Synthesis and spectroscopic properties of 4-ethoxymethylene-2-(1)-naphthyl-5(4H)-oxazolone-labeled fluorescent peptides

Strategies for the preparation of new fluorescent oligopeptide conjugates labeled with 4-ethoxymethylene-2-[1]-naphthyl-5(4H)-oxazolone (naOx-OEt) at the N-terminal on solid support or in solution have been devised. These procedures are simple and easy to carry out by reacting naOx-OEt or N(alpha)-naOx-amino acid with side chain protected peptide chains attached to resins. The integrity of the N-alkyl bond was maintained even after the trifluoracetic acid or HF based cleavages procedures. Our data show that the naOx fluorophore is compatible with both Fmoc/tBu and Boc/Bzl methods and also suggest that naOx-amino acid could be utilized as building blocks for solid phase peptide synthesis. Comparative analysis of fluorescence properties of naOx-conjugates indicated that the spectral properties of the fluorophore do not change after incorporating into peptides. The compact size, the definite chemical reaction for its introduction in combination with the appropriate spectral features (e.g., intense emission, pH independent fluorescent characteristics, and beneficial photobleaching dose constant and rates) and with chemical and spectral stability, naOx-based labeling could be attractive for novel cellular fluorescent techniques (e.g., in laser scanning confocal FRET) to study peptide-protein and protein-protein interactions even in biological matrices.     

Primary structure of protein L19 from the large subunit of Escherichia coli ribosomes.

Protein L19, a component of the Escherichia coli 50S ribosomal subunit implicated in 30S-50S subunit interaction was sequenced by the dansyl-Edman method. L19 consists of a single polypeptide chain of 114 amino acids giving a calculated molecular weight of 13 002. Peptides obtained from various enzymatic cleavages were isolated on thin-layer peptide maps or gel filtration. Automated Edman degradation using a liquid phase sequenator was carried out on the whole protein as well as on a large 58-residue fragment arising from digestion with Staphylococcus aureus protease. Every position in protein L19 was confirmed at least twice. Results of secondary structure estimation and homologies with other E. coli ribosomal protein sequences are presented.     

Preparation of protected peptide amides using the Fmoc chemical protocol. Comparison of resins for solid phase synthesis.

Different resins were examined for their potential use in the solid phase synthesis of protected peptide amides using the 9-fluorenylmethoxycarbonyl (Fmoc) chemical protocol. The model protected peptide amide BocTyr-Gly-Gly-Phe-Leu-Arg(Pmc)NH2 (1) was synthesized on both the acid-labile 4-(2',4'-dimethoxyphenyl-Fmoc-aminomethyl)phenoxy resin (Rink amide resin) (2) and on resins containing the base-labile linker 4-hydroxymethylbenzoic acid. Of the resins examined only the methylbenzhydrylamine resin containing the 4-hydroxymethylbenzoic acid linkage, which was cleaved by ammonolysis in isopropanol, gave the model peptide 1 in good overall yield (53% including functionalization). Thus the synthesis of protected peptide amides by solid phase synthesis using Fmoc-protected amino acids with t-butyl-type side chain protecting groups is feasible. The choice of peptide-resin linkage and its cleavage conditions, however, are critical to the success of such syntheses. The potential application of this synthetic strategy to the preparation of novel peptide amides is discussed.     

A synthetic strategy for ON-resin amino acid specific multiple fatty acid acylation of peptides

Covalent modification with fatty acids is observed in several proteins that play crucial roles in cellular physiology. In this paper, a convenient method for the generation of multiple fatty acylated synthetic peptides is described. Peptides were synthesized using solid phase procedures with fluorenylmethoxycarbonyl a-amino protected amino acids. Acetamidomethyl protected cysteines were employed. The thiol protecting group was selectively deprotected and acylation was carried out on the resin-bound peptides. The strategy described in this report is applicable to any peptide sequence.     

Does trypsin cut before proline?

Trypsin is the most commonly used enzyme in mass spectrometry for protein digestion with high substrate specificity. Many peptide identification algorithms incorporate these specificity rules as filtering criteria. A generally accepted "Keil rule" is that trypsin cleaves next to arginine or lysine, but not before proline. Since this rule was derived two decades ago based on a small number of experimentally confirmed cleavages, we decided to re-examine it using 14.5 million tandem spectra (2 orders of magnitude increase in the number of observed tryptic cleavages). Our analysis revealed a surprisingly large number of cleavages before proline. We examine several hypotheses to explain these cleavages and argue that trypsin specificity rules used in peptide identification algorithms should be modified to "legitimatize" cleavages before proline. Our approach can be applied to analyze any protease, and we further argue that specificity rules for other enzymes should also be re-evaluated based on statistical evidence derived from large MS/MS data sets.     

P134-M Solid Phase Synthesis of C-Terminus Fluorescent Peptide: Comparison of Fmoc-Lys(5-FAM)-Resin and Fmoc-Lys[5-FAM(Trt)]-Resin

Many FRET (Fluorescent Resonance Energy Transfer) peptides require a C-terminus fluorescent label. In order to facilitate the synthesis of C-terminus fluorescent peptides, we prepared and compared two kinds of resins, Fmoc-Lys(5-FAM)-resin (I) and Fmoc-Lys[5-FAM(trt)]-resin (II).¹ Resin (II) has a phenolic hydroxyl group protected with trityl group. The reason for introducing the protecting group was supposedly to prevent the phenolic hydroxyl groups from reacting with the activated amino acids during peptide synthesis.In this report, a fluorescent peptide [EREQTVDLS-VKRPRTGRKKRRQ-RRRK(5-FAM)-NH₂] was synthesized using each of these resins. Syntheses were carried out under similar standard conditions. The peptides obtained showed no significant difference in purity. These results showed that resin (I) is also suitable for synthesis of C-terminus fluorescent peptide.     

Comparison of procedures for directly obtaining protected peptide acids from peptide-resins.

The preparation of small-sized protected peptide acids related to cholecystokinin and gomesin was attempted using peptide-Kaiser oxime resins (KOR) as starting materials. For comparison, peptide-2-Cl-trityl resin (CLTR) was also employed. While peptide detachment from KOR was achieved through the oxime ester bond hydrolysis mediated by DBU, hydroxide ion or Ca(+2) ion, peptide release from CLTR was accomplished through acid-catalysed hydrolysis of the peptide-resin ester linkage. Amino acid analysis of the peptide-resins before and after peptide release allowed the calculation of the reaction yields. RP-HPLC and LC/ESI-MS of the resulting crude peptides allowed estimation of their quality. The data collected indicated that: (i) among the procedures used for peptide displacement from KOR, the one employing DBU was the most efficient since it furnished all model protected peptide acids with the highest quality in a very short time; (ii) although slow, Ca(+2)-assisted peptide detachment from KOR was selective and was suitable for generating high-quality protected peptide acids containing up to five residues; (iii) even though the protocols employed for peptide release from CLTR have shown to be appropriate, the one employing 1% TFA/DCM was the most productive; (iv) in terms of product quality, DBU-catalysed peptide detachment from KOR was similar to TFA-catalysed peptide release from CLTR although the latter was more productive. These findings are relevant to peptide chemists in general, but especially to those interested in preparing acyl donors for convergent peptide syntheses by the t-Boc chemistry.     

Synthesis of cyclooctapeptides: constraints analogues of the peptidic neurotoxin, ω‐agatoxine IVB—an experimental point of view

ω‐AGA IVB is an important lead structure when considering the design of effectors of glutamate release inducting P/Q‐type calcium channels. The best route to achieve the analogues possessing the three‐dimensional arrangement corresponding to the native binding loop was the introduction of constraint by ring formation via side chain to side chain lactamization for suitably protected Lys and Glu residues. Since tryptophane residue located at position 14 of this neuropeptide has been suggested as essential for binding, analogues in which this amino acid was replaced by aza‐tryptophane and alanine were synthesized. The synthesis was carried out on various acid‐labile resins (BARLOS chlorotrityl, Rink amide, PEG‐based or Wang resins), by Fmoc strategy. In this paper, we describe optimization of the peptide cyclization with various protecting groups, and on resin or in solution cyclization experimental parameters. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.     

Swellographic Study of Peptide Resin Swelling Behavior during Solid Phase Peptide Synthesis

A representative array of peptide resin swelling data obtained using swellographic monitoring technique was analyzed to determine general tendencies in swelling volume dynamics in the course of Boc- and Fmoc-SPPS. Efficiency of the approach based on analyzing swelling volume changes (ΔV) as a function of nominal molecular weight change (ΔM) of the pendant peptide chain was demonstrated. The conclusion was made that a linear relationship between swelling volume and weight changes of peptide resin is a normal basic trend in line with results of early model studies carried out by Merrifield and coworkers. Excellent linear ΔV vs. ΔM correlations (r > 0.97) throughout SPPS for peptide resins swollen in DMF appeared to be typical of >60% of analyzed peptides and also are invariably observed for incorporation of the first four C-terminal amino acids and Boc-deprotected peptide resins swollen in 50% TFA-DCM. Formal theoretical interpretation of the observed regularities and anomalies of swelling volume dynamics and related solvation changes was made in terms of solvation numbers defined as a number of solvent molecules associated with a specific molecular segment of peptide-resin.     

Convenient reduction of S-oxides in synthetic peptides, lipopeptides and peptide libraries

Summary The oxidation of thioether bonds in peptides is still one of the major side reactions during peptide synthesis and it is easily detected by electrospray mass spectrometry. A fast reduction of oxidized methionine, biotin and tripalmitoyl-S-glyceryl-cysteine in synthetic peptides is possible using mixtures of trimethylsilylbromide and ethanedithiol as additives in trifluoroacetic acid. Simple procedures have been worked out which are especially suitable for handling the reduction of large numbers of peptides, prepared by multiple peptide synthesis, and of peptide libraries.     

A solid-phase synthetic strategy for the preparation of peptide-based affinity labels: synthesis of dynorphin A analogs.

Solid-phase synthetic methodology was developed for the preparation of peptide-based affinity labels. The initial peptides synthesized were dynorphin A (Dyn A) analogs [Phe(p-X)4,D-Pro10]Dyn A(1-11)NH2 containing isothiocyanate (X=-N=C=S) and bromoacetamide (X=-NHCOCH2Br) groups. The peptides were assembled on solid supports using Fmoc-protected amino acids, and the side chain amine to be functionalized, Phe(p-NH2), was protected by the Alloc (allyloxycarbonyl) group. Following removal of the Alloc group by palladium(O), the reactive isothiocyanate and bromoacetamide functionalities were successfully introduced while the peptides were still attached to the resin. Synthesis of these peptides was carried out on polystyrene (PS) and polyethylene glycol-polystyrene (PEG-PS) resins containing the PAL [peptide amide linker, 5-(4-Fmoc-aminomethyl-3,5-dimethoxyphenoxy)valeric acid] linker. Both the rate of Alloc deprotection and the purity of the crude affinity-labeled peptides obtained were found to be dependent on the resin used for peptide assembly.     

Rapid semi-on-line monitoring of Fmoc solid-phase peptide synthesis by matrix-assisted laser desorption/ionization mass spectrometry

A simple yet highly effective application of matrix-assisted laser desorption/ionization massspectrometry (MALDI-MS) for the rapid monitoring of Fmoc solid-phase peptide synthesisis described. A few beads of the resin are removed at any desired step during synthesis, thefully protected peptide is cleaved from the resin and an MS spectrum of the analytes presentis produced. Some standard side-chain protecting groups may be cleaved off during samplepreparation for MS analysis; however, these cleavages are readily identified. Using thisapproach, incomplete amino acid acylations are readily detected in approximately the sametime as by traditional tests such as ninhydrin. The semi-on-line method also lends itself toready optimization of synthesis protocols and to the examination of resin-bound peptide sidereactions which may not be detectable by chemical means.     

Efficient method of circumventing insolubility problems with fully protected peptide carboxylates via in situ direct thioesterification reactions

A straightforward and convenient protocol is presented for the direct thioesterification of fully protected peptide C‐terminal carboxylates synthesized by Fmoc strategy. This methodology specifically serves to overcome the frequent insolubility problem of these fully protected carboxolate isolates during the thioesterification process by carrying out the reaction as an in situ procedure on the freshly cleaved 1% TFA/DCM solution of carboxylate. The direct thioesterification of a number of insolubility prone peptide systems is explored and compared with some control systems for ease of conversion to the corresponding thioesters. It is shown that although the fully protected carboxylates are indeed insoluble to varying degrees in the thioesterification reactions carried out using the classical approach, full dissolution is maintained and complete conversion is evident using the in situ methodology. This protocol serves to remove a frequent stumbling block in the preparation of peptide thioesters via the direct approach, allowing for facile entry into previously difficult systems traditionally unapproachable through this method. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

Cleavage of cell surface proteins by thrombin

This study was based on our previous findings that the mitogenic action of thrombin on cultured fibroblasts can result from interaction of thrombin with the cell surface in the absence of internalization, and that the proteolytic activity of thrombin is required for stimulation of cell division. This prompted us to look for thrombin-mediated cleavages using 2-dimensional gel electrophoresis of labeled cell surface proteins. Surface membrane components were labeled by 3 procedures: (1) proteins were labeled by lactoperoxidase-catalyzed iodination using ¹²⁵I^?; (2) galactose and galactosamine residues of glycoproteins were oxidized with galactose oxidase and reduced with ³H-NaBH₄; and (3) glycoproteins were metabolically labeled by incubating cells with ³H-fucose. Labeling with the first 2 procedures was carried out after thrombin treatment; in contrast, cells metabolically labeled with ³H-fucose were subsequently treated with thrombin to look for proteolytic cleavages. Collectively, these studies indicated that only about 5 cell surface proteins were thrombin-sensitive, consistent with the high specificity of this protease. Each of the labeling procedures revealed a thrombin-sensitive cell surface glycoprotein which was identified as fibronectin by immunoprecipitation experiments. In addition, cell surface proteins of about 140K and 55K daltons were thrombin-sensitive. However, cell surface proteins of about 45K daltons and 130K to 1 50K daltons were increased after thrombin treatment. These experiments were conducted on an established line of Chinese hamster lung cells with the eventual goal of studying thrombin-mediated cleavages of cell surface proteins in a large number of cloned populations derived from this line that are either responsive or unresponsive to the mitogenic action of thrombin. This approach should permit identification of proteolytic cleavages that are necessary for thrombin-stimulated cell division.     

Rapid semi-on-line monitoring of Fmoc solid-phase peptide synthesis by matrix-assisted laser desorption/ionization mass spectrometry

Summary A simple yet highly effective application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the rapid monitoring of Fmoc solid-phase peptide synthesis is described. A few beads of the resin are removed at any desired step during synthesis, the fully protected peptide is cleaved from the resin and an MS spectrum of the analytes present is produced. Some standard side-chain protecting groups may be cleaved off during sample preparation for MS analysis; however, these cleavages are readily identified. Using this approach, incomplete amino acid acylations are readily detected in approximately the same time as by traditional tests such as ninhydrin. The semi-on-line method also lends itself to ready optimization of synthesis protocols and to the examination of resin-bound peptide side reactions which may not be detectable by chemical means.     

Acid-labile anchoring linkages for solid phase synthesis of C-terminal asparagine peptides using the Fmoc strategy

Two acid-labile substituted benzylamine type anchoring linkages, 4-benzoxy-2,6-dimethoxybenzylamine and 2-benzoxy-4,6-dimethoxybenzylamine, for solid phase synthesis of peptide amides were prepared. The Na-9-fluorenylmethyloxycarbonyl (Fmoc) amino acids could be easily attached to the resins with DCC/HOBt (loading 0.5-0.6 mmol/g resin). After final removal of the Na-protecting groups, treatment with TFA (50-95%) yielded amino acid and peptide amides in high purity. As we could show for the synthesis of thymulin (FTS, pGlu-Ala-Lys-Ser-Gln-Gly-Gly-Ser-Asn), these two resins with anchoring linkages are well suited for the synthesis of C-terminal Asn peptides using protected aspartic acid derivative as starting material.     

Polypeptide synthesis by the thioester method

A novel method for polypeptide synthesis, in which partially protected peptide thioesters are used as building blocks, has been developed. Partially protected peptide thioesters are easily prepared by solid-phase methodology. The thioester moiety is converted to an active ester in the presence of a silver compound such as AgNO(3) or AgCl and an active ester component such as 1-hydroxybenzotriazole or 3,4-dihydro-3-hydro-4-oxo-1,2, 3-benzotriazine. Segment condensation can be accomplished using partially protected peptide segments. The consecutive condensation of the partially protected peptide segments is realized by the selective removal of the 9-flourenylmethoxycarbonyl group, for terminal amino protection, after segment condensation has been achieved. In this method, large peptide segments can easily be used. Thus, the products obtained by the thioester method can be separated from by-products by reverse phase high performance liquid chromatography, even when no purification process was performed during the prior segment condensation procedures. This indicates that proteins that have no specific features such as enzymatic or biological activities can be obtained after isolation, solely based on their chromatographic profiles. Thus, the thioester method will provide a new basis for protein studies including phosphorylated and glycosylated polypeptides.     

Affinity chromatographic purification of papain.

The reinvestigation of the affinity chromatographic method of purifying papain has been carried out. It has been reported that papain could be purified by taking advantage of the affinity of the enzyme for the insolubilized peptide inhibitor, agarose-Gly-Gly-Tyr(Bz)-Arg. Using pure tetrapeptide obtained commercially and standard coupling procedures, a significant purification of papain could not be achieved. Both active and nonactivatible enzyme bound to a column prepared in this manner were eluted together by the use of deionized water. An affinity medium with properties similar to those reported by Blumberg et al. was obtained by removal of the benzyl group on tyrosine prior to coupling with agarose. The deprotected tetrapeptide was also synthesized by an independent route and inhibition constants for the binding of the protected and deprotected tetrapeptide to papain were determined in kinetic experiments.     

Conventional and microwave‐assisted SPPS approach: a comparative synthesis of PTHrP(1–34)NH2

Attracted by the possibility to optimize time and yield of the synthesis of difficult peptide sequences by MW irradiation, we compared Fmoc/tBu MW‐assisted SPPS of 1–34 N‐terminal fragment of parathyroid hormone‐related peptide (PTHrP) with its conventional SPPS carried out at RT. MWs were applied in both coupling and deprotection steps of SPPS protocol. During the stepwise elongation of the resin‐bound peptide, monitoring was conducted by performing MW‐assisted mini‐cleavages and analyzing them by UPLC‐ESI‐MS. Identification of some deletion sequences was helpful to recognize critical couplings and as such helped to guide the introduction of MW irradiations to these stages. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Immobilization of animal cells using photo-crosslinkable resin

A photo-crosslinkable resin, BIX12, was selected from among various photo-crosslinkable resins for the immobilization of animal cells. BIX12 had no cytotoxic effect on the growth of hybridoma cells and the production of monoclonal antibody, although other photo-crosslinkable resins had significant inhibitory effects. Using BIX12-alginate hybrid gel particles, hybridoma cells could grow in the resins and produce monoclonal antibody. For the continuous production of monoclonal antibody, perfusion culture using a fluidized-bed bioreactor with direct air bubbling was carried out. By this cultivation, monoclonal antibody could be produced stably for more than 50 d. A high viable cell density of more than 10⁷ cells/ml-gel was attained, and the antibody productivity was improved 8.5-fold compared with conventional suspension culture using a spinner flask. Anchorage-dependent cells were also immobilized in the resin particles by three immobilization procedures. Among these procedures, porous BIX12 formed by adding gelatin powder provided good support strength and allowed the cells to grow on the surface inside of the support.