Greef, J. (Jan) van der | Leiden University (original) (raw)

Uploads

Papers by Greef, J. (Jan) van der

Research paper thumbnail of Acetoxy drug: protein transacetylase of buffalo liver—characterization and mass spectrometry of the acetylated protein product

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2004

The purification and characterization of the buffalo liver microsomal transacetylase (TAase) cata... more The purification and characterization of the buffalo liver microsomal transacetylase (TAase) catalyzing the transfer of acetyl groups from a model acetoxy drug: 7,8-diacetoxy-4-methylcoumarin (DAMC) to GST3 -3 has been described here. The enzyme was routinely assayed using DAMC and cytosolic GST as the substrates and was partially purified from microsomes of the buffalo liver. The enzyme was found to have approximate molecular weight of 65 kDa. The action of TAase and DAMC on liver cytosolic GST resulted in the formation of monoacetoxymonohydroxy-4-methylcoumarin (MAMHC) and 7,8-dihydroxy-4-methylcoumarin (DHMC), although the former was the major metabolite. The buffalo liver microsomal TAase exhibited hyperbolic kinetics and yielded K m (1667 AM) and V max (192 units) when the concentration of DAMC was varied keeping the concentration of GST constant. After having characterized the nature of the substrates and a product of the TAase-catalyzed reaction, we set out to identify the acetylated protein which is another product of the reaction. GST3 -3 was used as a model protein substrate for the action of TAase using DAMC as the acetyl donor. The subunit of control and modified GST3 -3 were separated by SDS-polyacrylamide gel electrophoresis (PAGE) and digested with trypsin. The tryptic peptides were extracted from the gel pieces and analyzed by matrix assisted laser desorption/ionization -time of flight -mass spectrometry (MALDI-TOFMS). The data search for calibrated and labeled mass peaks of peptides was performed on the Matrix Science Server using the search engine Mascot. The peptide maps so obtained covered 97% of the GST3 -3 sequence. On comparison of MALDI peptide maps of modified and control GST, seven new peaks were recognized corresponding to the potentially acetylated peptides in peptide map. The mass value of each of them was 42 Da higher than the theoretical mass of a non-modified GST3 -3 tryptic peptide, strongly suggesting acetylation. By examining the fragmentation patterns and by comparing experimental and predicted values for MS/MS daughter ions, the identity of the seven acetylated GST tryptic peptides could be confirmed by the application of LC/MS/MS. In the modified GST, N-terminal proline and six lysines (Lys 51 , Lys 82 , Lys 123 , Lsy 181 , Lys 191 and Lys 210 ) were found to be acetylated. The structure of acetylated GST revealed that the lysines that underwent acetylation were peripheral in positions. D

Research paper thumbnail of A15N labelling, FD and FAB study of ammonia loss from protonated arginine molecules

Journal of Mass Spectrometry, 1983

The positive ion field desorption (FD) spectrum of arginine taken at the best anode temperature o... more The positive ion field desorption (FD) spectrum of arginine taken at the best anode temperature only contains a peak due to [M+H]+ ions. At higher emitter temperatures a considerable amount of fragmentation is induced and the [M+HNH3]+ ions become most abundant. Specific 15N labelling reveals that the eliminated ammonia molecule, exclusively, contains one of the terminal nitrogen atoms of the guanidyl group. This also applies to the ammonia loss from metastably decomposing [M+H]+ ions. The positive ion fast atom bombardment (FAB) spectrum shows more fragmentation than the FD spectrum. In contrast with the FD results, the [M+H]+ ions generated upon FAB with ion lifetimes <10−6 s eliminate both ammonia containing one of the terminal nitrogen atoms of the guanidyl group and ammonia containing the α-amino group in the ratio of 1.35, as found by 15N labelling. The metastably decomposing [M+H]+ ions, however, eliminate only the former ammonia molecule. In the negative ion FD and FAB spectra no other peak than that corresponding to the [MH]− ion is observed. Some attention has been paid to the thermal degradation of arginine on the basis of a few Curie-point pyrolysis experiments.

Research paper thumbnail of Direct Sequencing of Neuropeptides in Biological Tissue by MALDI−PSD Mass Spectrometry

Analytical Chemistry, 1999

Dissected tissue pieces of the pituitary pars intermedia from the amphibian Xenopus laevis was di... more Dissected tissue pieces of the pituitary pars intermedia from the amphibian Xenopus laevis was directly subjected to matrix-assisted laser desorption/ionization (MALDI) mass analysis. The obtained MALDI peptide profile revealed both previously known and unexpected processing products of the proopiomelanocortin gene. Mass spectrometric peptide sequencing of a few of these neuropeptides was performed by employing MALDI combined with postsource decay (PSD) fragment ion mass analysis. The potential of MALDI-PSD for sequence analysis of peptides directly from unfractionated tissue samples was examined for the first time for the known desacetyl-r-MSH-NH 2 and the presumed vasotocin neuropeptide. In addition, the sequence of an unknown peptide which was present in the pars intermedia tissue sample at mass 1392.7 u was determined. The MALDI-PSD mass spectrum of precursor ion 1392.7 u contained sufficient structural information to uniquely identify the sequence by searching protein sequence databases. The determined amino acid sequence corresponds to the vasotocin peptide with a C-terminal extension of Gly-Lys-Arg ("vasotocinyl-GKR"), indicating incomplete processing of the vasotocin precursor protein in the pituitary pars intermediate of X. laevis. Both vasotocin and vasotocinyl-GKR are nonlinear peptides containing a disulfide (S-S) bridge between two cysteine residues. Interpretation of the spectra of these two peptides reveals three different forms of characteristic fragment ions of the cysteine side chain: peptide-CH 2 -SH (regular mass of Cys-containing fragment ions), peptide-CH 2 -S-SH (regular mass + 32 u) and peptidedCH 2 (regular mass -34 u) due to cleavage on either side of the sulfur atoms.

Research paper thumbnail of Diagnostic markers based on a computational model of lipoprotein metabolism

Background Dyslipidemia is an important risk factor for cardiovascular disease and type II diabet... more Background
Dyslipidemia is an important risk factor for cardiovascular disease and type II diabetes. Lipoprotein diagnostics, such as LDL cholesterol and HDL cholesterol, help to diagnose these diseases. Lipoprotein profile measurements could improve lipoprotein diagnostics, but interpretational complexity has limited their clinical application to date. We have previously developed a computational model called Particle Profiler to interpret lipoprotein profiles. In the current study we further developed and calibrated Particle Profiler using subjects with specific genetic conditions. We subsequently performed technical validation and worked at an initial indication of clinical usefulness starting from available data on lipoprotein concentrations and metabolic fluxes. Since the model outcomes cannot be measured directly, the only available technical validation was corroboration. For an initial indication of clinical usefulness, pooled lipoprotein metabolic flux data was available from subjects with various types of dyslipidemia. Therefore we investigated how well lipoprotein metabolic ratios derived from Particle Profiler distinguished reported dyslipidemic from normolipidemic subjects.
Results
We found that the model could fit a range of normolipidemic and dyslipidemic subjects from fifteen out of sixteen studies equally well, with an average 8.8% ± 5.0% fit error; only one study showed a larger fit error. As initial indication of clinical usefulness, we showed that one diagnostic marker based on VLDL metabolic ratios better distinguished dyslipidemic from normolipidemic subjects than triglycerides, HDL cholesterol, or LDL cholesterol. The VLDL metabolic ratios outperformed each of the classical diagnostics separately; they also added power of distinction when included in a multivariate logistic regression model on top of the classical diagnostics.
Conclusions
In this study we further developed, calibrated, and corroborated the Particle Profiler computational model using pooled lipoprotein metabolic flux data. From pooled lipoprotein metabolic flux data on dyslipidemic patients, we derived VLDL metabolic ratios that better distinguished normolipidemic from dyslipidemic subjects than standard diagnostics, including HDL cholesterol, triglycerides and LDL cholesterol. Since dyslipidemias are closely linked to cardiovascular disease and diabetes type II development, lipoprotein metabolic ratios are candidate risk markers for these diseases. These ratios can in principle be obtained by applying Particle Profiler to a single lipoprotein profile measurement, which makes clinical application feasible.

Research paper thumbnail of Acetoxy drug: protein transacetylase of buffalo liver—characterization and mass spectrometry of the acetylated protein product

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2004

The purification and characterization of the buffalo liver microsomal transacetylase (TAase) cata... more The purification and characterization of the buffalo liver microsomal transacetylase (TAase) catalyzing the transfer of acetyl groups from a model acetoxy drug: 7,8-diacetoxy-4-methylcoumarin (DAMC) to GST3 -3 has been described here. The enzyme was routinely assayed using DAMC and cytosolic GST as the substrates and was partially purified from microsomes of the buffalo liver. The enzyme was found to have approximate molecular weight of 65 kDa. The action of TAase and DAMC on liver cytosolic GST resulted in the formation of monoacetoxymonohydroxy-4-methylcoumarin (MAMHC) and 7,8-dihydroxy-4-methylcoumarin (DHMC), although the former was the major metabolite. The buffalo liver microsomal TAase exhibited hyperbolic kinetics and yielded K m (1667 AM) and V max (192 units) when the concentration of DAMC was varied keeping the concentration of GST constant. After having characterized the nature of the substrates and a product of the TAase-catalyzed reaction, we set out to identify the acetylated protein which is another product of the reaction. GST3 -3 was used as a model protein substrate for the action of TAase using DAMC as the acetyl donor. The subunit of control and modified GST3 -3 were separated by SDS-polyacrylamide gel electrophoresis (PAGE) and digested with trypsin. The tryptic peptides were extracted from the gel pieces and analyzed by matrix assisted laser desorption/ionization -time of flight -mass spectrometry (MALDI-TOFMS). The data search for calibrated and labeled mass peaks of peptides was performed on the Matrix Science Server using the search engine Mascot. The peptide maps so obtained covered 97% of the GST3 -3 sequence. On comparison of MALDI peptide maps of modified and control GST, seven new peaks were recognized corresponding to the potentially acetylated peptides in peptide map. The mass value of each of them was 42 Da higher than the theoretical mass of a non-modified GST3 -3 tryptic peptide, strongly suggesting acetylation. By examining the fragmentation patterns and by comparing experimental and predicted values for MS/MS daughter ions, the identity of the seven acetylated GST tryptic peptides could be confirmed by the application of LC/MS/MS. In the modified GST, N-terminal proline and six lysines (Lys 51 , Lys 82 , Lys 123 , Lsy 181 , Lys 191 and Lys 210 ) were found to be acetylated. The structure of acetylated GST revealed that the lysines that underwent acetylation were peripheral in positions. D

Research paper thumbnail of A15N labelling, FD and FAB study of ammonia loss from protonated arginine molecules

Journal of Mass Spectrometry, 1983

The positive ion field desorption (FD) spectrum of arginine taken at the best anode temperature o... more The positive ion field desorption (FD) spectrum of arginine taken at the best anode temperature only contains a peak due to [M+H]+ ions. At higher emitter temperatures a considerable amount of fragmentation is induced and the [M+HNH3]+ ions become most abundant. Specific 15N labelling reveals that the eliminated ammonia molecule, exclusively, contains one of the terminal nitrogen atoms of the guanidyl group. This also applies to the ammonia loss from metastably decomposing [M+H]+ ions. The positive ion fast atom bombardment (FAB) spectrum shows more fragmentation than the FD spectrum. In contrast with the FD results, the [M+H]+ ions generated upon FAB with ion lifetimes <10−6 s eliminate both ammonia containing one of the terminal nitrogen atoms of the guanidyl group and ammonia containing the α-amino group in the ratio of 1.35, as found by 15N labelling. The metastably decomposing [M+H]+ ions, however, eliminate only the former ammonia molecule. In the negative ion FD and FAB spectra no other peak than that corresponding to the [MH]− ion is observed. Some attention has been paid to the thermal degradation of arginine on the basis of a few Curie-point pyrolysis experiments.

Research paper thumbnail of Direct Sequencing of Neuropeptides in Biological Tissue by MALDI−PSD Mass Spectrometry

Analytical Chemistry, 1999

Dissected tissue pieces of the pituitary pars intermedia from the amphibian Xenopus laevis was di... more Dissected tissue pieces of the pituitary pars intermedia from the amphibian Xenopus laevis was directly subjected to matrix-assisted laser desorption/ionization (MALDI) mass analysis. The obtained MALDI peptide profile revealed both previously known and unexpected processing products of the proopiomelanocortin gene. Mass spectrometric peptide sequencing of a few of these neuropeptides was performed by employing MALDI combined with postsource decay (PSD) fragment ion mass analysis. The potential of MALDI-PSD for sequence analysis of peptides directly from unfractionated tissue samples was examined for the first time for the known desacetyl-r-MSH-NH 2 and the presumed vasotocin neuropeptide. In addition, the sequence of an unknown peptide which was present in the pars intermedia tissue sample at mass 1392.7 u was determined. The MALDI-PSD mass spectrum of precursor ion 1392.7 u contained sufficient structural information to uniquely identify the sequence by searching protein sequence databases. The determined amino acid sequence corresponds to the vasotocin peptide with a C-terminal extension of Gly-Lys-Arg ("vasotocinyl-GKR"), indicating incomplete processing of the vasotocin precursor protein in the pituitary pars intermediate of X. laevis. Both vasotocin and vasotocinyl-GKR are nonlinear peptides containing a disulfide (S-S) bridge between two cysteine residues. Interpretation of the spectra of these two peptides reveals three different forms of characteristic fragment ions of the cysteine side chain: peptide-CH 2 -SH (regular mass of Cys-containing fragment ions), peptide-CH 2 -S-SH (regular mass + 32 u) and peptidedCH 2 (regular mass -34 u) due to cleavage on either side of the sulfur atoms.

Research paper thumbnail of Diagnostic markers based on a computational model of lipoprotein metabolism

Background Dyslipidemia is an important risk factor for cardiovascular disease and type II diabet... more Background
Dyslipidemia is an important risk factor for cardiovascular disease and type II diabetes. Lipoprotein diagnostics, such as LDL cholesterol and HDL cholesterol, help to diagnose these diseases. Lipoprotein profile measurements could improve lipoprotein diagnostics, but interpretational complexity has limited their clinical application to date. We have previously developed a computational model called Particle Profiler to interpret lipoprotein profiles. In the current study we further developed and calibrated Particle Profiler using subjects with specific genetic conditions. We subsequently performed technical validation and worked at an initial indication of clinical usefulness starting from available data on lipoprotein concentrations and metabolic fluxes. Since the model outcomes cannot be measured directly, the only available technical validation was corroboration. For an initial indication of clinical usefulness, pooled lipoprotein metabolic flux data was available from subjects with various types of dyslipidemia. Therefore we investigated how well lipoprotein metabolic ratios derived from Particle Profiler distinguished reported dyslipidemic from normolipidemic subjects.
Results
We found that the model could fit a range of normolipidemic and dyslipidemic subjects from fifteen out of sixteen studies equally well, with an average 8.8% ± 5.0% fit error; only one study showed a larger fit error. As initial indication of clinical usefulness, we showed that one diagnostic marker based on VLDL metabolic ratios better distinguished dyslipidemic from normolipidemic subjects than triglycerides, HDL cholesterol, or LDL cholesterol. The VLDL metabolic ratios outperformed each of the classical diagnostics separately; they also added power of distinction when included in a multivariate logistic regression model on top of the classical diagnostics.
Conclusions
In this study we further developed, calibrated, and corroborated the Particle Profiler computational model using pooled lipoprotein metabolic flux data. From pooled lipoprotein metabolic flux data on dyslipidemic patients, we derived VLDL metabolic ratios that better distinguished normolipidemic from dyslipidemic subjects than standard diagnostics, including HDL cholesterol, triglycerides and LDL cholesterol. Since dyslipidemias are closely linked to cardiovascular disease and diabetes type II development, lipoprotein metabolic ratios are candidate risk markers for these diseases. These ratios can in principle be obtained by applying Particle Profiler to a single lipoprotein profile measurement, which makes clinical application feasible.