Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
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Phenylketonuria (PKU) is a disease in which phenylalanine and phenylalanine-derived metabolites build up to neurotoxic levels due to mutations in the phenylalanine hydroxylase gene (PAH). Enzyme replacement therapy is a viable option to supply active PAH. However, the inherent protease sensitivity and potential immunogenicity of PAH have precluded adoption of this approach. In this report, we have used polyethylene glycol derivatization (PEGylation) to produce protected forms of PAH for potential therapeutic use. Three recombinantly produced PAH enzymes were reacted with activated PEG species, with the aim of developing a stable and active PKU enzyme replacement. Tetrameric full-length human PAH, dimeric double-truncated (DeltaN102-DeltaC428) human PAH, and monomeric Chromobacterium violaceum PAH were PEGylated with succinimidyl succinate polyethylene glycol of molecular weight 5000 or 20,000 Da. Characterization of the PEGylated species was accomplished with MALDI-TOF mass spectrometry, SDS-PAGE, and specific activity measurements using ESI mass spectrometry. All PEG-derivatized PAH species retained catalytic activity, and, at low numbers of PEG molecules attached, these PEGylated PAH proteins were found to be more active and more stable than their non-derivatized PAH counterparts.
Mol Ther 2004 Jan
PMID:Toward PKU enzyme replacement therapy: PEGylation with activity retention for three forms of recombinant phenylalanine hydroxylase. 1474 85

To isolate high molecular weight (HMW) or low-abundance proteins we exploited the high resolving power provided by the molecular sieves of polyacrylamide gel matrices. Rice-leaf protein extracts were applied to a single well of an SDS-polyacrylamide gel with prestained molecular size markers at both ends. After electrophoresis, the gel was cut into 4 segments according to size, and each segment was ground in extraction buffer. The eluted proteins were separated from the gel matrix by centrifugation followed by acetone precipitation, and the precipitated proteins were subjected to SDS-PAGE and 2-DE. The SDS-PAGE-based prefractionation method provided non-overlapping discrete sample pools. About 27% more protein spots were detected in the fractionated samples than in the unfractionated samples, and 17% were enhanced. The improvement was especially prominent in the case of HMW proteins. Well-separated HMW proteins were analyzed by MALDI-TOF mass spectrometry. The molecular masses of the identified proteins in the > 48 kDa gel segment were distributed between 50 and 112 kDa, thus validating this prefractionation method. Identified HMW proteins with similar mass but different pI were mostly isoforms. Thus SDS-PAGE-based size prefractionation provides improved separation and detection of HMW proteins.
Mol Cells 2003 Dec 31
PMID:Prefractionation of protein samples for proteome analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. 1474 21

The primary structure of proteins is nowadays determined by DNA sequencing, and a variety of genomes are already known. Nevertheless, protein sequencing/identification is still indispensable to analyze the proteins expressed in a cell, to identify specific proteins, and to determine posttranslational modifications. Proteins of interest are typically available in low microgram amounts or even less. The separation method of choice is gel electrophoresis, followed by blotting to PVDF membrane for N-terminal sequencing or by in-gel digestion to generate peptides that can be separated by HPLC. Structural analysis can be done by Edman degradation or mass spectrometry (MS). Edman degradation is the older method based on successive removal of N-terminal amino acids by chemical methods. Sequencing of a peptide requires many hours, the sensitivity is in the range of 2-5 pmol of a purified peptide. Nevertheless, Edman degradation is still the workhorse in the lab for routine work such as identification of blotted proteins. It is also the method of choice for sequencing unknown proteins/ peptides and modified peptides. MS has routinely been used with peptides in the range of 100 fmol or even less. In contrast to Edman degradation, complex mixtures such as tryptic digests can be analyzed, making HPLC separation of peptides unnecessary. MS is a very fast method that can be automated. It is the method of choice for sensitive analysis and large-scale applications (proteomics). Two different ionization methods are commonly used to generate peptide/protein ions for MS analysis. These are MALDI (matrix assisted laser desorption and ionization) and ESI (electrospray ionization). They can be combined with a variety of mass analyzers (TOF, quadrupole, ion trap). Proteins are either identified by searching databases with the masses of proteolytic peptides (peptide mass fingerprinting) or using fragmentation data (raw MS/MS spectra or sequence tags). This approach requires that the protein is known and listed in the database. De novo sequencing by MS of peptides is possible, but very time consuming and not a routine application, in contrast to Edman degradation. The aim of this chapter is to introduce to basic theory, practical applications and limitations of the various methods, to enable the non-expert scientist to decide which method is best suited for his project and which kind of sample preparation is necessary.
Methods Mol Med 2004
PMID:Structural characterization of proteins and peptides. 1495 36

Alterations in the phospholipid (PL) composition of spermatozoal membranes occur during the fertilization process. Furthermore, membrane lipid composition is of high interest with respect to cryopreservation. The PL and fatty acid compositions of human and boar spermatozoa are compared by using matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) in combination with thin-layer chromatography and 31P NMR spectroscopy. The extreme sensitivity of alkenyl-linked PL against acid treatment was used to estimate the plasmalogen content of spermatozoa. Compared with humans, boar spermatozoa are characterized by a lower variability of their PL and fatty acid composition. Additionally, boar spermatozoa contain much higher moieties of alkyl-linked compounds, e.g. 1-palmityl-2-docosapentaenoyl-sn-glycero-3-phosphocholine and 1-palmityl-2-docosahexaenoyl-sn-glycero-3-phosphocholine as well as the corresponding phosphatidylethanolamine (PE), while human spermatozoa are characterized by high contents of diacyl-PL, e.g. 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine. A considerable plasmalogen moiety, for instance 1-palmitenyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine is a typical feature of both, human and boar spermatozoa. It will be shown that these differences in PL composition can be very rapidly and conveniently assessed by MALDI-TOF MS in combination with TLC and also by 31P NMR.
Comp Biochem Physiol B Biochem Mol Biol 2004 Feb
PMID:Analysis of the lipid composition of human and boar spermatozoa by MALDI-TOF mass spectrometry, thin layer chromatography and 31P NMR spectroscopy. 1499 Feb 23

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common X-linked hereditary enzymopathy. We describe here the techniques based on matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and multiprimer extension (multi-PEX) to detect the most common Chinese G6PD mutations, which are the single-point mutations G-->T at nt 1376, G-->A at nt 1388, A-->G at nt 95, G-->T at nt 392, C-->T at nt 1024, and C-->T at nt 1311. Fifteen samples were genotyped using this method coupled with direct sequencing, after identification of G6PD mutations by ARMS. In this study, we identified a mutation G-->T at nt 1376, which had been G-->A at nt 1388 using ARMS, while the result of sequencing corresponds with ours. This indicates the reliability of this method. Furthermore, since it can scan six common Chinese G6PD mutations simultaneously in one mass spectrum, this approach could be used to fast diagnose these G6PD mutations accurately in large-scale analysis.
Blood Cells Mol Dis
PMID:Rapid detection of six common Chinese G6PD mutations by MALDI-TOF MS. 1500 24

The muscle larva of Trichinella spiralis is an intracellular parasite of mammalian skeletal muscle, encapsulating within a portion of the myofiber and resulting in muscle de-differentiation. Parasite-derived factors secreted or excreted by the muscle larva are thought to play a role in the formation of the host-parasite complex and in the induction of changes in the host cell. We screened a library enriched for T. spiralis-specific cDNAs and identified a clone encoding a protein with similarity to a predicted secreted or extracellular Caenorhabditis elegans protein. The region of similarity included a conserved cysteine-glycine (CCG) domain, which we have identified as being nematode-specific. This domain is present in the predicted T. spiralis protein, Ts-CCG-1, and in a second protein, Ts-CCG-2, which we identified from subsequent analysis. We showed that while the Ts-ccg-1 gene is constitutively expressed, Ts-ccg-2 gene expression is restricted to the muscle L1 larva. Both predicted proteins contain an N-terminal signal peptide and we subsequently confirmed by MALDI-TOF mass spectrometric analyses of excretory/secretory peptide spots excised from two-dimensional gels that Ts-CCG-2 is secreted.
Mol Biochem Parasitol 2004 Apr
PMID:Developmental regulation and secretion of nematode-specific cysteine-glycine domain proteins in Trichinella spiralis. 1500 45

Cellular response to the external environment is often controlled by one or more protein kinases. We report a methodology for simultaneously monitoring multiple kinase activities across multiple signal-transduction pathways using ProteinChip Array technology. Based on the addition of specific peptide reporters, kinase activity is detected by the presence of a mass shift of 80 Da (or multiple thereof) corresponding to the addition of one or more phosphate groups. These phosphorylated peptide substrates are then enriched using an immobilized metal affinity capture (IMAC)-Ga array and detected directly by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). SELDI-TOF MS is sensitive, tagless (nonradioactive, nonfluorescent), can be easily multiplexed for the analysis of several different kinases in a single reaction mixture (limited only by the specificity of the kinase for its substrate peptides), and is directly scalable through the use of robotic sample processing. By multiplexing kinase assays, one can dramatically increase the amount of information obtained from rare or volume-limited samples. More important, results reflect closely the complex interrelationships between kinases and show high correlation with in vivo assays.
Methods Mol Biol 2004
PMID:Simultaneous monitoring of multiple kinase activities by SELDI-TOF mass spectrometry. 1502 Jul 92

Amyloid-beta (A beta) fragments are found in plaques of patients with Alzheimers. Three secretases cleave the amyloid precursor protein, producing multiple A beta fragments that accumulate in the brain and fluids of patients with Alzheimers. A beta peptides are difficult to detect using standard methods because of their small size and multiple isoforms. However, multiple peptide fragments can be detected using a single ProteinChip Array-Based assay. Specific antibodies recognizing various amyloid epitopes are immobilized on a ProteinChip Array. Crude samples, such as tissue lysates, serum, cerebral spinal fluid (CSF), or cell culture media, are applied to the antibody-coated arrays. A beta peptides are specifically retained by the antibody, whereas other sample components are removed by washing. The multiple peptide fragments are detected by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), which can easily resolve the different fragments because of the corresponding changes in peptide mass.
Methods Mol Biol 2004
PMID:ProteinChip array-based amyloid beta assays. 1502 Jul 95

The high-resolution two-dimensional protein gel electrophoresis technique combined with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to analyse the oxidative stress response in Staphylococcus aureus COL. Exponentially growing cells were supplemented with 100 mM H2O2 leading to a growth arrest lasting 30 min. The comparison of the two-dimensional pattern of cytoplasmic protein extracts of stressed and unstressed cells revealed only a few changes in the protein synthesis profile. However, the isoelectric points of Gap (glyceraldehyde-3-phosphate dehydrogenase), AhpC (alkylhydroperoxide reductase) and MvaS (HMG-CoA-synthase) changed strikingly. For analysis of the modification of Gap, tandem hybrid mass spectrometry (Q-Star) was used. The observed pI shift resulted from the oxidation to sulphonic acid of cysteine 151, which is crucial for catalytic activity. A drop in ATP and a complete inactivation of Gap was accompanied by the growth arrest. About 30 min after the addition of H2O2, the damaged Gap was still present, but a new protein spot at the original location became visible, representing the newly synthesized enzyme that is active again. This is accompanied by the restoration of Gap enzyme activity, ATP levels and recovery of growth. There is a strong correlation between growth, ATP level and Gap activity under oxidative stress conditions, indicating that the H2O2-triggered Gap inactivation might be one reason for growth arrest under these conditions. Our data indicate that the damaged Gap protein was not repaired.
Mol Microbiol 2004 Apr
PMID:Oxidative stress triggers thiol oxidation in the glyceraldehyde-3-phosphate dehydrogenase of Staphylococcus aureus. 1504 16

The "inositol depletion hypothesis" has been widely held to be the explanation for both the effect of lithium on brain function, apropos of its use in mood disorders, and on the impairment of development and induction of embryonic malformations in diverse organisms. The essence of the hypothesis is that a deficiency in cellular myo-inositol (Ins), secondary to lithium inhibition of inositol monophosphatase and/or multiple inositol polyphosphate phosphatase activities with trapping of Ins as inositol phosphates, leads to a depression of phosphatidylinositol (PtdIns) and a secondary impairment in inositide signaling. However, the ability of relatively low micromolar levels of Ins to reduce mammalian PtdIns synthetase activity in vivo has never been adequately tested. We have generated a lethal murine brain Ins deficiency model and measured PtdIns content using a novel MALDI-TOF MS method. Our results show that in the most severe Ins deficiency ever recorded in a mammal, the brain PtdIns levels do not decrease. We conclude that PtdIns deficiency due to "inositol depletion" is not a mechanism of lithium action in brain, and that Ins plays another unidentified role in the mammalian brain.
Mol Genet Metab 2004 May
PMID:Phosphoinositide deficiency due to inositol depletion is not a mechanism of lithium action in brain. 1511 Mar 28


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