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Identification of domains on the extrinsic 23 kDa protein possibly involved in electrostatic interaction with the extrinsic 33 kDa protein in spinach photosystem IIFEBS JOURNAL, Issue 5 2004
To elucidate the domains on the extrinsic 23 kDa protein involved in electrostatic interaction with the extrinsic 33 kDa protein in spinach photosystem II, we modified amino or carboxyl groups of the 23 kDa protein to uncharged methyl ester groups with N -succinimidyl propionate or glycine methyl ester in the presence of a water-soluble carbodiimide, respectively. The N -succinimidyl propionate-modified 23 kDa protein did not bind to the 33 kDa protein associated with PSII membranes, whereas the glycine methyl ester-modified 23 kDa protein completely bound. This indicates that positive charges on the 23 kDa protein are important for electrostatic interaction with the 33 kDa protein associated with the PSII membranes. Mapping of the N -succinimidyl propionate-modified sites of the 23 kDa protein was performed using Staphylococcus V8 protease digestion of the modified protein followed by determination of the mass of the resultant peptide fragments with MALDI-TOF MS. The results showed that six domains (Lys11,Lys14, Lys27,Lys38, Lys40, Lys90,Lys96, Lys143,Lys152, Lys166,Lys174) were modified with N -succinimidyl propionate. In these domains, Lys11, Lys13, Lys33, Lys38, Lys143, Lys166, Lys170 and Lys174 were wholly conserved in the 23 kDa protein from 12 species of higher plants. These positively charged lysyl residues on the 23 kDa protein may be involved in electrostatic interactions with the negatively charged carboxyl groups on the 33 kDa protein, the latter has been suggested to be important for the 23 kDa binding [Bricker, T.M. & Frankel, L.K. (2003) Biochemistry42, 2056,2061]. [source]
On choosing the right ether for peptide precipitation after acid cleavageJOURNAL OF PEPTIDE SCIENCE, Issue 3 2008
Beatriz G. de La Torre
Abstract Methyl tert -butyl ether (MTBE) and diethyl ether (DEE) tend to be regarded as interchangeable for the ,cold ether' workup concluding the final acidolytic cleavage and deprotection step of solid-phase peptide syntheses. However, the use of MTBE to precipitate peptides from strong acid solutions is shown to give rise to t -butyl alkylation byproducts, readily detectable by MALDI-TOF MS. The problem can attain undesirable dimensions in the cleavage of peptide resins containing high proportions of aromatic residues, particularly in peptide nucleic acid (PNA) syntheses. In those cases, DEE workup is advisable, as it consistently leads to cleaner products. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source]
Staphylococcus aureus ClpC ATPase is a late growth phase effector of metabolism and persistencePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 5 2009
Indranil Chatterjee Dr.
Abstract Staphylococcus aureus Clp ATPases (molecular chaperones) alter normal physiological functions including an aconitase-mediated effect on post-stationary growth, acetate catabolism, and entry into death phase (Chatterjee et al., J. Bacteriol. 2005, 187, 4488,4496). In the present study, the global function of ClpC in physiology, metabolism, and late-stationary phase survival was examined using DNA microarrays and 2-D PAGE followed by MALDI-TOF MS. The results suggest that ClpC is involved in regulating the expression of genes and/or proteins of gluconeogenesis, the pentose-phosphate pathway, pyruvate metabolism, the electron transport chain, nucleotide metabolism, oxidative stress, metal ion homeostasis, stringent response, and programmed cell death. Thus, one major function of ClpC is balancing late growth phase carbon metabolism. Furthermore, these changes in carbon metabolism result in alterations of the intracellular concentration of free NADH, the amount of cell-associated iron, and fatty acid metabolism. This study provides strong evidence for ClpC as a critical factor in staphylococcal energy metabolism, stress regulation, and late-stationary phase survival; therefore, these data provide important insight into the adaptation of S. aureus toward a persister state in chronic infections. [source]
Evaluation of the SELDI-TOF MS technique for protein profiling of pancreatic islets exposed to glucose and oleatePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 17 2007
Henrik Ortsäter Dr.
Abstract The aim of the study was to evaluate the SELDI-TOF MS technique for pancreatic islet research. Mouse islets were cultured at low or high glucose levels in the absence or presence of oleate and characterized by measuring insulin secretion and oxygen tension. Subsequently, the islets were protein profiled. Up to 200 different peaks could be detected in a single experiment with the majority of peaks corresponding to proteins with masses below 30,kDa. By combining different protein arrays, the number of detected peaks could be increased further. The optimal binding of islet proteins was achieved using the anionic exchange array and phosphate buffer (pH,6) when the binding of insulin was low, which allowed other less abundant proteins to be captured. When islets from different culture conditions were profiled and analyzed, in total 25 proteins were found to be oleate/glucose-regulated. An oleate-regulated protein was chosen for identification work, which was conducted by passive elution from SDS-PAGE gels and subsequent in-gel trypsin digestion and MALDI-TOF MS. The protein was identified as peptidyl-prolyl isomerase B (PPI-B). In conclusion, the study demonstrates that SELDI-technique can be used not only to obtain islet protein patterns but is also helpful in the subsequent identification of differentially expressed proteins. [source]
Fe3+ immobilized metal affinity chromatography with silica monolithic capillary column for phosphoproteome analysisPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2007
Abstract Immobilized metal affinity chromatography (IMAC) is a commonly used technique for phosphoproteome analysis due to its high affinity for adsorption of phosphopeptides. Miniaturization of IMAC column is essential for the analysis of a small amount of sample. Nanoscale IMAC column was prepared by chemical modification of silica monolith with iminodiacetic acid (IDA) followed by the immobilization of Fe3+ ion inside the capillary. It was demonstrated that Fe3+ -IDA silica monolithic IMAC capillary column could specifically capture the phosphopeptides from tryptic digest of ,-casein with analysis by MALDI-TOF MS. The silica monolithic IMAC capillary column was manually coupled with nanoflow RPLC/nanospray ESI mass spectrometer (,RPLC,nanoESI MS) for phosphoproteome analysis. The system was validated by analysis of standard phosphoproteins and then it was applied to the analysis of protein phosphorylation in mouse liver lysate. Besides MS/MS spectra, MS/MS/MS spectra were also collected for neutral loss peak. After database search and manual validation with conservative criteria, 29 singly phosphorylated peptides were identified by analyzing a tryptic digest of only 12,,g mouse liver lysate. The results demonstrated that the silica monolithic IMAC capillary column coupled with ,RPLC-nanoESI MS was very suitable for the phosphoproteome analysis of minute sample. [source]
Searching cell-secreted proteomes for potential urinary bladder tumor markersPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 15 2006
Abstract To search for biomarkers critical for bladder carcinoma diagnosis and prognosis, secreted proteomes of highly malignant U1 and pre-malignant U4 cell lines were initially analyzed. Proteins in the culture media of the U1 and U4 cell lines were systematically examined by SDS-PAGE combined with MALDI-TOF MS. Among them, expression of pro-u-plasminogen activator (pro-u-PA) was confirmed by Western blot analysis and further evaluated. In analyzing urine samples from bladder cancer patients and normal subjects, we established a statistically significant relationship between the low level and absence of pro-u-PA in urine with high stages and grades of the tumor samples. Constitutive expression of Ras dominant negative protein led to increased expression of pro-u-PA in culture media, indicating that the loss of pro-u-PA is associated with oncogenic transformation. Analysis of cancer-secreted proteomes can be a feasible, non-invasive and efficient strategy for searching potential bladder tumor biomarkers. Our work also has identified the loss of pro-u-PA in urine as potential marker of more advanced bladder carcinoma. [source]
A proteomic analysis of 14-3-3 binding proteins from developing barley grainsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2006
Ross D. Alexander
Abstract 14-3-3 proteins are important eukaryotic regulatory proteins. Barley (Hordeum vulgare,L.) 14-3-3A was over-expressed, immobilised and used to affinity purify 14-3-3 binding proteins from developing barley grains. Binding was shown to be phosphorylation-dependent. These proteins were fractionated by PAGE and identified by MALDI-TOF MS. In total, 54,14-3-3 binding proteins were identified, 49,of these interactions are novel to plants. These proteins fell into a number of functional categories. The largest category was for carbohydrate metabolism, including plastidic enzymes for starch synthesis and modification. 14-3-3 was shown to be present in isolated plastids. Four of five enzymes involved in sucrose biosynthesis from triose phosphates were identified, suggesting co-ordinated regulation of this pathway. Invertase and sucrose synthase, which break down sucrose to hexoses, were found. Sucrose synthase activity was shown to be inhibited by exogenous 14-3-3 in a dosage-dependent manner. The second-largest functional group was for proteins involved in stress and defence responses; for example, RGH2A, closely related to the MLA powdery mildew resistance protein, was found. This work illustrates the broad range of processes in which 14-3-3 may be involved, and augments previous data demonstrating key roles in carbohydrate metabolism and plant defence. [source]
Carbohydrate-Encapsulated Gold Nanoparticles for Rapid Target-Protein Identification and Binding-Epitope MappingCHEMBIOCHEM, Issue 7 2005
Yu-Ju Chen Dr.
Carbohydrate,lectin recognition plays important roles in cell,cell communication, proliferation, and differentiation. We report here a new approach of using a carbohydrate-encapsulated gold nanoparticle (shown in purple) as an affinity probe for the efficient separation and enrichment of target proteins, and then protein identification and epitope mapping by MALDI-TOF MS. [source]