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PubMed2004

Characterization of covalently inhibited extracellular lipase from Streptomyces rimosus by matrix-assisted laser desorption/ionization time-of-flight and matrix-assisted laser desorption/ionization quadrupole ion trap reflectron time-of-flight mass spectrometry: localization of the active site serine.

A chemical modification approach combined with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to identify the active site serine residue of an extracellular lipase from Streptomyces rimosus R6-554W. The lipase, purified from a high-level overexpressing strain, was covalently modified by incubation with 3,4-dichloroisocoumarin, a general mechanism-based serine protease inhibitor. MALDI time-of-flight (TOF) mass spectrometry was used to probe the nature of the intact inhibitor-modified lipase and to clarify the mechanism of lipase inhibition by 3,4-dichloroisocoumarin. The stoichiometry of the inhibition reaction revealed that specifically one molecule of inhibitor was bound to the lipase. The MALDI matrix 2,6-dihydroxyacetophenone facilitated the formation of highly abundant [M + 2H](2+) ions with good resolution compared to other matrices in a linear TOF instrument. This allowed the detection of two different inhibitor-modified lipase species. Exact localization of the modified amino acid residue was accomplished by tryptic digestion followed by low-energy collision-induced dissociation peptide sequencing of the detected 2-(carboxychloromethyl)benzoylated peptide by means of a MALDI quadrupole ion trap reflectron TOF instrument. The high sequence coverage obtained by this approach allowed the confirmation of the site specificity of the inhibition reaction and the unambiguous identification of the serine at position 10 as the nucleophilic amino acid residue in the active site of the enzyme. This result is in agreement with the previously obtained data from multiple sequence alignment of S. rimosus lipase with different esterases, which indicated that this enzyme exhibits a characteristic Gly-Asp-Ser-(Leu) motif located close to the N-terminus and is harboring the catalytically active serine residue. Therefore, this study experimentally proves the classification of the S. rimosus lipase as GDS(L) lipolytic enzyme.

Amino Acid Sequence↗

PubMed2004

A combination of protein profiling and isotopomer analysis using matrix-assisted laser desorption/ionization-time of flight mass spectrometry reveals an active metabolism of the extracellular matrix of 3T3-L1 adipocytes.

Differential gel electrophoresis followed by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a commonly used protein profiling method. However, observed changes can be explained in multiple ways, one of which is by the protein turnover rate. In order to easily and rapidly obtain information on both the identity and turnover of individual proteins, we applied a combination of protein labeling with L-(ring-2,3,4,5,6 2H5) phenylalanine and MALDI-TOF MS. While the spectrum reveals the identity of a protein, mass isotopomer analysis provides information about the rate of protein labeling as a measure of synthesis or turnover. Using this approach on mature 3T3-L1 adipocytes, we were able to discriminate between rapidly and slowly metabolised proteins. In our isolate, proteins of the cytoskeleton appeared to be slowly metabolised, whereas components of the extracellular matrix, in particular collagen type I alpha 1 (COL1A1) and collagen type I alpha 2 (COL1A2) showed rapid accumulation of newly synthesized proteins. Both proteins appeared to be metabolised in the same ratio as they are present in collagen fibers, i.e. 2:1 (COL1A1: COL1A2). In addition, functionally related proteins were also readily labeled. Taken together, we have shown that a combination of stable isotope labeling and protein profiling by gel electrophoresis and MALDI-TOF analysis can simultaneously provide information on the identity and relative metabolic rate of proteins in eukaryotic cells in a simple, nonhazardous and rapid-throughput way.

3T3-L1 Cells↗

PubMed2003

Identification of proteins separated by one-dimensional sodium dodecyl sulfate/polyacrylamide gel electrophoresis with matrix-assisted laser desorption/ionization ion trap mass spectrometry; comparison with matrix-assisted laser desorption/ionization time-of-flight mass fingerprinting.

Digests from ten gel bands containing low abundance proteins were analyzed by both matrix-assisted laser desorption/ionization ion trap (MALDI-IT) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) methods. MALDI-TOF techniques were able to identify only one protein from all 10 gel bands, while MALDI-IT identified eight proteins from the same 10 bands. The ability to perform MS/MS experiments with a MALDI-IT instrument leads to protein identifications based on both peptide molecular mass and sequence information, and is much less prone to errors and uncertainties introduced by peptide fingerprinting methodologies in which protein identification is based on peptide molecular masses alone.

Amino Acid Sequence↗

PubMed2003

Matrix-assisted laser desorption/ionization analysis of lipids and high molecular weight hydrocarbons with lithium 2,5-dihydroxybenzoate matrix.

Lithium 2,5-dihydroxybenzoate (LiDHB) is shown to be a very effective matrix for matrix-assisted laser desorption/ionization (MALDI) analysis of nonpolar long-chain lipids, hydrocarbons and polymers. Under standard desorption and ionization conditions using a conventional nitrogen UV laser (337 nm), hydrocarbons (C(24)-C(40)), diverse lipids (triglycerides, diglycerides, wax esters from leaves) and saturated polymers are effectively lithiated providing [M+Li](+) ions. The formation of lithiated hydrocarbons is not accompanied by an elimination of hydrogen or other fragmentation reactions and, due to the relatively simple isotopic distribution of lithium, seems to be more useable for analysis of hydrocarbon mixtures than the previously used silver cationization agents. The mass calibration can be conveniently performed either externally or internally using poly(ethylene glycol) commercial standards.

Gentisates↗

PubMed2004

A mixed matrix of 3-hydroxypicolinic acid and pyrazinecarboxylic acid for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of oligodeoxynucleotides.

A mixed matrix of 3-hydroxypicolinic acid (3-HPA) and pyrazinecarboxylic acid (PCA) was used for analysis of a variety of synthetic oligodeoxynucleotides ranging in length from 8-108-mers by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The experimental results showed that DNA segments with masses in the range from 5000 to 10,500 Da can be analyzed with high resolution (isotopic peaks resolved) when 3-HPA/PCA was prepared by mixing saturated 3-HPA solution and saturated PCA solution (in 50% of a 0.5 mol/L solution of diammonium hydrogen citrate plus 50% acetonitrile) at the volume ratio of 4:1. Each component of a mixture of d(A)1-10 gave a well-resolved peak. Moreover, when 3-HPA/PCA was used to analyze two mixtures, one containing two 23-mer DNA segments with a 9 Da difference (A and T) and the other with a 7 Da difference (AA and TG), the two 23-mer ion peaks were well separated from each other and an isotopically resolved spectrum of each component was recorded. Under the identical experimental conditions, the sample-to-sample reproducibility, resolution, signal-to-noise ratio and the tolerance to metal salts, with 3-HPA/PCA, were superior to those observed using 3-HPA alone for analysis of DNA segments.

Base Sequence↗

PubMed2004

Removal of sodium and potassium adducts using a matrix additive during matrix-associated laser desorption/ionization time-of-flight mass spectrometric analysis of peptides.

Monovalent cations often associate with peptides and proteins under mass spectrometry (MS) conditions, resulting in a discernable, but often misleading, adduct cluster pattern. These adduct cluster peaks reduce the signal intensity of specific peptide species by splitting the ion population into multiple mass peaks, suppressing the ionization of neighboring low-abundance peaks, and interfering with identification of post-translational modifications. Further, monovalent contaminants tend to form a distribution of matrix cluster peaks in matrix-associated laser desorption/ionization time-of-flight (MALDI-TOF) spectra causing interference and suppression in the mass range below 1400 Da. The most common method for reduction or elimination of adduct clusters is solid-phase extraction via a pipette tip or spin column, which often leads to loss of low-abundance peptide components. In this study we describe the use of a commercially available surfactant blend that markedly reduces the adduction of monovalent cations during peptide analysis by MALDI-TOFMS.

Animals↗

PubMed2005

Oxidized carbon nanotubes as matrix for matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of biomolecules.

Oxidized carbon nanotubes (CNTs), which can form a stable homogeneous suspension in water close to a solution phase, were synthesized and used for matrix-assisted desorption/ionization mass spectrometric (MALDI-MS) analysis of biomolecules. Infrared (IR) spectra, transmission electron microscopy (TEM) and particle size analysis were used for the characterization of the oxidized CNTs. The results indicate that the physical structure of the CNTs was not damaged, but carboxylate groups were introduced onto the surface of the CNTs. In addition, impurities including amorphous carbon, which is one of the main reasons for ion source contamination, were destroyed by the oxidization. The carboxyl groups on the oxidized surface of the CNTs can not only provide an additional proton source, but can also increase the surface polarity and solubility of the CNTs, making it easier to manipulate which is important for MALDI analysis of some biomolecules, especially larger peptides and proteins. The oxidized CNTs were successfully applied to the analysis of neutral oligosaccharides, peptides, and insulin, and thus promise to be an efficient matrix for MALDI-MS analysis of biomolecules.

Microscopy, Electron, Transmission↗

PubMed2002

Identification of acetylation and methylation sites of histone H3 from chicken erythrocytes by high-accuracy matrix-assisted laser desorption ionization-time-of-flight, matrix-assisted laser desorption ionization-postsource decay, and nanoelectrospray ionization tandem mass spectrometry.

A new strategy has been employed for the identification of the covalent modification sites (mainly acetylation and methylation) of histone H3 from chicken erythrocytes using low enzyme/substrate ratios and short digestion times (trypsin used as the protease) with analysis by HPLC separation, matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF), matrix-assisted laser desorption ionization-postsource decay, and tandem mass spectrometric techniques. High-accuracy MALDI-TOF mass measurements with representative immonium ions (126 for acetylated lysine, 98 for monomethylated lysine, and 84 for di-, tri-, and unmethylated lysine) have been effectively used for differentiating methylated peptides from acetylated peptides. Our results demonstrate that lysines 4, 9, 14, 27, and 36 of the N-terminal of H3 are methylated, while lysines 14, 18, and 23 are acetylated. Surprisingly, a non-N-terminal residue, lysine 79, in the loop region hooking up to the bound DNA, was newly found to be methylated (un-, mono-, and dimethylated isoforms coexist). The reported mass spectrometric method has the advantages of speed, directness, sensitivity, and ease over protein sequencing and Western-blotting methods and holds the promise of an improved method for determining the status of histone modifications in the field of chromosome research.

Acetylation↗

PubMed1994

A role for extracellular matrix degradation and matrix metalloproteinases in senile dementia?

In brain as in cartilage, the extracellular matrix contains aggregates formed by hyaluronic acid (HA) and proteoglycans. In osteoarthritic cartilage, release of the proteoglycans from the aggregates by cleavage of the HA-binding region results in the accumulation of the HA-binding region and in the fragmentation of the released proteoglycans. Stromelysin, a matrix neutral metalloproteinase, is one of the enzymes responsible for the cleavage of the HA-binding region. We suggest that a similar process also occurs in senile dementia. The brain proteoglycan contains sequences identical to those of aggrecan, which are recognized and cleaved by stromelysin, and is, in fact, susceptible to stromelysin digestion. Monoclonal antibodies reacting with glial HA-binding protein, but not with the parent protein, stained several senile plaques as defined by their reactivity with antibodies to the amyloid-beta protein in double-labeling experiments.

Aged↗

PubMed2003

Automated coupling of capillary-HPLC to matrix-assisted laser desorption/ionization mass spectrometry for the analysis of small molecules utilizing a reactive matrix.

This study describes the application of a novel, reactive matrix for the mass spectral analysis of steroids by capillary-high performance liquid chromatography (capillary-HPLC) coupled to matrix-assisted laser desorption/ionization (MALDI). The mass spectral analysis of steroids was accomplished after fully automated peak deposition of chromatographic peaks onto MALDI targets. The seven corticosteroids used as test compounds were: triamcinolone, prednisone, cortisone, fludrocortisone, dexamethasone, deoxycorticosterone, and budesonide. They were separated using a PepMap C(18) (3 microm particle size, 100 A pore width) column at five different concentration levels of 25, 15, 7.5, 2.5 and 1 ng/microL, and the peaks were detected at a wavelength of 237 nm. The column effluent was mixed with 2,4-dinitrophenylhydrazine (DNPH) directly following the UV detector. The chromatographic peaks were then deposited onto the MALDI target with a robotic micro-fraction collector triggered by the UV detector signals. A special hydrophobic surface coating allowed the deposition of up to 4 microL (up to 90 % of the chromatographic peak volume) onto one sample spot. The compounds were then identified by MALDI mass spectrometry. Depending on the nature of the analyte, radical cations ([M](+.)) and sodium adduct ions ([M+Na](+)) of the steroids as well as protonated steroid-dinitrophenylhydrazone derivatives ([M(D)+H](+)) were detected in positive ion mode. The detection limits were between 0.5 and 15 ng injected with capillary-HPLC-MALDI-TOF-MS and between 0.3 and 3 ng on target with MALDI-TOF when deposited manually.

Chromatography, High Pressure Liquid↗

PubMed1992

Extracellular matrix contraction by cultured mesangial cells: modulation by transforming growth factor-beta and matrix components.

Cultured glomerular mesangial cells (MCs) have the ability to contract the surrounding collagen gel matrix (CGM). To investigate this phenomenon, we examined the effect of growth factors and extracellular matrix (ECM) components. Among some growth factors tested, transforming growth factor-beta (TGF-beta) and fetal calf serum (FCS) enhanced CGM contraction dose dependently. These factors acted through distinct mechanisms because: (1) when growth-arrested MCs were used, the effect of FCS was inhibited partially but that of TGF-beta was not; and (2) anti-TGF-beta had no influence on CGM contraction induced by FCS. Among the ECM components such as laminin, fibronectin, type IV collagen, and heparin-like proteoglycans (heparan sulfate and heparin), which were each mixed separately with CGM before gelling, heparin-like proteoglycans and type IV collagen inhibited contraction by MCs. The inhibitory effect of heparin was mediated by the interaction both with CGM and with MCs because: (1) when heparin was added to the culture medium, not into the gel, the inhibitory effect was diminished but still noted; and (2) using growth-arrested MCs, the inhibitory effect of heparin in the medium was reduced but still observed. This culture assay is useful for elucidating the tensional interaction between MCs and surrounding ECM.

Animals↗

PubMed1992

Selective binding of anchorin CII (annexin V) to type II and X collagen and to chondrocalcin (C-propeptide of type II collagen). Implications for anchoring function between matrix vesicles and matrix proteins.

Anchorin CII is a collagen binding protein of the annexin family associated with plasma membranes of chondrocytes, osteoblasts, and many other cells. As a major constituent of cartilage-derived matrix vesicles it has been shown to bind to native type II and X collagen. In accordance with this observation, here we show the localization of anchorin CII in the extracellular matrix of calcifying cartilage in the fetal human growth plate, and that it was restricted to the chondrocyte surface in proliferating and resting cartilage. Furthermore, we present evidence, using a slot blot assay, that anchorin CII not only binds to native type II and X collagen, but also to chondrocalcin, the carboxy-terminal extension of type II procollagen, in a calcium-independent manner. Pepsin digestion of type II collagen results in loss of anchorin CII binding, confirming our previous notion that the telopeptide region of type II collagen carries anchorin CII binding sites.

Animals↗

PubMed2006

Quantitative analysis of free fatty acids in rat plasma using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with meso-tetrakis porphyrin as matrix.

Quantitative analysis of free fatty acids was achieved using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with a meso-tetrakis porphyrin matrix. Cesium acetate was employed as a cationizing agent. The MALDI signal was reproducible and dominated by cesiated cesium carboxylates [RCOOCs + Cs]+. The addition of two Cs ions resulted in a mass shift of 264.8 Da for each fatty acid and greatly reduced background peaks. A linear relationship between fatty acid concentration and corresponding fatty acid to internal standard peak intensity ratio was observed for three representative fatty acids analyzed across a concentration range from 4.40 to 150 microM, with correlation coefficients between 0.986 and 0.987. The application of this method was demonstrated with the analysis of free fatty acids in nonfasted and fasted rat plasmas. A total of eight free fatty acids (14:0, 16:0, 16:1, 17:0, 18:0, 18:1, 18:2, and 20:4) were detected. The relative peak height ratios of the fatty acids to the internal standard allow quantitative measurements of the free fatty acids. It was shown that the levels of free fatty acids were higher in fasted rats than in rats in a nonfasted state. This method is simple, sensitive, and fast. Thus, it provides an appealing tool for the analysis of free fatty acids or other low-molecular weight compounds during drug discovery and/or development.

Acetates↗

PubMed2006

Matrix metalloproteinase-9 (MMP-9) and tissue inhibitor of matrix metalloproteinase (TIMP-1) in patients with relapsing-remitting multiple sclerosis treated with interferon beta.

OBJECTIVES: Matrix metalloproteinases (MMPs), particularly MMP-9, facilitate T-cell migration into the central nervous system. They play a key role in the disruption of the blood-brain barrier (BBB) and thus in the pathogenesis of multiple sclerosis. Interferon beta's (IFNbeta) ability to alter the balance between MMP-9 and MMP-9s natural inhibitor, tissue inhibitor of matrix metalloproteinase-1 (TIMP-1), may play a role in stabilizing the BBB. The aim of this study, was to evaluate serum MMP-9 and TIMP-1 and cerebrospinal fluid (CSF) TIMP-1 levels in patients with relapsing-remitting multiple sclerosis (RRMS) treated with IFNbeta-1a. PATIENTS AND METHODS: Blood and CSF samples from 14 patients with RRMS before and 6 months after IFNbeta therapy and 14 age and sex-matched controls were obtained. Levels of MMP-9 and TIMP-1 were measured using ELISA. RESULTS: Before treatment, patients with MS had higher levels of serum MMP-9 and a higher MMP-9/TIMP-1 ratio than the controls. Although serum levels of TIMP-1 were lower in RRMS patients than in the controls, the differences did not reach statistical significance. CSF levels of TIMP-1 were significantly lower in RRMS patients. In the sixth month of IFNbeta therapy serum MMP-9 and the MMP-9/TIMP-1 ratio were significantly decreased, whereas the changes in serum TIMP-1 were not statistically significant. There was a significant increase in CSF TIMP-1 levels in the sixth month of IFNbeta therapy. CONCLUSIONS: Our result shows that RRMS patients have an impaired MMP-9 and TIMP-1 balance, and that 6 months of IFNbeta therapy is beneficial in restoring this balance.

Adjuvants, Immunologic↗

PubMed2004

Regulation of matrix metalloproteinase-1 and tissue inhibitor of matrix metalloproteinase-1 by dichloroacetic acid in human fibroblasts from normal peritoneum and adhesions.

OBJECTIVE: To examine the role of stimulation of aerobic metabolism on the differential expression of matrix metalloproteinase-1 (MMP-1) and tissue inhibitor of matrix metalloproteinase-1 (TIMP-1), which are differentially regulated in fibroblasts isolated from normal human peritoneum and adhesions. DESIGN: Tissue culture study. SETTING: University research laboratory. PATIENT(S): Human fibroblasts cultures from normal peritoneum and adhesions that were exposed to dichloroacetic acid (DCA; 0 and 100 microg/mL) for 24 hours under normal and hypoxic conditions. MAIN OUTCOME MEASURE(S): Real-time reverse-transcription polymerase chain reaction of MMP-1, TIMP-1, and beta-actin. RESULT(S): Dichloroacetic acid stimulated peritoneal fibroblast MMP-1 mRNA expression under normoxic conditions; this stimulation was lost during hypoxia. In adhesion fibroblasts, DCA increased MMP-1 mRNA expression; this effect was reversed by hypoxia. Expression of TIMP-1 mRNA was insignificantly increased by DCA in normal peritoneal and adhesion fibroblasts under normoxic conditions; however under hypoxic conditions, DCA reduced TIMP-1 mRNA expression from both. CONCLUSION(S): Regulation of metabolic activity of peritoneal cells may provide a target for future interventions for reduction of development of postoperative adhesions, particularly as it relates to healing of peritoneal sites that did not previously have adhesions as opposed to sites that underwent lysis of preexistent adhesions.

Cell Hypoxia↗

PubMed2004

Determination of the serum matrix metalloproteinase-9 (MMP-9) and tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) in patients with either advanced small-cell lung cancer or non-small-cell lung cancer prior to treatment.

This study was undertaken to examine the relationship between circulating matrix metalloproteinase (MMP-9) and tissue inhibitor of matrix metalloproteinase (TIMP-1) in our patients with either advanced small-cell lung cancer (SCLC) or non-small-cell lung cancer (NSCLC) prior to treatment. Thirty-one male and female patients with either stage III or IV NSCLC and 17 with either stage III or IV SCLC were compared to 117 age matched non-smoking controls of both sexes. Prior to any treatment of the patient, a baseline serum sample was obtained from each of the patients for the determination of circulating MMP-9 and TIMP-1 by ELISA. The results indicate that both MMP-9 and TIMP-1 are elevated in the serum of lung cancer patients when compared to the controls. This observation was true for both SCLC and NSCLC. However, the mean values for both MMP-9 and TIMP-1 in the two tumors were not different from each other. The natural physiological relationship between MMP-9 and the inhibitor TIMP-1 was lost in both SCLC and NSCLC, indicative of abnormal alterations by the tumor. The data from this study suggests that advanced lung cancer does alter the normal circulatory pattern of MMP-9 and TIMP-1. This could aid in the processes of tumor invasion and/or metastasis.

Adult↗

PubMed2003

Matrix metalloproteinase and tissue inhibitor of matrix metalloproteinase expression in human preimplantation embryos.

OBJECTIVE: To examine human embryos at various stages of preimplantation development for simultaneous expression of matrix metalloproteinases (MMPs) and tissue inhibitor of matrix metalloproteinases (TIMPs). DESIGN: mRNAs of specific MMPs and TIMPs were examined in single human embryos, at different stages of preimplantation development, by reverse transcription-polymerase chain reaction (RT-PCR). Single embryo immunohistochemistry was applied to examine the protein expression. SETTING: University-affiliated IVF-ET program. PATIENT(S): Couples, attending the university-affiliated IVF-ET program, electing to donate poor prognosis embryos with anomalous morphology. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): The expression of MMP-1, MMP-2, MMP-9, TIMP-1, TIMP-2, and TIMP-3 in preimplantation embryos. RESULT(S): The MMP-2 mRNA was expressed consistently during development from one-cell to blastocyst stage. The TIMP-1 and TIMP-3 mRNAs were detected in embryos at all stages; however, in the later preimplantation developmental stages, an increasing proportion of embryos expressing TIMP-1 and TIMP-3 mRNA were noted. The MMP-1, MMP-9, and TIMP-2 mRNAs were detected in only a minority of human embryos studied. Immunohistochemistry showed MMP-1 and TIMP-1 protein expression in preimplantation embryos. CONCLUSION(S): The existence of MMP and TIMP mRNA expression in human preimplantation embryos argues for a role for these metalloproteinases and their inhibitors during the process of implantation in humans.

Blastocyst↗

PubMed1998

Matrix metalloproteinase degradation of extracellular matrix: biological consequences.

Targeted mutagenesis has allowed investigators to perform controlled experiments in mammals and determine the contribution of individual proteins to physiologic and pathologic processes. Recent lessons learned from matrix metalloproteinase gene targeted mice and other in vivo observations have given new life to old concepts regarding the role of proteolytic fragments of extracellular matrix proteins in regulating a variety of critical processes in cell biology.

Cardiovascular Diseases↗