PrP with neuronal cells.

Amino acid analysis by high-performance liquid chromatography after derivatization with 1-fluoro-2,4-dinitrophenyl-5-L-alanine amide.

Amino acids are quantitatively determined by precolumn derivatization with 1-fluoro-2,4-dinitrophenyl-5-L-alanine amide and reversed-phase high-performance liquid chromatography with photometric detection at 340 nm. Excellent chromatographic resolution of a mixture of the derivatives of 20 amino acids including proline and cystine is achieved within 110 min by linear gradient elution with acetonitrile in 13 mM trifluoroacetate plus 4% (by vol) tetrahydrofuran. The limit of detection is 50 pmol. Amino acid analyses of acid hydrolysates of the several proteins gave results equivalent to those obtained by conventional ion-exchange-based amino acid analysis. The simplicity of the procedure allows its use on any multipurpose high-performance liquid chromatographic system.

Chemical evidence for syncatalytic conformational changes in aspartate aminotransferase

Conformational changes in proteins are well established experimentally, as the structural changes correlate with the transitions between different functional states. In enzymes, particularly, conformational alterations appear to play a fundamental role for both the regulation of activity and the mechanism of action. In a number of instances they have been found to accompany the formation of the enzyme-substrate adsorption complex [cf. 21 . However, chemical modification studies with aspartate aminotransferase have recently indicated that conformational changes may also occur during the subsequent phase of catalysis when covalent bonds are formed and broken [3] . These structural alterations have now been explored by probing the reactivity of sulfhydryl groups toward Nethylmaleimide in different enzyme-substrate intermediates of the multistep reaction sequence. In a distinct phase of catalysis, most probably in the ketimine complex, two sulfhydryl groups are at least one order of magnitude more reactive than either in the other enzymesubstrate complexes or in the free enzyme. Blocking of these two groups reduces enzymatic activity about a hundred-fold.