Peptide Synthesis In Organic Solvents Research Articles

Trypsin-Catalyzed N-Terminal Labeling of Peptides with Stable Isotope-Coded Affinity Tags for Proteome Analysis

An enzymatic approach to label peptide N-termini with isotope-coded affinity tags is presented. This method exploits the high activity of trypsin for peptide synthesis in organic solvents. A cosubstrate containing a stable isotope-coded Arg residue and a biotin tag was synthesized. When the cosubstrate was incubated with tryptic peptides and trypsin in ethanol solution, the stable isotope-coded affinity tag was specifically coupled onto the N-termini of peptides via the formation of new peptide bonds. The labeled peptides were specifically enriched by avidin affinity chromatography and then were submitted to liquid chromatography-tandem mass spectrometry (LC/MS/MS) for quantification. This enrichment step effectively reduced the interference by unlabeled peptides. The excellent performance of this approach was demonstrated by labeling standard peptides as well as a mouse liver digest. In addition to one amino acid residue, a few dipeptide tags were also introduced to the N-termini of peptides successfully by this enzymatic approach. It was found that the identifications for samples labeled with these tags were highly complementary. Coupling a short sequence tag onto peptides could be an effective approach to improve the coverage for proteome analysis.

The role of N-glycosylation sites in the activity, stability, and expression of the recombinant elastase expressed by Pichia pastoris

The Pseudomonas aeruginosa elastase (PAE), produced by Pseudomonas aeruginosa (P. aeruginosa), is a promising biocatalyst for peptide synthesis in organic solvents. As P. aeruginosa is an opportunistic pathogen, the enzyme has been heterologously over-expressed in the safe and efficient host, Pichia pastoris (P. pastoris) for its industrial application. The recombinant elastase (rPAE) contains three potential N-glycosylation sites (Asn-Xaa-Ser/Thr consensus sequences), and is heterogeneously N-glycosylated. To investigate the role of N-glycosylation in the activity, stability, and expression of rPAE, these potential N-glycosylation sites (N43, N212, and N280) were mutated using site-directed mutagenesis. Specifically the asparagine (Asn, N) residues were converted to glutamine (Gln, Q). The enzymatic activity and stability of non-glycosylated and glycosylated rPAE were then compared. The results indicated that the influence of N-glycosylation on its activity was insignificant. The non- and glycosylated isoforms of rPAE displayed similar kinetic parameters for hydrolyzing casein in aqueous medium, and when catalyzing bipeptide synthesis in 50% (v/v) DMSO, they exhibited identical substrate specificity and activity, and produced similar yields. However, N-glycosylation improved rPAE stability both in aqueous medium and in 50% (v/v) organic solvents. The half-lives of the glycosylated and non-glycosylated forms of rPAE at 70°C were 32.2 and 23.1min, respectively. Mutation of any potential N-glycosylation site was detrimental to its expression in P. pastoris. There was a 23.9% decrease in expression of the N43Q mutant, 63.6% of the N212Q mutant, and 63.7% of the N280Q mutant compared with the wild type. Furthermore, combined mutation of these sites resulted in an additional decrease in the caseinolytic activities of the mutants. These results indicated that all of the N-glycosylation sites were necessary for high-level expression of rPAE.

N‐Terminal Labeling of Peptides by Trypsin‐Catalyzed Ligation for Quantitative Proteomics

Labeling tryptic peptides with stable isotopes is one of the most important methods for quantitative proteomics, and many ingenious chemical labeling strategies have been developed. Incorporation of one isotopically labeled tag onto a peptide terminus represents an ideal labeling approach, as it would simplify the interpretation of mass spectra. Moreover, the absence of labels on the side chains would facilitate the quantification of post-translational modifications (PTMs). However, to date all the reported chemical labeling strategies, including dimethyl labeling, iTRAQ (isobaric tags for absolute and relative quantification), and ICAT (isotope-coded affinity tags), result in the modification of side chains. One promising method to achieve the incorporation of a single tag is enzymatic labeling. Proteolytic O labeling can specifically label tryptic peptide termini without modification of side chains, but the small change in mass and O/O back-exchange, i.e. the exchange of O with O after the labeling process hinder its wide application in quantitative proteomics. Herein, we report a novel enzymatic labeling approach, in which trypsin is used as a ligase to specifically incorporate amino acids labeled with stable isotopes onto the N termini of peptides for quantitative analysis. Trypsin is a serine protease that specifically hydrolyzes peptide bonds in proteins after arginine and lysine residues. However, trypsin also catalyses peptide synthesis in organic solvents. Therefore, it is possible to covalently link isotopically labeled amino acids to tryptic peptides by using trypsin as a ligase. In this study, arginine, the prototype substrate for trypsin, was used as an acyl moiety donor. The primary amine group of arginine was protected with a benzoyl group (Bz) to prevent the formation of dipeptides or oligopeptides, and the carboxy group was esterified with ethanol to activate the acyl donor (see the Supporting Information, Figure S1). The final product, Na-benzoyl-l-arginine ethyl ester (Bz–R–OEt), was used as a substrate for the trypsin-catalyzed ligation. The quantitative proteomics workflow based on the trypsincatalyzed N-terminal labeling is shown in Figure 1a. Trypsin was first used as a protease to digest proteins in an aqueous solution (1m urea/50 mm Tris-HCl, pH 8.0). Then, the generated tryptic peptides were lyophilized and transferred to an ethanol solution containing 4% aqueous buffer (0.1m TrisHCl, pH 8.0). Next, trypsin immobilized on magnetic nanoparticles (IM-trypsin) and Bz–R–OEt were added to the ethanol solution for the N-terminal labeling of peptides with Bz–R based on a kinetically controlled mechanism (see the Supporting Information). Finally, quantification of the proteins was achieved by the differential labeling of two samples by using Bz–R–OEt (light label) and Bz–(C6)R–OEt (bearing six C atoms; heavy label), the incorporation of which are indicated by mass shifts of 260 and 266 Da, respectively. We first validated the protease and ligase activities of trypsin by using the synthetic peptide VGKANEELAGVVAEVQK (Figure 1b; m/z= 1740.86), which contains one trypsin cleavage site. In aqueous solution, treatment with IMtrypsin generated a shorter peptide ANEELAGVVAEVQK (Figure 1b, m/z= 1456.82). Treatment of the obtained peptide with an ethanol solution containing Bz–R–OEt and IMtrypsin gave an N-terminus labeled peptide Bz–RANEELAGVVAEVQK (Figure 1b, m/z= 1716.9). Similar results were also obtained for three other synthetic peptides that contained one trypsin cleavage site (Supporting Information, Figure S2). These examples clearly illustrate that trypsin functions as a protease in an aqueous solution whereas it acts as an N-terminus ligase in an ethanol solution. Thus, these results imply that this enzymatic labeling approach can be used to label peptides generated by trypsin digestion of a proteome sample. In this study, free trypsin was used for the digestion of proteins, as is conventional in proteomics analysis, whereas IM-trypsin (trypsin from the same source) was used for ligation because it is more tolerant to organic solvents and it is readily removed using magnetism. We tested whether the labeling of side-chain primary amino groups would also be facilitated by trypsin ligase. A synthetic peptide VIFIEHAKRKG, containing two sidechain amino groups and one terminal primary amino group, was labeled by trypsin. The Arg tag was incorporated only onto the terminal primary amino group and not onto the sidechain amino groups (see the Supporting Information, Figure S3a). These results are markedly different from those of other amine labeling approaches. For example, for labeling [*] Y. Pan, Prof. Dr. M. Ye, Dr. L. Zhao, K. Cheng, M. Dong, C. Song, H. Qin, Dr. F. Wang, Prof. Dr. H. Zou CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 (China) E-mail: mingliang@dicp.ac.cn hanfazou@dicp.ac.cn

Can lipases hydrolyze a peptide bond?

Several research groups reported that lipase catalyzes peptide synthesis in organic solvents. Structural studies revealed that the catalytic triad of lipase consists of Ser, His, and Asp, the same as serine proteases. Lipase has a potential to have peptidase activity. In this report, we investigated the peptidase activity of lipases. Of 13 lipases of diverse origin tested, only commercially available porcine pancreatic lipase (PPL) exhibited peptidase activity. However, purification of PPL by gel permeation chromatography separated the peptidase and lipolytic activities of PPL. This study clearly demonstrated that all the lipases tested do not hydrolyze a peptide bond.

ChemInform Abstract: Enzymatic Peptide Synthesis in Organic Solvent with Different Zeolites as Immobilization Matrixes.

A series of zeolite immobilized α-chymotrypsin and thermolysin with microporous Y zeolites (HY, NH4Y, NaY) and mesoporous dealuminized DAY zeolites (HDAY, HNH4DAY) as matrixes have been prepared to catalyze peptide bond formation in organic solvents for the first time. The results indicated that most zeolite immobilized enzymes were active for peptide syntheses in organic media, and still had catalytic activity to some extent after being reused five times. According to the results, the immobilization effect of microporous Y zeolite was better than that of mesoporous DAY zeolite, suggesting that microporous Y zeolite can form more powerful hydrogen bonds with enzyme molecules since there are more hydroxyl groups on the Y zeolite than on the DAY zeolite. In addition, the influences of some reaction conditions such as reaction time and water content of the solvent on the enzymatic peptide synthesis were also studied and optimized. For the two kinds of proteases, NH4Y zeolite did not show its advantages for thermolysin, but was more suitable for α-chymotrypsin as an immobilization matrix.

Highly-substituted benzhydrylamine resin: An alternative chromatographic support for ganglioside and neutral glycosphingolipid purification

Benzhydrylamine resin (BHAR) is a copolymer of (styrene-1% divinylbenzene) containing phenylmethylamine groups and commonly used as a solid support for peptide synthesis in organic solvents. We have demonstrated that a larger number of NH3+ groups distributed throughout the BHAR matrix improves bead solvation under more polar conditions. As this characteristic might allow this aminated-polymer to be used as a stationary phase for liquid chromatography, a hyghly substituted BHAR (2.4 mmol.g−1 of amine groups) was synthesized under forceful conditions. Neutral glycosphingolipids and negatively charged gangliosides and sulfatide obtained from rat brain extracts were successfully purified and fractionated in this BHAR batch by single-step, reverse-phase anion-exchange chromatography. Additionally, the anion-exchange potential of BHAR was also compared to that of commercial dimethylaminoethyl (DEAE)-Sephadex A25 resin.

Enzymatic Peptide Synthesis in Organic Solvent with Different Zeolites as Immobilization Matrixes

A series of zeolite immobilized α-chymotrypsin and thermolysin with microporous Y zeolites (HY, NH 4Y, NaY) and mesoporous dealuminized DAY zeolites (HDAY, HNH 4DAY) as matrixes have been prepared to catalyze peptide bond formation in organic solvents for the first time. The results indicated that most zeolite immobilized enzymes were active for peptide syntheses in organic media, and still had catalytic activity to some extent after being reused five times. According to the results, the immobilization effect of microporous Y zeolite was better than that of mesoporous DAY zeolite, suggesting that microporous Y zeolite can form more powerful hydrogen bonds with enzyme molecules since there are more hydroxyl groups on the Y zeolite than on the DAY zeolite. In addition, the influences of some reaction conditions such as reaction time and water content of the solvent on the enzymatic peptide synthesis were also studied and optimized. For the two kinds of proteases, NH 4Y zeolite did not show its advantages for thermolysin, but was more suitable for α-chymotrypsin as an immobilization matrix.

Effect of water and enzyme concentration on thermolysin-catalyzed solid-to-solid peptide synthesis

We have studied a thermolysin-catalyzed solid-to-solid dipeptide synthesis using equimolar amounts of Z-Gln-OH and H-Leu-NH2 as model substrates. The high substrate concentrations make this an effective alternative to enzymatic peptide synthesis in organic solvents. Water content was varied in the range of 0 to 600 mL water per mol substrate and enzyme concentration in the range of 0.5 to 10 g/mol of substrates. High yields around 80% conversion and initial rates from 5 to 20 mmol s-1 kg-1 were achieved. The initial rate increases 10-fold on reducing the water content, to reach a pronounced optimum at 40 mL water per mol substrate. Below this, the rate falls to much lower values in a system with no added water, and to zero in a rigorously dried system. This behavior is discussed in terms of two factors: At higher water contents the system is mass transfer limited (as shown by varying enzyme content), and the diffusion distances required vary. At low water levels, effects reflect the stimulation of the enzymatic activity by water.

Effect of water activity on thermolysin-catalyzed peptide synthesis in organic solvents

The effect of water activity on the rate of thermolysin-catalyzed synthesis of an aspartame precursor has been investigated in water-miscible and water-immiscible solvents. In both cases, the enzyme reaction rate at a given water activity was found to be significantly different depending on the nature of the solvent. The reaction rates in water-immiscible solvents, where the water activities were close to 1.0, were found to be significantly dependent on the volume ratio of water to organic media and the hydrophobicity of the solvent. These data suggest that the enzyme reaction in the solvent is influenced appreciably by other factors in addition to the water activity.

Peptide Synthesis in Organic Solvents Catalyzed by an Industrial Alkaline Protease “Alcalase”

AbstractAn industrial alkaline protease “Alcalase” is stable (half life > 5 days in ethanol or in t‐butanol) and active in alcoholic solvents (except methanol), and usable as a catalyst for kinetically controlled peptide bond formation in these solvents. We give an overview of our use of alcalase as catalyst in peptide synthesis; it includes 1) the stability of alcalase in various organic solvents; 2) the resolution of N‐protected amino acids at large concentration of organic solvent; 3) the saponification of Fmoc‐peptide esters in high concentration of organic solvent; 4) kinetically controlled peptide bond formation in alcoholic solvent, and 5) enzymatic synthesis of a Cathepsin inhibitor, peptidyl Q‐acyl hydroxamates.

Enzymatic peptide synthesis in organic solvent mediated by gels of copolymerized acrylic derivatives of α‐chymotrypsin and polyoxyethylene

Copolymers of acrylated derivatives of alpha-chymotrypsin and polyethylene glycol (PEG) have been prepared and used as biocatalysts for the synthesis of model peptides in organic solvent containing a low quantity of water. Other peptide couplings have been tried to point out the chemico- and stereoselectivity and examples of segment couplings are given.

Immobilization of proteases to porous chitosan beads and their catalysis for ester and peptide synthesis in organic solvents

α-Chymotrypsin (CT), subtilisin BPN' (STB), and subtilisin Carlsberg (STC) were immobilized by adsorption to porous chitosan beads (Chitopearl, CP). The immobilized enzymes showed higher catalytic activities than free enzymes for amino acid esterification in many hydrophilic organic solvents except for methanol and DMF. In ethanol, the initial rate of the esterification increased with water content, whereas in ethyl acetate, the maximum rate was obtained at 2%–3% water. CP-immobilized CT also catalysed transesterification of Ac-Tyr-OMe in ethanol and peptide synthesis in acetonitrile from Ac-Tyr-OH or its ethyl ester and amino acid amides. The immobilized enzymes are highly stable in organic solutions, and can easily be separated from the reaction solutions. Repeated esterifications of Ac-Tyr-OH in acetonitrile by a CP-immobilized CT gave almost constant yields of the ester for more than 3 weeks.

The use of biosensors in bioorganic synthesis: Peptide synthesis by immobilized α-chymotrypsin assessed with an enzyme thermistor

Biosensor analysis of peptide synthesis in organic solvents using immobilized α-chymotrypsin is described. It is shown that with the enzyme thermistor sensor used, a direct correlation exists between the negative ΔT-values registered and the amount of peptides formed (essentially various N-acetyldipeptide amides) allowing concentrations of 0.1 mM peptide and lower to be determined directly in the reaction medium.

Enzymatic reactions in aqueous-organic media. VIII. Medium effect and nucleophile specificity in subtilisin-catalyzed peptide synthesis in organic solvents

Subtilisin Carlsberg and subtilisin BPN' (nagarse) catalyze peptide bond formation from aromatic amino acid esters and glycinamide in hydrophilic organic solvents. The activities of subtilisin and product compositions are different in several organic solvents; reactions in acetonitrile, tetrahydrofuran, and propylene carbonate gave the peptide in excellent yields, while in N,N-dimethylformamide and methanol the enzyme activity was largely retarded. The yield of the peptide is also dependent on water content in the reaction solutions. Optimum water contents are in the range from 3 to 7 %. The reaction is strongly specific for glycinamide as an amine component, and amides of alanine, valine, and leucine gave the corresponding peptides in poor yields.

Unusual specificity of polyethylene glycol-modified thermolysin in peptide synthesis catalyzed in organic solvents

Polyethylene glycol-modified thermolysin was found to efficiently catalyze peptide synthesis in organic solvents. As in aqueous media, the reaction occurred through a rapid equilibrium random bireactant mechanism. However, the substrate specificity of modified thermolysin was actually changed since hydrophilic as well as acidic amino acids were better carboxyl group donors than hydrophobic residues, contrary to what is observed in both the enzyme-catalyzed synthesis and hydrolysis of peptide bonds in water.

Peptide synthesis catalyzed by polyethylene glycol-modified chymotrypsin in organic solvents.

Chymotrypsin modified with polyethylene glycol was successfully used for peptide synthesis in organic solvents. The benzene-soluble modified enzyme readily catalyzed both aminolysis of N-benzoyl-L-tyrosine p-nitroanilide and synthesis of N-benzoyl-L-tyrosine butylamide in the presence of trace amounts of water. A quantitative reaction was obtained when either hydrophobic or bulky amides of L- as well as D-amino acids were used as acceptor nucleophiles, while almost no reaction occurred with free amino acids or ester derivatives. The acceptor nucleophile specificity of modified chymotrypsin as a catalyst in the formation of both amide and peptide bonds in organic solvents was quite comparable to that in aqueous solution as well as to that of the leaving group in hydrolysis reactions. By contrast, the substrate specificity of modified chymotrypsin in organic solvents was different from that in water since arginine and lysine esters were found to be as effective as aromatic amino acids to form the acyl-enzyme with subsequent synthesis of a peptide bond.

Enzymatic reactions in aqueous-organic media. IV. Chitin-alpha-chymotrypsin complex as a catalyst for amino acid esterification and peptide synthesis in organic solvents

Chitin-α-chymotrypsin complex was found to be an effective catalyst for the esterification of N-acetyl-L-tryptophan in ethanol and for peptide synthesis from N-acetyl-L-tyrosine and glycinamide in acetonitrile. In the former reaction both initial rate of ester formation and equilibrium yield of the ester markedly increased by the complexation of chymotrypsin with chitin compared to free chymotrypsin.