PubMed Health⌕ Search

Biomedical subjects

M Meldal

Publications and source records attributed to M Meldal.

At least 37 records · Page 2Linked to original sources
PubMed1998

Kinetic analysis of the mechanism and specificity of protein-disulfide isomerase using fluorescence-quenched peptides.

Protein-disulfide isomerase (PDI) is an abundant folding catalyst in the endoplasmic reticulum of eukaryotic cells. PDI introduces disulfide bonds into newly synthesized proteins and catalyzes disulfide bond isomerizations. We have synthesized a library of disulfide-linked fluorescence-quenched peptides, individually linked to resin beads, for two purposes: 1) to probe PDI specificity, and 2) to identify simple, sensitive peptide substrates of PDI. Using this library, beads that became rapidly fluorescent by reduction by human PDI were selected. Amino acid sequencing of the bead-linked peptides revealed substantial similarities. Several of the peptides were synthesized in solution, and a quantitative characterization of pre-steady state kinetics was carried out. Interestingly, a greater than 10-fold difference in affinity toward PDI was seen for various substrates of identical length. As opposed to conventional PDI assays involving larger polypeptides, the starting material for this assay is homogenous. It is furthermore simple and highly sensitive (requires less than 0.5 microgram of PDI/assay) and thus opens the possibility for quantitative determination of PDI activity and specificity.

Amino Acid Sequence↗
PubMed1998

Analysis of organic reactions by thin layer chromatography combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

The products of a wide variety of organic reactions were rapidly identified by their masses through a combination of thin layer chromatography (TLC) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). Crude mixtures of peptides and glycopeptides, complex carbohydrate reactions, and a classical organic reaction were analysed using the following standard protocol. The components of the reaction mixtures were first separated on the TLC plate, scraped off, extracted and analysed by MALDI-TOFMS. The technique used is easy and applicable to most organic reactions, becoming a very powerful technique in reaction optimization once composition and identity of TLC spots have been established by MS. Moreover, the TLC/MALDI-TOFMS method was used to identify low molecular weight compounds with masses within the matrix region (100-500 u), a goal which is normally difficult to achieve. We successfully detected low molecular weight compounds by suppression of the matrix peaks using a relatively low matrix:analyte ratio (15:1 or lower). Doping both matrix and analyte solutions with [Cs]+ ions resulted in suppression of both [Na]+ and [K]+ peaks, thus enhancing the spectral signals and making identification of low molecular weight compounds more facile.

Carbohydrates↗
PubMed1998

Preparation of fluorescence quenched libraries containing interchain disulphide bonds for studies of protein disulphide isomerases.

Protein disulphide isomerase is an enzyme that catalyses disulphide redox reactions in proteins. In this paper, fluorogenic and interchain disulphide bond containing peptide libraries and suitable substrates, useful in the study of protein disulphide isomerase, are described. In order to establish the chemistry required for the generation of a split-synthesis library, two substrates containing an interchain disulphide bond, a fluorescent probe and a quencher were synthesized. The library consists of a Cys residue flanked by randomized amino acid residues at both sides and the fluorescent Abz group at the amino terminal. All the 20 natural amino acids except Cys were employed. The library was linked to PEGA-beads via methionine so that the peptides could be selectively removed from the resin by cleavage with CNBr. A disulphide bridge was formed between the bead-linked library and a peptide containing the quenching chromophore (Tyr(NO2)) and Cys(pNpys) activated for reaction with a second thiol. The formation and cleavage of the interchain disulphide bonds in the library were monitored under a fluorescence microscope. Substrates to investigate the properties of protein disulphide isomerase in solution were also synthesized.

Cystine↗
PubMed1998

Inhibition of cruzipain visualized in a fluorescence quenched solid-phase inhibitor library assay. D-amino acid inhibitors for cruzipain, cathepsin B and cathepsin L.

A PEGA-resin was derivatized with a 3:1 mixture of hydroxymethyl benzoic acid and Fmoc-Lys(Boc)-OH and the fluorogenic substrate Ac-Y(NO2)KLRFSKQK(Abz)-PEGA was assembled on the lysine using the active ester approach. Following esterification of the hydroxymethyl benzoic acid with Fmoc-Val-OH a library XXX-k/r-XXXV containing approximately 200,000 beads was assembled by split synthesis. The resulting 'one bead, two peptides' library was subjected to extensive hydrolysis with cruzipain. One hundred darker beads were isolated and the 14 most persistently dark beads were collected and sequenced. The putative inhibitor peptides and several analogues were synthesized and found to be competitive microM to nM inhibitors of cruzipain in solution. The inhibitory activity was found to be unspecific to cruzipain when compared with cathepsins B and L and specific when compared with kallikrein. One of the inhibitors was docked into the active site of cathepsin B and was found most probably to bind to the enzyme cavity in an unusual manner, owing to the inserted D-amino acid residue.

Amino Acids↗
PubMed1998

PEGA supports for combinatorial peptide synthesis and solid-phase enzymatic library assays.

Permeable resins cross-linked with long PEG chains were synthesized for use in solid-phase enzyme library assays. High molecular weight bis-amino-polyethylene glycol (PEG) 4000, 6000, 8000 were synthesized by a three-step reaction starting from PEG-bis-OH. Macromonomers were synthesized by partial or di-acryloylation of bis-amino-PEG derivatives. Bis/mono-acrylamido-PEG were copolymerized along with acrylamide by inverse suspension copolymerization to yield a less cross-linked resin (Type I, compounds 6-9). Furthermore, acryloyl-sarcosin ethyl ester was co-polymerized along with bis-acrylamido PEG to obtain more crosslinked capacity resin (Type II, compounds 13-19). N,N-Dimethylacrylamide was used as a co-monomer in some cases. The polymer was usually obtained in a well-defined beaded form and was easy to handle under both wet and dry conditions. The supports showed good mechanical properties and were characterized by studying the swelling properties, size distribution of beads, and by estimating the amino group capacity. Depending on the PEG chain length, the monomer composition and the degree of cross-linking the PEGA supports showed a high degree of swelling in a broad range of solvents, including water, dichloromethane, DMF, acetonitril, THF and toluene: no swelling was observed in diethyl ether. The PEGA resins (Type I) with an amino acid group capacity between 0.07 and 1.0 mmol/g could be obtained by variation of the monomer composition in the polymerization mixture. Fluorescent quenched peptide libraries were synthesized on the new polymer using a multiple column library synthesizer and incubated with the matrix metalloproteinase MMP-9 after it had been activated by 4-aminophenyl mercuric acetate resulting in 67/83 kDa active enzyme. The bright beads were separated manually under a fluorescence microscope and sequenced to obtain peptide substrates for MMP-9. After treatment with ethylene diamine, high-loaded resins (Type II) have been employed in continuous flow peptide synthesis to yield peptides in excellent yield and purity.

Acetamides↗
PubMed1998

Fluorescent properties of amino acids labeled with ortho-aminobenzoic acid.

ortho-Aminobenzoic acid (Abz) has been used as a convenient fluorescent donor group in internally quenched fluorescent peptides, which are employed as substrates for several proteolytic enzymes. As Abz is usually bound to the N-amino terminal of these peptides, it is of interest to investigate the Abz group fluorescent properties bound to different amino acids. We report in this article the optical absorption and fluorescent properties, in aqueous media, of Abz bound to the alpha-amino group of Ala, Gly, Leu, Ile, Val, Pro, Phe, Arg, Glu, Met, Asn, Tyr, and Trp, with monomethylamidated alpha-carboxyl group. In order to explore the origin of the drastic reduction of Abz attached to Nalpha amino group of prolyl-peptides, we also examined the fluorescence properties of Abz-NHCH3, Abz-N(CH3)2, and Abz-pyrrolidine. Molecular dynamics simulation and NMR data indicated a lack of periplanarity of the Abz-dimethylamide, which could be the origin of low fluorescence quantum yield of Abz-prolyl-peptides.

Amides↗
PubMed1998

The extracellular polysaccharide of Pichia (Hansenula) holstii NRRL Y-2448: the phosphorylated side chains.

The exopolysaccharide produced by Pichia (Hansenula) holstii NRRL Y-2448 is composed of a phosphomannan core to which oligosaccharide diester phosphate side chains are appended. The oligosaccharides of the side chains were released as oligosaccharide phosphates and neutral oligosaccharides by mild hydrolysis with aqueous acetic acid and aqueous hydrogen fluoride, respectively. The liberated oligosaccharide phosphates were studied by NMR spectroscopy and by electrospray and fast atom bombardment mass spectrometry. The structures of the neutral oligosaccharides were determined by 1D and 2D NMR spectroscopic experiments. Further insight into the length of the side chains was obtained from a matrix assisted laser desorption ionisation-time of flight mass spectrometric study of high and low molecular weight fragments obtained from partial acid hydrolysis of the native polysaccharide.

Carbohydrate Conformation↗
PubMed1998

Substrate specificity of barley cysteine endoproteases EP-A and EP-B.

The cysteine endoproteases (EP)-A and EP-B were purified from green barley (Hordeum vulgare L.) malt, and their identity was confirmed by N-terminal amino acid sequencing. EP-B cleavage sites in recombinant type-C hordein were determined by N-terminal amino acid sequencing of the cleavage products, and were used to design internally quenched, fluorogenic peptide substrates. Tetrapeptide substrates of the general formula 2-aminobenzoyl-P2-P1-P1'-P2'-tyrosine(NO2)-aspartic acid, in which cleavage occurs between P1 and P1', showed that the cysteine EPs preferred phenylalanine, leucine, or valine at P2. Arginine was preferred to glutamine at P1, whereas proline at P2, P1, or P1' greatly reduced substrate kinetic specificity. Enzyme cleavage of C hordein was mainly determined by the primary sequence at the cleavage site, because elongation of substrates, based on the C hordein sequence, did not make them more suitable substrates. Site-directed mutagenesis of C hordein, in which serine or proline replaced leucine, destroyed primary cleavage sites. EP-A and EP-B were both more active than papain, mostly because of their much lower Km values.

Amino Acid Sequence↗
PubMed1997

T-cell recognition of tumor-associated carbohydrates: the nature of the glycan moiety plays a decisive role in determining glycopeptide immunogenicity.

Aberrant glycosylation is one of the most constant traits of the malignant cell phenotype. To study T-cell responses to tumor-associated glycans, the mouse hemoglobin-derived decapeptide Hb(67-76), which binds well to the MHC class II molecule E(k) and is nonimmunogenic in CBA/J mice, was either O- or N-glycosylated at its primary T-cell receptor contact residue, position 72, with different glycans attached to either threonine, serine, or asparagine. The carbohydrate moieties included tumor-associated mucins, i.e., the Tn and T antigens, mucin-related glycans, and mucin-unrelated glycans. The side chain of the amino acid in position 72 points away from the MHC binding site when the Hb(67-76) peptide is bound to E(k), so the assumption was that this was also the case for glycans attached to this position. The glycosylated Hb(67-76) peptide analogues were then studied for binding to E(k) and for immunogenicity in CBA/J mice. All 16 glycopeptides bound well to E(k), although those with the more complex carbohydrates bound more weakly than those with monosaccharides. Six of 12 O-glycosylated and 0 of 4 N-glycosylated glycopeptides were able to induce a T-cell proliferative response with a stimulation index above 3.0. Some glycopeptides were not immunogenic, suggesting that there may be holes in the T-cell repertoire due to a lack of T-cell receptor regions accommodating certain glycan structures. The four strongest immunogenic glycopeptides were all O-glycosylated, and interestingly, three of them carried the tumor-associated Tn or T antigen. On the other hand, the Hb(67-76) peptide analogue with the natural mucin Core2 structure attached did not elicit any T-cell response. T cells primed to a glycopeptide with a simple glycan structure such as Tn did not cross-respond significantly to other glycopeptides, indicating a high degree of carbohydrate specificity in T-cell recognition. T cells primed to a glycopeptide carrying the more complex T antigen showed a complicated pattern of cross-responses to glycopeptides with simpler glycan moieties. The fact that it is possible to raise MHC class II-restricted T-cell responses against tumor-associated carbohydrate structures opens new perspectives for the designing of cancer vaccines.

Animals↗
PubMed1997

Characterization of the substrate specificity of the major cysteine protease (cruzipain) from Trypanosoma cruzi using a portion-mixing combinatorial library and fluorogenic peptides.

The substrate specificity of the major cysteinyl proteinase of the parasitic protozoan Trypanosoma cruzi (cruzipain) was investigated, by combinatorial replacement of amino acid residues at positions P5-P'5, using a fluorescent quenched solid-phase library assay. Positively charged residues appear to be a general preference in the P5-P3 and the P'5-P'3 positions, while a hydrophobic residue was always required at the P2 position. A broad range of amino acids could be accepted at the P'1 position. A clear difference in terms of specificity between cruzipain and human cathepsin L was observed for the accommodation of Pro at the P2 position. The P1 specificity was investigated by a more detailed enzyme kinetic analysis using peptidyl-MCA (where MCA is methylcoumarin amide) and Abz-peptidyl-EDDnp [where Abz is o-aminobenzoic acid and EDDnp is N-(2,4-dinitrophenyl)ethylenediamine] as substrates, and the results were compared with those obtained using human cathepsin L. Cruzipain showed a clear preference for benzyl-Cys or Arg at the P1 position. Human cathepsin L presented similar behaviour to that of cruzipain for the hydrolysis of the epsilon-NH2-Cap-Leu-Xaa-MCA (where Cap is epsilon-aminocaproyl) and Abz-Lys-Leu-Xaa-Phe-Ser-Lys-Gln-EDDnp series, whereas the mammalian enzyme was able to tolerate large P1 residues, such as phenylalanine, better than cruzipain in the latter series.

Alanine↗
PubMed1997

Carbohydrate and peptide specificity of MHC class II-restricted T cell hybridomas raised against an O-glycosylated self peptide.

MHC class II E(k)-restricted, IL-2 secreting T cell hybridomas were raised against the synthetic glycopeptide Hb(67-76)-alpha-GalNAc, (T72(Tn)), in CBA/J mice (H-2(k)). The fine specificity of the hybridomas against the glycan moiety was investigated by testing their response against a panel of Hb(67-76)-derived glycopeptides, all with a glycan attached to serine or threonine at the position 72 in the peptide, but with different glycans. The hybridomas showed a high degree of specificity for the alpha-GalNAc moiety with few and faint cross-responses to the glycopeptides having other glycans attached even though some of these were structurally very similar to alpha-GalNAc. The fine specificity of the hybridomas for the peptide moiety was investigated by testing their responses to a panel of Hb(67-76)-alpha-GalNAc glycopeptides with alanine substitutions at all positions except at the two MHC binding anchor positions, I68 and K76, and the T72 to which the alpha-GalNAc was attached. Glycopeptides substituted with alanine at positions where the amino acid side chain pointed toward the TCR did not stimulate the hybridomas, whereas glycopeptides substituted with alanine at positions orientated down into the MHC binding groove stimulated many of the hybridomas. These results indicate that the glycan attached to the peptide as well as solvent-accessible parts of the peptide are recognized with a high degree of specificity by the T cells, whereas the parts of the peptide buried in the MHC binding site are less important or totally ignored by the T cells.

Animals↗
PubMed1997

Synthesis and characterisation of highly glycosylated glycopeptides with Tn-antigenic structures corresponding to human glycophorin AN.

Two highly glycosylated O-glycopeptides corresponding to human glycophorin AN with Tn-antigenic structures were synthesised. The first glycopeptide has two glycosylated clusters with three and six adjacent 2-acetamido-2-deoxy-D-galactose (GalNAc) glycosylation sites and represents the N-terminal octadecapeptide from Leu-1 to Lys-18. The second glycopeptide, a decapeptide from His-9 to Lys-18, contains as a compact cluster six adjacent GalNAc glycosylation sites. The solid phase synthesis was realised by using the carbohydrate-containing building blocks Fmoc-Ser(Ac3GalN3)-Pfp and Fmoc-Thr(Ac3GalN3)-Pfp. The synthesised substances were characterised by NMR spectroscopic techniques. The main techniques used were homonuclear TOCSY and NOESY as well as HMQC and HMBC for 13C,1H correlations.

Amino Acid Sequence↗
PubMed1997

Properties of solid supports.

Many supports including composite materials and functionalized surfaces are available for solid-phase synthesis. In the process of selecting the proper support it is important to consider the optimal performance during solid-phase synthesis. For most purposes the mechanically stable beaded gel resins are preferred. These resins are homogeneous, and the loading and physical and chemical properties can easily be varied. Optimal properties have been obtained by radical polymerization of end group acryloylated long-chain polyethylene glycols. However, polystyrene resins or amide bond free PEG-based resins may be more suited for general organic synthesis where reactivity of radicals, carbenes, carbanions, carbenium ions, or strong Lewis acids have to be considered. Loading of the resins can have a dramatic effect on the outcome of a synthesis and has to be considered separately for each synthesis. Synthesis of long peptides with 50-100 amino acids imposes completely different requirements on the performance, swelling, and loading than a large-scale synthesis of, for example, the pentapeptide enkephalin. Automated multiple synthesizers constructed for columns of beaded gel or composite supports are available from many suppliers. It is therefore expected that the optimization of support properties will continue in order to meet new synthetic challenges. In the synthesis for solid-phase screening of binding of biomolecules to ligands directly on the resin beads, it is an advantage if the resin is not permeable to the biomolecule so unbound molecules can easily be removed by washing. This is the case with polystyrene-based resins, but they do, however, often show nonspecific adhesion of proteins owing to the hydrophobic character of the polystyrene. Modification of the functional groups of polystyrene with polyethylene glycol as spacers for synthesis of the binding ligands can increase the available ligand concentration on the bead surface and eliminate most of the nonspecific adhesion. In contrast to binding studies, solid-phase assays of enzymes require beads that are permeable to the enzyme, as the progress of reaction can be followed and the product of reaction analyzed. The available amount on the surface of the polystyrene-based beads (approximately 0.3%) is not enough for product analysis. Therefore, in the case of enzyme assays, highly swelling permeable PEG-based gel resins or functionalized surfaces of a polar and porous matrix are preferred.

Chemistry↗
PubMed1997

Constrained glycopeptide ligands for MPRs. Limitations of unprotected phosphorylated building blocks.

A new methodology for the synthesis of cyclic and phosphorylated glycopeptide templates was developed. First, fully protected building blocks containing mannose and mannose disaccharides with bis-trichloroethyl phosphate on Fmoc-Thr-OPfp were synthesized. These were used in solid-phase assembly through side chain anchoring of glycosylated hexa- and octa-peptides protected at the C-terminal carboxylate as the allyl ester. Selective allyl ester cleavage and head-to-tail cyclization under pseudodilution conditions gave a high yield of pure cyclic peptide templates. Unprotected phosphate in the building block was evaluated as an alternative to the problematic trichloroethyl group. It was found that one unprotected phosphate is readily incorporated, whereas the second unprotected phosphorylated building block react very slowly due to electrostatic repulsion in the solid-phase synthesis. For comparison with previous binding studies modified glycopeptide templates containing only phosphorylated mannose monosaccharides or templates modified in the peptide part were synthesized. All the structures were tested for their binding to the mannose 6-phosphate receptor, and it was found that although mannose disaccharides are required for optimal interaction, the detailed structure of the peptide template has a strong influence on binding to the receptor. The restricted conformations of the cyclic peptides decreased the binding considerably.

Chromatography, High Pressure Liquid↗