Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity.

In order to investigate issues of selectivity and specificity in protein-ligand interactions, we have undertaken the reconstruction of the binding pocket of human factor Xa in the structurally related rat trypsin by site-directed mutagenesis. Three sequential regions (the "99"-, the "175"- and the "190"- loops) were selected as representing the major structural differences between the ligand binding sites of the two enzymes. Wild-type rat trypsin and variants X99rT and X(99/175/190)rT were expressed in yeast, and analysed for their interaction with factor Xa and trypsin inhibitors.

S' subsite mapping of serine proteases based on fluorescence resonance energy transfer.

A microassay based on fluorescence resonance energy transfer has been developed to determine the S' specificity of serine proteases. The protease-catalyzed acyl transfer from a fluorescing acyl donor ester to a P'1/P'2 variable hexapeptide library of nucleophiles labeled with a fluorescence quencher leads to an internally quenched peptide product and a fluorescent hydrolysis product. The amount of fluorescence quenching allows one to draw conclusions about the interaction of the nucleophile at the S' sites of the protease.

Design and synthesis of fluorogenic trypsin peptide substrates based on resonance energy transfer.

An assay based on new internally quenched fluorogenic peptide substrates with the general structure 4-(4-dimethylaminophenylazo)benzoic acid (DABCYL)-Gly-Pro-Ala-Xaa-Leu-Ala-Ile-Gly-5-(2-aminoethylamino++ +)naphtha lene-1-sulfonic acid (EDANS), where Xaa = Arg, Lys, has been developed to measure proteolytic activity of trypsin and similar proteases. The kinetic parameters for the tryptic hydrolysis of DABCYL-Gly-Pro-Ala-Arg-Leu-Ala-Ile-Gly-EDANS are Km = 34 microM, kcat = 40 s-1, and kcat/Km = 1.17 x 10(6) M-1 s-1.

The specificity of prolyl endopeptidase from Flavobacterium meningoseptum: mapping the S' subsites by positional scanning via acyl transfer.

The S1'-S3' subsite specificity of prolyl endopeptidase from Flavobacterium meningoseptum was studied by acyl transfer to libraries of amino acid amides and peptides. Whereas the S1' and S3' subsites influence the specificity for the amino component by approximately one order of magnitude, the S2' subsite possesses a markedly higher specificity. Besides the high specificity for hydrophobic residues at P1'-P3', proline was efficiently bound by the S2' and S3' subsites of the enzyme.

Engineering the S1' subsite of trypsin: design of a protease which cleaves between dibasic residues.

The serine protease trypsin was converted into a site-specific protease which hydrolyzes peptides between dibasic residues. Trypsin exhibits a high S1 specificity for Arg and Lys residues. However, the S1' specificity of trypsin is very broad, with only a slight preference for hydrophobic residues in P1'.

Reverse catalysis of elastase from porcine pancreas in frozen aqueous systems.

The reverse action of a trypsin-free elastase isolated from porcine pancreas was studied in frozen aqueous systems. Under frozen state conditions, porcine pancreatic elastase was able to catalyse peptide bond formation more effectively than in solution at room temperature. The acceptance of free amino acids as nucleophilic amino components indicates a changed specificity of the endoprotease in frozen reaction mixtures.

Subsite specificity studies on the unusual cysteine protease clostripain: charged residues in the P3 position indicate a narrow subsite region.

The importance of electrostatic interactions between charged residues at the P3 position of substrates and the S3 subsite of the cysteine protease clostripain was investigated. For this purpose quantitative enzymatic hydrolysis studies using steady state kinetics have been carried out within a set of N alpha-protected synthetic dipeptide ester substrates with systematic changes of their charge in the P3 position. It was demonstrated that, in contrast to the former postulated second anionic S3 subsite, the lowest specificity was for the hydrolysis of the positively charged substrates.

Converting trypsin to chymotrypsin: structural determinants of S1' specificity.

Trypsin and chymotrypsin differ strikingly in substrate specificities despite great similarity in their primary and tertiary structures. This work analyzes the role of two surface loops, loop 40 and loop 60, as structural determinants of the specificity of the S1'-subsite in chymotrypsin and trypsin. Chymotrypsin prefers P1' Arg/Lys residues, while trypsin prefers hydrophobic P1' residues.

Solid-phase acyl donor as a substrate pool in kinetically controlled protease-catalysed peptide synthesis.

Recently we have demonstrated the advantage of solid-phase substrate pools mainly in equilibrium controlled protease-catalysed peptide syntheses. The extension of this approach to protease-catalysed acyl transfer reactions will be presented. The model reaction was systematically investigated according to both the influence of solid phases present in the system on enzyme activity as well as nucleophile concentration on peptide yield.

Synthesis of dipeptides by suspension-to-suspension conversion via thermolysin catalysis: from analytical to preparative scale.

When using proteases in direct reversal of their normal hydrolytic function, the equilibrium position is very important in limiting the attainable yield in equilibrium-controlled enzymic peptide synthesis. Analysis of the equilibrium position reveals a favourable shift towards the peptide product if starting materials are largely undissolved in the reaction medium and the product precipitates. This approach enabled us to obtain high peptide yields in thermolysin-catalysed reactions in high-density aqueous media with an equimolar supply of substrates.

Proteolytically stable peptides by incorporation of alpha-Tfm amino acids.

A series of model peptides containing alpha-trifluoromethyl-substituted amino acids in five different positions relative to the predominant cleavage site of the serine protease alpha-chymotrypsin was synthesized by solution methods to investigate the influence of alpha-Tfm substitution on the proteolytic stability of peptides. Proteolysis studies demonstrated absolute stability of peptides substituted to the P1 position and still considerable proteolytic stability for peptides substituted at the P2 and P'2 positions compared with the corresponding unsubstituted model peptide. Comparison with peptides containing the fluorine-free disubstituted amino acid alpha-aminoisobutyric acid allowed to separate electronic from steric effects.

Influence of freeze-concentration effect on proteinase-catalysed peptide synthesis in frozen aqueous systems.

Freezing of the reaction mixture is a powerful tool in proteinase-catalysed peptide synthesis. In this study, the considerable yield-increasing effect of freezing has been analysed by physical and analytical methods. 1H-NMR relaxation time measurements have been used to determine the amount of unfrozen water in partially frozen systems thus quantifying the extent of the 'freeze concentration effect' for the first time.

Enzymatic peptide synthesis in frozen aqueous solution: use of N alpha-unprotected peptide esters as acyl donors.

The ability of the endopeptidase alpha-chymotrypsin (EC 3.4.21.

Reverse action of ribonuclease T1 in frozen aqueous systems.

We have studied ribonuclease T1 (EC 3.1-27.3)-catalysed synthesis of guanylyl-(3'-->5')cytidine in frozen aqueous reaction mixtures at -10 degrees C and in solution at 0 degree C in order to investigate whether ribonuclease-catalysed synthetic reactions can take advantage of the yield-increasing effect of freezing as was reported for protease-catalysed peptide synthesis.

Peptide modification by incorporation ofα-trifluoromethyl substituted amino acids.

Metabolic stabilization of pharmacologically active peptides can be achieved by incorporation of sterically hindered non-natural amino acids, e.g. C (α,α) -disubstituted amino acids.

Reverse action of hydrolases in frozen aqueous solutions.

The reverse action of hydrolases provides an attractive alternative to the chemical synthesis of peptides, oligosaccharides and oligonucleotides. Freezing the reaction mixture has proved to suppress competitive reactions in enzyme-catalysed peptide synthesis. After a short discussion of the influence of freezing on enzyme-catalysed reactions the current manuscript gives an overview of protease-catalysed peptide synthesis and the possible reasons of the yield-enhancing effect of freezing.

Nonconventional protease catalysis in frozen aqueous solutions.

During the past decade proteases have been widely used as catalysts in peptide synthesis. Unfortunately, they are not ideal ligases. Enzymatic peptide synthesis in frozen aqueous systems has been developed as an approach towards the suppression of competitive reactions.

Non-conventional enzyme catalysis: application of proteases and zymogens in biotransformations.

One of the attractions of using enzymes for chemical syntheses is the control of stereochemistry: problems of racemization that attend chemical C-N ligation methods are completely avoided. Furthermore, the enzymatic approach has the advantage that only minimal protection-deprotection steps are involved. The Impetus to develop non-conventional catalysis procedures has sprung from the lack of usable native enzymes that normally catalyze the formation of peptide bonds for biotransformation.

Nucleophile specificity of subtilisin in an organic solvent with low water content: investigation via acyl transfer reactions.

Nucleophile specificity of subtilisin (subtilopeptidase A) was studied via acyl transfer reactions in acetonitrile containing piperidine and 10 vol% of water. Ac-Tyr-OEt was used as acyl donor and a series of amino acid derivatives, di- and tripeptides of the general structure Xaa-Gly, Gly-Xaa, Gly-Gly-Xaa (Xaa represents all natural L-amino acids except cysteine) were used as nucleophiles. The nucleophilic efficiencies of these peptides were characterized by the values of the apparent partition constants, p(app), determined from the HPLC analysis of the reactions.

The application of papain, ficin and clostripain in kinetically controlled peptide synthesis in frozen aqueous solutions.

The capability of the cysteine proteases ficin, papain and clostripain to form peptide bonds in frozen aqueous solutions was investigated. Freezing the reaction mixture resulted in increased peptide yields in kinetically controlled coupling of Bz-Arg-OEt with various amino acid amides and dipeptides. Under these conditions, peptide yields increased up to 70% depending on the enzyme and the amino component used.

Peptide modification by introduction ofα-trifluoromethyl substituted amino acids.

Methodology for the synthesis and incorporation ofα-trifluoromethyl substituted amino acids into N- and C-terminal position of peptides is described. The incorporation ofα-trifluoromethyl substituted amino acids into strategical positions of peptides enhances proteolytic stability and lipophilicity. Furthermore, it improves transport rates in vivo and permeability through certain body barriers.

Enzymic peptide synthesis in microaqueous, solvent-free systems.

Thermolysin-catalyzed (EC 3.4.24.

Enzymatic peptide synthesis in frozen aqueous systems: influence of modified reaction conditions on the peptide yield.

The alpha-chymotrypsin (EC 3.4.21.

Enzymatic approach to the synthesis of taurine-containing peptides.

Subtilisins (subtilopeptidase A, nagarse) and proteinase K were able to catalyze the synthesis of taurine-containing peptides from various N-acylated amino acid or peptide esters and nonprotected taurine. The synthesis was optimized using a model reaction between Boc-Tyr-OMe and taurine. The best results were obtained under strongly alkaline conditions in acetonitrile with low water content as the reaction medium.

The specificity of clostripain from Clostridium histolyticum. Mapping the S' subsites via acyl transfer to amino acid amides and peptides.

The S' subsite specificity of clostripain from Clostridium histolyticum was investigated by acyl transfer to libraries of amino acid amides, Ala-Xaa dipeptides, proline derivatives and pentapeptides using N alpha-benzoyl-L-arginine ethyl ester as acyl donor. A pentapeptide library consisting of 29 pentapeptides with general structure Xaa-Ala-Ala-Ala-Gly, Ala-Xaa-Ala-Ala-Gly and Ala-Ala-Xaa-Ala-Gly, where Xaa represents Gly, Ala, Pro, Leu, Phe, Asp, Glu, Arg and Lys, was prepared by solid-phase synthesis. The data analysis was performed by HPLC and evaluated by statistical algorithms.