The proteolysis of proteins during folding.
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L-Lactate Dehydrogenase↗
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Cobalamin (Cbl) C/D deficiency: clinical, neurophysiological and neuroradiologic findings in 14 cases.
The early onset type of cobalamin (Cbl) C/D deficiency is characterised by feeding difficulties, failure to thrive, hypotonia, seizures, microcephaly and developmental delay. It has an unfavourable outcome, often with early death and significant neurological impairment in survivors. While clinical and biochemical features of Cbl C/D deficiency are well known, only a few isolated case reports are available concerning neurophysiological and neuroimaging findings. We carried out clinical, biochemical, neurophysiological and neuroradiologic investigations in 14 cases with early-onset of the Cbl CID defect. Mental retardation was identified in most of the cases. A variable degree of supratentorial white matter atrophy was detected in 11 cases by MR imaging and tetraventricular hydrocephalus was present in the remaining 3 patients. Waking EEG showed a clear prevalence of epileptiform abnormalities, possibly related to the high incidence of seizures in these cases. Increased latency of evoked responses and/or prolongation of central conduction time were the most significant neurophysiological abnormalities. The selective white matter involvement, shown both by neuroradiologic and neurophysiological studies, seems to be the most consistent finding of Cbl C/D deficiency and may be related to a reduced supply of methyl groups, possibly caused by the dysfunction in the methyl-transfer pathway.
5-Methyltetrahydrofolate-Homocysteine S-Methyltran↗
A cobalamin metabolic defect with homocystinuria, methylmalonic aciduria and macrocytic anemia.
We have identified a patient with methylmalonic aciduria and homocystinuria due to a defect in cobalamin metabolism of the cb1C type mutant. At the time of admission at eight months of age the patient was malnourished, hypotonic and had macrocytic anemia. Neonatal screening for hypermethioninemia associated with homocystinuria had been normal. Serum vitamin B12 was markedly increased and folate concentration was above normal, as were urinary homocystine and methylmalonic acid. The patient had abnormal brain stem auditory and visual evoked potentials. Fibroblast activity of N5-methyltetrahydrofolate: homocysteine methyltransferase was reduced to approximately 10% of concurrent controls. A course of therapy with hydroxocobalamin resulted in a 90% reduction in excretion of methylmalonic acid and normalization of the evoked potentials. These studies support the efficacy of hydroxocobalamin therapy in this disease, suggest that methylmalonic acid may be the most appropriate metabolite to monitor for therapeutic response, and in importance of electrophysiologic studies in character in objectively monitoring the response to treatment metabolic disease.
5-Methyltetrahydrofolate-Homocysteine S-Methyltran↗
Prenatal therapy of a patient with vitamin-B12-responsive methylmalonic acidemia.
Methylmalonic acidemia due to deficient synthesis of 5'-deoxyadenosylcobalamin was discovered in a mid-term fetus by culture of amniotic-fluid cells. Elevated concentrations of methylmalonic acid were also found in amniotic fluid and maternal urine. Treatment during the last nine weeks of gestation with large doses of vitamin B12 given to the mother reversed the increasing maternal excretion of methylmalonic acid, which was 23 mug per milligram of creatinine at 31 weeks' gestation. Just before delivery, the mother was excreting 5 mug, two to three times normal. At birth the methylmalonic acid content of the baby's urine (67 mug per milligram of creatinine) and serum (2.0 mug per milliliter) was only moderately elevated, and serum vitamin B12 concentration was very high. Acid levels rose in serum and urine in response to oral protein loading, but subsided after vitamin B12 administration. The infant is developing normally on a restricted protein diet alone at present. Prenatal therapy of methylmalonic acidemia is possible with large amount of vitamin B12 administered to the mother.
Amino Acid Metabolism, Inborn Errors↗
Hereditary defect of cobalamin metabolism (cblG mutation) presenting as a neurologic disorder in adulthood.
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5-Methyltetrahydrofolate-Homocysteine S-Methyltran↗
Combinatorial methods for small-molecule placement in computational enzyme design.
The incorporation of small-molecule transition state structures into protein design calculations poses special challenges because of the need to represent the added translational, rotational, and conformational freedoms within an already difficult optimization problem. Successful approaches to computational enzyme design have focused on catalytic side-chain contacts to guide placement of small molecules in active sites. We describe a process for modeling small molecules in enzyme design calculations that extends previously described methods, allowing favorable small-molecule positions and conformations to be explored simultaneously with sequence optimization. Because all current computational enzyme design methods rely heavily on sampling of possible active site geometries from discrete conformational states, we tested the effects of discretization parameters on calculation results. Rotational and translational step sizes as well as side-chain library types were varied in a series of computational tests designed to identify native-like binding contacts in three natural systems. We find that conformational parameters, especially the type of rotamer library used, significantly affect the ability of design calculations to recover native binding-site geometries. We describe the construction and use of a crystallographic conformer library and find that it more reliably captures active-site geometries than traditional rotamer libraries in the systems tested.
Catalytic Domain↗
The yeast A kinases differentially regulate iron uptake and respiratory function.
Yeast has three A kinase catalytic subunits, which have greater than 75% identity and are encoded by the TPK genes (TPK1, TPK2, and TPK3) [Toda, T., Cameron, S., Sass, P., Zoller, M. & Wigler, M. (1987) Cell 50, 277-287]. Although they are redundant for viability, the three A kinases are not redundant for pseudohyphal growth [Robertson, L. S. & Fink, G. R. (1998) Proc. Natl. Acad. Sci. USA 95, 13783-13787; Pan, X. & Heitman, J. (1999) Mol. Cell. Biol. 19, 4874-4887]; Tpk2, but not Tpk1 or Tpk3, is required for pseudohyphal growth. Genome-wide transcriptional profiling has revealed unique signatures for each of the three A kinases leading to the identification of additional functional diversity among these proteins. Tpk2 negatively regulates genes involved in iron uptake and positively regulates genes involved in trehalose degradation and water homeostasis. Tpk1 is required for the derepression of branched chain amino acid biosynthesis genes that seem to have a second role in the maintenance of iron levels and DNA stability within mitochondria. The fact that TPK2 mutants grow better than wild types on nonfermentable carbon sources and on media deficient in iron supports the unique role of Tpk2 in respiratory growth and carbon source use.
2-Acetolactate Mutase↗
The near attack conformation approach to the study of the chorismate to prephenate reaction.
Standard free energies (DeltaGN degree) for formation of near attack conformers, those ground state conformers that can convert directly to the transition state, were calculated for the Claisen rearrangement of chorismate to prephenate in six different environments: water, wild-type enzymes from Bacillus subtilis and Escherichia coli, their Arg90Cit and Glu52Ala mutants, and the 1F7 catalytic antibody. Values of the calculated DeltaGN degrees and the experimentally determined activation energies (DeltaG++) are linearly related with the slope of approximately equal to 1. This demonstrates that the relative rate of the chorismate --> prephenate reaction is overwhelmingly dependent on the efficiency of formation of near attack conformers in the ground state.
Animals↗
How an enzyme surmounts the activation energy barrier.
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Catalysis↗
Handedness of crossover connections in beta sheets.
In a crossover connection, the polypeptide chain leaves one end of a beta sheet, forms a loop of any length and any conformation, and reenters the same beta sheet from the opposite end. Of the 85 examples of crossover connections which occur in the known protein structures, 83 are righthanded and only two are lefthanded. It is proposed that consistent handedness, even in long irregular loops, could be produced by the preferred twist direction of extended chain and the righthandedness of alpha-helices, provided certain conditions hold during the protein folding process.
Carboxypeptidases↗
Protein phosphorylation in pancreatic islets induced by 3-phosphoglycerate and 2-phosphoglycerate.
We have shown previously that 3-phosphoglycerate, which is a glycolytic metabolite of glucose, induces protein phosphorylation in bovine and rat brain and in rat heart, kidney, liver, lung, and whole pancreas. Since glycolytic metabolism of glucose is of paramount importance in insulin release, we considered the possibility that 3-phosphoglycerate may act as a coupling factor, and we searched for evidence for the existence of 3-phosphoglycerate-dependent protein phosphorylation systems in freshly isolated normal rat pancreatic islets. Membrane and cytosol fractions were incubated with [gamma-32P]ATP and appropriate test substances and were subjected to NaDodSO4/PAGE and autoradiography. As little as 0.005 mM 3-phosphoglycerate or 2-phosphoglycerate stimulated the phosphorylation of a 65-kDa cytosol protein by as early as 0.25 min. The phosphate bond of the 65-kDa phosphoprotein was sufficiently stable to withstand dialysis; the radioactivity could not be chased out by subsequent exposure to ATP, ADP, 3-phosphoglycerate, or 2,3-bisphosphoglycerate. Moreover, cAMP, cGMP, phorbol 12-myristate 13-acetate, or calcium failed to stimulate the phosphorylation of the 65-kDa protein. Phosphoglycerate-dependent protein phosphorylation in islets may have relevance to stimulation of insulin secretion.
Bisphosphoglycerate Mutase↗
The enigma of cobalamin (Vitamin B12) biosynthesis in Porphyromonas gingivalis. Identification and characterization of a functional corrin pathway.
The ability of Porphyromonas gingivalis to biosynthesize tetrapyrroles de novo has been investigated. Extracts of the bacterium do not possess activity for 5- aminolevulinic-acid dehydratase or porphobilinogen deaminase, two key enzymes involved in the synthesis of uroporphyrinogen III. Similarly, it was not possible to detect any genetic evidence for these early enzymes with the use of degenerate polymerase chain reaction. However, the bacterium does appear to harbor some of the enzymes for cobalamin biosynthesis since cobyric acid, a pathway intermediate, was converted into cobinamide. Furthermore, degenerate polymerase chain reaction with primers to cbiP, which encodes cobyric-acid synthase, produced a fragment with a high degree of identity to Salmonella typhimurium cbiP. Indeed, the recently released genome sequence data confirmed the presence of cbiP together with 14 other genes of the cobalamin pathway. A number of these genes were cloned and functionally characterized. Although P. gingivalis harbors all the genes necessary to convert precorrin-2 into cobalamin, it is missing the genes for the synthesis of precorrin-2. Either the organism has a novel pathway for the synthesis of precorrin-2, or more likely, it has lost this early part of the pathway. The remainder of the pathway may be being maintained to act as a salvage route for corrin synthesis.
Base Sequence↗
Membrane binding modulates the quaternary structure of CTP:phosphocholine cytidylyltransferase.
CTP:phosphocholine cytidylyltransferase (CCT), a key enzyme that controls phosphatidylcholine synthesis, is regulated by reversible interactions with membranes containing anionic lipids. Previous work demonstrated that CCT is a homodimer. In this work we show that the structure of the dimer interface is altered upon encountering membranes that activate CCT. Chemical cross-linking reactions were established which captured intradimeric interactions but not random CCT dimer collisions. The efficiency of capturing covalent cross-links with four different reagents was diminished markedly upon presentation of activating anionic lipid vesicles but not zwitterionic vesicles. Experiments were conducted to show that the anionic vesicles did not interfere with the chemistry of the cross-linking reactions and did not sequester available cysteine sites on CCT for reaction with the cysteine-directed cross-linking reagent. Thus, the loss of cross-linking efficiency suggested that contact sites at the dimer interface had increased distance or reduced flexibility upon binding of CCT to membranes. The regions of the enzyme involved in dimerization were mapped using three approaches: 1) limited proteolysis followed by cross-linking of fragments, 2) yeast two-hybrid analysis of interactions between select domains, and 3) disulfide bonding potential of CCTs with individual cysteine to serine substitutions for the seven native cysteines. We found that the N-terminal domain (amino acids 1-72) is an important participant in forming the dimer interface, in addition to the catalytic domain (amino acids 73-236). We mapped the intersubunit disulfide bond to the cystine 37 pair in domain N and showed that this disulfide is sensitive to anionic vesicles, implicating this specific region in the membrane-sensitive dimer interface.
Animals↗
Proteome analysis of intact proteins in complex mixtures.
Analysis of intact protein mixtures by electrospray ionization mass spectrometry requires the resolution of a complex, overlapping set of multiply charged envelopes. To ascertain the ability of a moderate resolution mass spectrometer to resolve such mixtures, we have analyzed the soluble proteins of adult chick skeletal muscle. This is a highly specialized tissue showing a marked bias in expression of glycolytic enzymes in the soluble fraction. SDS-PAGE-resolved proteins were first identified by a combination of matrix-assisted laser desorption ionization time-of-flight (TOF) and electrospray ionization tandem mass spectrometry. Then the mixture of intact proteins was introduced into the electrospray source of a Q-TOF mass spectrometer either by direct infusion or via a C4 desalting trap. In both instances, the complex pattern of peaks could be resolved into true masses, and these masses could in many instances be reconciled with the masses predicted from the known protein sequences when qualified by expected co- and post-translational modifications. These included loss of the N-terminal initiator methionine residue and N-terminal acetylation. The ability to resolve such a complex mixture of proteins with a routine instrument is of considerable value in analyses of protein expression and in the confirmation of post-translational changes in mature proteins.
Amino Acid Sequence↗
The ILV5 gene of Saccharomyces cerevisiae is highly expressed.
The nucleotide sequence of the yeast ILV5 gene, which codes for the branched-chain amino acid biosynthesis enzyme acetohydroxyacid reductoisomerase, has been determined. The ILV5 coding region is 1,185 nucleotides, corresponding to a polypeptide with a molecular weight of 44,280. Transcription of the ILV5 mRNA initiates at position -81 upstream from the ATG translation start codon and terminates between 218 and 222 bases downstream from the stop codon. Consensus sequences have been identified for initiation and termination of transcription, and for general control of amino acid biosynthesis, as well as repression by leucine. The ILV5 gene is regulated slightly by general amino acid control. Codon usage of the ILV5 gene has the strong bias observed in yeast genes that are highly expressed. In agreement with this, the reductoisomerase monomer, with an apparent molecular weight of 40,000, has been identified in an SDS polyacrylamide gel pattern of total soluble yeast proteins as a gene dosage dependent band.
2-Acetolactate Mutase↗
Disruption of phase during PCR amplification and cloning of heterozygous target sequences.
PCR amplification of genomic DNA or cDNA has become a standard tool for identification of mutations underlying genetic disease. There are inherent limitations in the application of this method in compound heterozygotes. One problem which is encountered is the disruption of phase (linkage) between heterozygous polymorphisms represented on heterologous alleles. A test system was used to demonstrate and quantitate the disruption of phase between two polymorphic restriction sites. Phase is disrupted in approximately 1% of the PCR amplified material, possibly due to incomplete chain elongations and subsequent priming on the heterologous allele. Phase is disrupted in approximately 1/4 of cloned PCR fragments, possibly due to excision repair of heteroduplexes during cloning. The implications of these disruptions for the use of PCR in identifying mutations are discussed.
Base Sequence↗
Essential arginyl residues in yeast phosphoglyceromutase.
Inactivation of yeast phosphoglyceromutase (tetramer) with 1,2-cyclohexanedione correlates with the modification of six arginyl residues per mole of the enzyme. Protection experiments using 3-phosphoglycerate suggest that four arginyl residues (one residue per subunit) are involved in the binding of the substrate to the enzyme. The modified enzyme reversibly regained its activity upon incubation with hydroxylamine. The reactivity of lysyl residues which have been shown to be involved in the active site is markedly reduced in the enzyme inactivated with 1,2-cyclohexanedione, indicating that the lysyl and arginyl residues are in close proximity in the active site.
Arginine↗
The influence of nitrous oxide on methionine, S-adenosylmethionine, and other amino acids.
Fasting rats were exposed to nitrous oxide (70% N2O/30% O2) for 24 h, a period of time sufficient to inactivate methionine synthase (correct trivial name). A spectrum of amino acids was measured in the brain, plasma, and liver. In addition, S-adenosylmethionine was measured in the liver and brain and glutathione was measured in the liver. Nitrous oxide caused no changes in the circulating concentrations of amino acids except for a decrease in tyrosine and alanine. Many amino acids were decreased in the liver, including glycine, tyrosine, phenylalanine, and methionine. In the brain, only methionine and tyrosine were reduced. The administration of methionine did not reverse any of the amino acid changes except to increase methionine concentrations in the plasma and brain. Nitrous oxide reduced S-adenosylmethionine in the brain and liver. Administration of methionine to nitrous oxide-treated rats increased the level of S-adenosylmethionine in the liver and brain by 109% and 38% respectively above the control value. Liver glutathione (reduced) was unaffected by nitrous oxide. These results demonstrate that nitrous oxide can decrease the concentrations of two intermediary metabolites (methionine and S-adenosylmethionine) that are important in the control of methylation reactions and in the maintenance of the active form of tetrahydrofolic acid. Although nitrous oxide potentially is a strong oxidizing agent, there was no evidence of a disturbance in the liver glutathione pool.
5-Methyltetrahydrofolate-Homocysteine S-Methyltran↗