Johan Haverkamp

Johan Haverkamp
Utrecht University | UU · Bijvoet Institute for Biomolecular Research

PhD

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182
Publications
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Publications

Publications (182)
Article
An HPLC-ESI-MS/MS method using collision induced dissociation - multiple reaction monitoring was developed for the quantification of eight Hoodia gordonii steroid glycosides and their metabolites in porcine plasma samples. The method was validated for the three most important glycosides and was successfully applied also for the related glycosides a...
Article
Full-text available
A two-dimensional chromatographic method with mass spectrometric detection has been developed for identification of small, hydrophilic angiotensin I-inhibiting peptides in enzymatically hydrolysed milk proteins. The method involves the further separation of the poorly retained hydrophilic fraction from a standard C(18) reversed-phase column on a hy...
Article
A fast at-line method was developed for the identification of ACE inhibiting (ACEI) peptides in protein hydrolysates. The method consists of activity measurements of fractions collected from a two-dimensional HPLC fractionation of the peptide mixture followed by MS identification of the peptides in the inhibiting fractions. The inhibition assay is...
Article
Endothelial senescence contributes to endothelium dysfunctionality and is thereby linked to vascular aging. A dynamic proteomic study on human umbilical vein endothelial cells, isolated from three umbilical cords, was performed. The cells were cultured towards replicative senescence and whole cell lysates were subjected to 2-D difference gel electr...
Article
An HPLC-MRM-MS method was developed for the quantification of 17 small ACE inhibiting (ACEI) peptides in plasma samples collected from human volunteers after the consumption of a peptide-enriched drink. The assay shows the high selectivity and sensitivity necessary to monitor small changes in the levels of the ACEI peptides after consumption of dri...
Article
The desorption of neutrals, alkali ions and quasimolecular ions of sucrose was studied as function of substrate temperature in laser desorption mass spectrometry. These phenomena were also investigated in thermal desorption experiments. It was concluded that in these experiments gas phase cationization is the major ionization process.
Article
Short wet heat-treatment is presented as a new technique to release high-mass biomarkers to obtain strain-specific fingerprints of intact bacterial spores by matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). Wet heat-treatment was applied for several minutes (3-30) by two techniques using either a screw-cap tube submerged in...
Article
Heat-induced aggregation of bovine beta-lactoglobulin AB (10 mg/ml) was studied at 68.5 degrees C at two different pH values (6.7, 4.9) using gel electrophoresis techniques and matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF MS). Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis under non-reduci...
Article
Full-text available
In this report, we evaluate the validity of using hydrogen/deuterium exchange in combination with collision-induced dissociation mass spectrometry (CID MS) for the detailed structural and conformational investigation of peptides and proteins. This methodology, in which partly deuterated peptide ions are subjected to collision-induced dissociation i...
Article
Full-text available
Nano-electrospray ionization mass spectrometry (ESI-MS) was used to analyze hydrogen/deuterium (H/D) exchange properties of transmembrane peptides with varying length and composition. Synthetic transmembrane peptides were used with a general acetyl-GW(2)(LA)(n)LW(2)A-ethanolamine sequence. These peptides were incorporated in large unilamellar vesic...
Article
CDTA-extractable soybean pectic substances were subjected to enzymatic digestion with arabinogalactan degrading enzymes yielding a resistant polymeric pectic backbone and arabino-, galacto-, and arabinogalacto-oligomers. The complex digest was fractionated using size-exclusion chromatography. Monosaccharide composition analysis, HPAEC fractionation...
Article
Lipo-chitin oligosaccharides (LCOs) are usually produced and isolated for structural analysis from bacteria cultured under laboratory rather than field conditions. We have studied the influence of bacterial growth temperature on the LCO structures produced by different Rhizobium leguminosarum strains, using thin-layer chromatographic, high-performa...
Article
Salmonella enterica sv. Typhimurium strain 1135 possesses smooth(S)-form lipopolysaccharide (LPS). Although the structures of the core region and the O-specific polysaccharide were investigated intensively between the 1960s and the 1980s, the structure of the linkage region between the O-chain and the core was not elucidated unequivocally. By using...
Article
Full-text available
A method is described to study the precise positioning of transmembrane peptides in a phospholipid bilayer combining hydrogen/deuterium (H/D) exchange and nanoelectrospray ionization mass spectrometry. The method was tested by using model systems consisting of designed α-helical transmembrane peptides [acetylGW2(LA)5W2Aethanolamine (WALP16) and ace...
Article
Solid-like components in maltodextrin and inulin model gels were probed with NMR spectroscopy. 1H NMR cross-relaxation experiments yielded quantitative information about the ageing process during which the immobile fraction of the polymer increased. The increase of immobile protons was correlated with crystallization in the gels. From the growth ra...
Article
A systematic comparison between the up-front Collision induced dissociation (CID) mass spectra and low-energy CID tandem mass spectra from twenty-one singly and/or doubly charged peptides has been made. CID spectra of the peptides were recorded at different electrode voltages in the up-front source region of a single quadrupole instrument and diffe...
Article
In an attempt to find the best approach for the mass spectrometric analysis of the whole range of lipopolysaccharide (LPS) structures from Klebsiella pneumoniae ssp. pneumoniae rough strain R20 (O1-:K20-), various methods of LPS preparation were applied and the products were analyzed using a range of mass spectrometric techniques. The most producti...
Article
A mixture of oligosaccharides produced by β-galactosidase using lactose as a substrate was fractionated according to degree of polymerization using gel filtration, followed by high-pH anion-exchange chromatography. The fractions obtained were analyzed using monosaccharide analysis, methylation analysis, mass spectrometry, and NMR spectroscopy. Twel...
Article
The phenomenon of 'internal residue loss' of protonated native- and per-O-methylated oligosaccharides has recently been described as occurring on high-energy collision conditions. Awareness of this phenomenon in the mass spectrometric analysis of oligosaccharides is of great importance since the rearrangement ions produced by this process may compl...
Article
Oxindolylalanine and oxindolylalanine-containing peptides were prepared by treatment of tryptophan and tryptophan-containing peptides with mixtures of dimethyl sulfoxide and hydrochloric acid in acetic acid (DMSO–HCl–HAc). The reaction between tryptophan and DMSO–HCl–HAc was monitored by fast atom bombardment mass spectrometry (FAB-MS) and the prop...
Article
A method has been developed for the rapid molecular mass determination and structural elucidation of mixtures of oligosaccharides derived from plant cell walls. The oligosaccharides were fractionated using gel permeation chromatography and 'analytical' high-performance anion-exchange chromatography (HPAEC), neutralized, dried and the mixtures of el...
Article
Mesorhizobium loti has been described as a microsymbiont of plants of the genus Lotus. Lipo-chitin oligosaccharides (LCOs), or Nod factors, produced by several representative M. loti strains all have similar structures. Using fast-atom-bombardment tandem mass spectrometry and NMR spectroscopy, we have now examined the LCOs from the type strain NZP2...
Article
Nitric oxide (NO) is formed by a class of NO synthases (NOS), which convert arginine into citrulline. A decreased in vivo NO availability can be the result of an increased NO inactivation or a decreased NO production. The latter can be assessed by measurement of isotopic enrichment of plasma citrulline during infusion of isotopically labeled argini...
Article
 For the first time, the complete structure of a lipopolysaccharide (LPS) core region fromSalmonella enterica has been identified that is different from the Ra core type generally thought to be present in allSalmonella LPS. The LPSs from two rough mutants and the smooth form of S. enterica sv. Arizonae IIIa O62, which all failed to react with an Ra...
Article
Full-text available
For the first time, the complete structure of a lipopolysaccharide (LPS) core region fromSalmonella enterica has been identified that is different from the Ra core type generally thought to be present in allSalmonella LPS. The LPSs from two rough mutants and the smooth form of S. enterica sv. Arizonae IIIa O62, which all failed to react with an Ra...
Article
Apple fruit xyloglucan is predominantly built up from XXXG, XXFG, and XLFG units (G = beta-D-Glcp-, X = alpha-D-Xylp-(1-->6)-beta-D-Glcp-, L = beta-D-Galp-(1-->2)-alpha-D-Xylp-(1-->6)-beta-D-Glcp-, F = alpha-L-Fucp-(1-->2)-beta-D-Galp-(1-->2)-alpha-D-Xyl p-(1-->6)-beta-D-Glcp-). However, small amounts of oligosaccharides with a less heavily branche...
Article
Slow molecular motion of polysaccharide chains in native starch and in retrograding starch gels was investigated by one- and two-dimensional exchange solid-state NMR spectroscopy. In native starch, no evidence of molecular motion of the polysaccharide chains on a time-scale of seconds was found. Molecular motion of polysaccharide chains during retr...
Article
The primary proteolysis of caseins by chymosin in Gouda cheese was assessed by identifying the peptides present in the watersoluble fraction of a starter-free cheese. The results show that the selectivity of chymosin, as observed in solution, is affected by the cheese environment.Of all known preferred cleavage sites in αs1- and β-caseins in soluti...
Article
The fragmentation behavior of [M + H]+ ions of a series of underivatized and per-O-methylated trisaccharides having 1 → 6 linked residues, of which one or two is a deoxy-fluoro or deoxy residue and thus has a unique mass, has been studied by using collision-induced dissociation fast-atom bombardment mass spectrometry. In addition to the usual fragm...
Article
The positive- and negative-ion collision-induced dissociation spectra of peptides containing methionine, methionine sulphoxide and methionine sulphone have been studied. Characteristic fragmentations were identified and evaluated as possible indicators for the presence of oxidized methionine residues in peptides. It was found that the elimination o...
Article
A statistical study of the fragmentation behaviour of 138 model peptides, containing 3-9 amino acid residues (n = 3-9) under high-energy collision conditions is presented. The aim was to identify characteristic patterns of ions in the spectra of peptides which can be translated into general rules to be used in the spectral interpretation and provid...
Article
Full-text available
The lipo-chitin oligosaccharides (LCO) or nodulation factors synthesized by Rhizobium leguminosarum bv. trifolii were analyzed using positive mode fast atom bombardment and positive and negative mode electrospray ionization mass spectrometry. From their mass spectrometric behavior it is clearly possible to distinguish between the [M + Na]+ pseudomo...
Article
The lantibiotic lacticin 481 is a bacteriocin produced by Lactococcus lactis ssp. lactis. This polypeptide contains 27 amino acids, including the unusual residues dehydrobutyrine and the thioether-bridging lanthionine and 3-methyllanthionine. Lacticin 481 belongs to a structurally distinct group of lantibiotics, which also include streptococcin A-F...
Article
From complex mixtures of non-glycosylated and differently glycosylated caseinomacropeptides (CMP; κ-casein fragment 106–169; Mr≈7000) various fractions were isolated and further purified by reversed-phase HPLC. The fractions were characterized by mass determination and composition analysis and also used in gel-permeation chromatography and NMR stud...
Article
The stability of the B1-ion from glycylglycine dipeptides was studied using collision-induced dissociation experiments and ab initio calculations. This study reveals that the B1-type ion from glycine should be considered as an electrostatically bound ion/moecule complex, which dissociates into a glycine immonium ion (A1) and a carbon monoxide molec...
Article
Full-text available
We have purified and characterized the nodulation factors produced by Rhizobium tropici CIAT899. This strain produces a large variety of nodulation factors, these being a mixture of sulfated or nonsulfated penta- or tetra-chito-oligosaccharides to which any of six different fatty acyl moieties may be attached to nitrogen of the nonreducing terminal...
Article
Rhizobium wild-type strain GRH2 was originally isolated from the tree, Acacia cyanophylla, and has a broad host-range which includes herbaceous legumes, such as Phaseolus and Trifolium species. Here we show that strains of Rhizobium sp. GRH2, into which heterologous nodD alleles have been introduced, produce a large diversity of both sulphated and...
Article
Plant lectins can be potent modulators of vertebrate immune functions. Biochemical characterization of lectins from animal tissues enables the determination of whether these endogenous activities display a comparable immunological potency. Focusing on chicken beta-galactoside-binding lectins, the monomeric intestinal (CL-14) and the dimeric liver l...
Article
Natural mixtures of sophorolipids produced by the yeast Candida bombicola have been analyzed by fast atom bombardment (FAB)-MS and collision-induced dissociation (CID)-MS. Some pure components have been analysed by two-dimensional NMR spectroscopy. The presence of acidic, lactonic, and O-acetylated forms and the position of double bonds in the fatt...
Article
Various components of the beta-casein fraction from bovine milk were separated by preparative reversed-phase high-performance liquid chromatography (RP-HPLC). They included the genetic variants beta A1, beta A2, beta A3, and an unknown component previously denoted beta X [S. Visser et al., J. Chromatogr. 548 (1991) 361-370]. Tryptic digests of thes...
Article
Numerous studies have shown that glycosylation of the alpha-subunit of human chorionic gonadotropin (alpha hCG) is essential for the biological activity of this hormone. To obtain detailed insight into the function of N-glycosylation, the availability of site-specifically and fully deglycosylated alpha-subunits obtained under non-denaturing conditi...
Article
Numerous studies have shown that glycosylation of the alpha-subunit of human chorionic gonadotropin (αCG) is essential for the biological activity of this hormone. To obtain detailed insight into the function of N-glycosylation, the availability of site-specifically and fully deglycosylated alpha-subunits obtained under non-denaturing conditions is...
Article
Previously, we have shown that the nodE gene is a major determinant of the difference in host range between Rhizobium leguminosarum biovars viciae and trifolii. A new genetic test system for stringent functional analysis of nodE genes was constructed. By testing chimeric nodE genes constructed by the exchange of polymerase chain reaction (PCR)-gene...
Article
The protonated and sodium cationized pseudomolecular ions of a series of reducing and non-reducing oligosaccharides possessing aldopentopyranosyl, 6-deoxyaldohexopyranosyl, ketohexofuranosyl, 4-O-methyl glucuronopyranosyl methyl ester and N-acetyl 2-deoxyglucopyranosylamine units were studied using collision-induced dissociation (CID) fast atom bom...
Article
Staphylococcus hyicus lipase is a serine hydrolase. In order to identify the active site histidine of S. hyicus lipase we have chemically modified S. hyicus lipase with 1-bromo-octan-2-one. The enzyme is rapidly inactivated by this inhibitor with a half-time of 578 s at pH 6.5 and 30 degrees C. Addition of the enzyme's cofactor calcium increases th...
Article
Fast atom bombardment and collisonal-induced dissociation tandem mass spectrometry were used to analyze 12 cationic organometallic palladium [Pd(L)(R)](OTf) complexes containing three different terdentate nitrogen ligands (L), an organic group (R) attached in the sigma bonding mode, and a trifluoromethanesulfonate anion (OTf is CF3SO3-) using m-nit...
Article
Motional heterogeneity in acrylate (AA)/laurylmethacrylate (LMA) copolymers was investigated by the two-dimensional 1H-13C heteronuclear wideline-separation n.m.r. technique. Qualitative information about molecular dynamics is reflected in the width of the proton wideline. It was found that a decrease of the AA/LMA ratio in the copolymer reduces th...
Article
Full-text available
Rhizobium etli is a microsymbiont of plants of the genus Phaseolus. Using mass spectrometry we have identified the lipo-chitin oligosaccharides (LCOs) that are produced by R. etli strain CE3. They are N-acetylglucosamine pentasaccharides of which the non-reducing residue is N-methylated and N-acylated with cis-vaccenic acid (C18:1) or stearic acid...
Article
The mass spectrometric characteristics of a number of different m/z 102 ions, which might occur in the fast-atom bombardment mass spectra of peptides, appeared to be sufficiently different for an unequivocal structural assignment and they have successfully been applied in the structural analysis of an unknown. Special attention has been paid to the...
Article
The positive-ion fast atom bombardment mass spectra of permethylated aldo- and pseudoaldobiouronic acids can be used to distinguish these classes of compounds. The collisional-induced dissociation spectra of the [M + H]+ ions show fragment ions resulting from glycosidic bond cleavage and successive losses of methanol molecules. These spectra togeth...
Article
The molecular mobility of polysaccharide chains and the water organization in maize starch forms A and B were investigated with the recently developed 2D H-1-C-13 heteronuclear wideline separation (WISE) method of solid-state NMR spectroscopy. Proton lines of starch yield information about the molecular motion. No evidence for molecular motion of t...
Article
Unknown, specific mutations in the sequence of an enzyme variant (a Bacillus subtilisin protease) produced by protein engineering were identified using High-performance Liquid Chromatographic/Fast Atom Bombardment Mass Spectrometric (HPLC/FAB MS) techniques. The variant and the highly homologous wild-type enzyme were treated with CNBr followed by t...
Article
The Rhizobium nodulation genes nodABC are involved in the synthesis of lipo-chitin oligosaccharides. We have analysed the metabolites which are produced in vivo and in vitro by Rhizobium strains which express the single nodA, nodB and nodC genes or combinations of the three. In vivo radioactive labelling experiments, in which D-[1-14C]-glucosamine...
Article
The specificity of the cell-envelope proteinase (CEPIII-type) from Lactococcus lactis subsp. cremoris AM1 in its action on bovine kappa-casein was studied. A 4-h digest (pH 6.2, 15 degrees C) of kappa-casein was made with the purified proteinase. The pH-4.6 soluble fraction, representing more than 95% of the whole hydrolysate, was ultrafiltered to...
Article
The specificity of the cell-envelope proteinase (CEPIII-type) from Lactococcus lactis subsp. cremoris AM1 in its action on bovine κ-casein was studied. A 4-h digest (pH 6.2, 15°C) of κ-casein was made with the purified proteinase. The pH-4.6 soluble fraction, representing more than 95% of the whole hydrolysate, was ultrafiltered to obtain a high-mo...
Article
In the unimolecular decomposition MS−MS spectra of the [M + H]+ ions of peracetylated β-methyl xylobiosides the α- and β-linked isomers show differences in fragmentation behaviour. The intensities of the oxonium ions at m/z 259 (formed by cleavage of the glycosidic bond) consistently turn out to be significantly higher (relative to the m/z 475 ions...
Article
Several rhamnolipid preparations from Pseudomonas strains were studied by thin-layer chromatography/fast atom bombardment (TLC/FAB) mass spectrometry and TLC/FAB tandem mass spectrometry (MS/MS). The preparations were separated with normal-phase (Silica 60) and reversed-phase (RP-8) chromatography. Silica 60 plates appeared to be very useful in the...
Article
A sensitive mass spectrometric method for the specific identification of O-glycosylation sites in glycopeptides is presented. Reductive β-elimination liberates a peptide containing a specifically modified amino acid at the former site of carbohydrate attachment. Mass spectrometry is used to determine the sequence of the modified peptide, in which t...
Article
Amino acid sequencing of a subtilisin-type bacterial protease and a bio-engineered variant was carried out by investigating various enzymatic digests using HPLC-frit fast atom bombardment MS methods. The fast atom bombardment mass spectral data allowed rapid identification of the enzymatically generated peptides and differentiation between both pro...
Article
The mechanism for the formation of C″-type ions from protonated peptides, produced under conditions of fast-atom bombardment and rollisional activation was investigated. Comparison of the tandem mass spectra of the [M + H]+ ions of a model peptide and the corresponding [Md + D]+ ions, in which all exchangeable hydrogens are replaced with deuterium,...
Article
Distinction between the linkage types 1-->2, 1-->3 and 1-->4 of xylobioses can be achieved on the basis of the unimolecular decomposition spectra of the oxonium ions of the per-O-acetylated methyl glycosides. The spectra of the oxonium ions of various unbranched xylotri-, tetra- and pentaoses allow determination of the linkage position between the...
Article
Unimolecular decomposition spectra of oxonium ions from peracetylated pentoses can be used for identification purposes. The fast-atom bombardment mass spectra of an oligosaccharide with a pentose residue at the non-reducing terminus also contain this oxonium ion, which allows identification of this monosaccharide residue by a tandem mass spectromet...
Article
Two rhamnobiose-lipid preparations have been studied by fast atom bombardment (FAB) tandem mass spectrometry. The principal rhamnobiose-lipids contain the beta-hydroxydecanoyl-beta-hydroxydecanoate Rha-Rha-C10-C10 and the beta-hydroxytetradecanoyl-beta-hydroxytetradecanoate Rha-Rha-C14-C14. Both preparations contain minor components which are heter...
Article
Fast Atom Bombardment (FAB) ionization of sucrose monocaprate and sucrose monolaurate in the presence of Na+ ions shows the formation of both [M+Na]+ and [M - H]- ions. The [M+Na]+ ions undergo charge-remote fragmentations when collisionally activated at high translational energy. These charge-remote fragmentations are useful for the structural det...
Article
The mechanism for the formation of C"-type ions from protonated peptides, produced under conditions of fast-atom bombardment and collisional activation was investigated. Comparison of the tandem mass spectra of the [M + H]+ ions of a model peptide and the corresponding [Md + D]+ ions, in which all exchangeable hydrogens are replaced with deuterium,...
Article
When mass-analysed ion kinetic energy (MIKE) spectra are required to discriminate between isomeric ions formed under conditons of fast atom bombardment (FAB) in the ion source, severe interference may be observed. The interfering peaks in MIKE spectra obtained with a reversed-geometry instrument can arise from different sources. Moreover, the inten...
Article
The positive ion fast atom bombardment mass spectrum of the aminoglycan N-[2-(acetamido)-2-deoxy-β-D-glucopyranosyl]-L-asparagine and the collisional activation spectrum of the protonated molecule are presented and its fragmentation scheme is proposed. To gain a further understanding of the mechanisms involved spectra of both methyl-2-(acetamido)-2...
Article
Mass spectra of peracetylated monosaccharides can be obtained by various ionization methods, including electron ionization, chemical ionization and fast atom bombardment. The structural information in the spectra of two relatively simple model compounds (acetyl 3,4-di-O-acetyl-D-digitoxose and acetyl 2,3,4-tri-O-acetyl-D-xylose) was compared. Addit...
Article
In some recent papers the use of fast atom bombardment (FAB) tandem mass spectrometry for the differentiation of various underivatized oligosaccharides was discussed. Because of the close structural resemblance of the isomers, the metastable ion (MI) and collisional activation (CA) spectra of isomeric ions generated from these compounds generally e...
Article
Liquid chromatography/fast-atom bombardment mass spectrometry was used to partially confirm the amino-acid sequence of the protein, beta-casein. The study demonstrates that the technique is capable of the rapid and accurate identification of peptide fragments from tryptic digests and that chromatographic integrity is maintained during the analysis....