Charge transport and mass transport in imidazolium-based ionic liquids.

The mechanism of charge transport in the imidazolium-based ionic liquid 1,3-dimethylimidazolium dimethylphosphate is analyzed by combining broadband dielectric spectroscopy (BDS) and pulsed field gradient nuclear magnetic resonance (PFG NMR). The dielectric spectra are dominated-on the low-frequency side-by electrode polarization effects while, for higher frequencies, charge transport in a disordered matrix is the underlying physical mechanism. Using the Einstein and Einstein-Smoluchowski equations enables one to determine-in excellent agreement with direct measurements by PFG NMR-the diffusion coefficient of the charge carriers. By that, it becomes possible to extract from the dielectric spectra separately the number density and the mobilities of the charge carriers and the type of their thermal activation. It is shown that the observed Vogel-Fulcher-Tammann (VFT) dependence of the dc conductivity can be traced back to a similar temperature dependence of the mobility while for the number density an Arrhenius-type thermal activation is found. Extrapolating the latter to room temperature indicates that nearly all charge carriers are participating in the conduction process.

Electrical conductivity and translational diffusion in the 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid.

Broadband dielectric and terahertz spectroscopy (10(-2)-10(+12) Hz) are combined with pulsed field gradient nuclear magnetic resonance (PFG-NMR) to explore charge transport and translational diffusion in the 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid. The dielectric spectra are interpreted as superposition of high-frequency relaxation processes associated with dipolar librations and a conductivity contribution. The latter originates from hopping of charge carriers on a random spatially varying potential landscape and quantitatively fits the observed frequency and temperature dependence of the spectra. A further analysis delivers the hopping rate and enables one to deduce--using the Einstein-Smoluchowski equation--the translational diffusion coefficient of the charge carriers in quantitative agreement with PFG-NMR measurements. By that, the mobility is determined and separated from the charge carrier density; for the former, a Vogel-Fulcher-Tammann and for the latter, an Arrhenius temperature dependence is obtained. There is no indication of a mode arising from the reorientation of stable ion pairs.

Substrate mimetics in protease catalysis: characteristics, kinetics, and synthetic utility.

This article reviews the latest developments in protease-catalyzed peptide synthesis focusing on the use of substrate mimetics. The substrate mimetics approach takes advantage of the characteristic of this novel type of substrates to direct the enzyme to recognize an alternative site on the acyl donor, i.e. the site-specific ester leaving group, mediating the acceptance of originally poorly reactive acyl moieties. At first the kinetics and catalytic mechanism of substrate mimetics-mediated reactions are discussed on the basis of hydrolysis, peptide synthesis, protein-ligand docking, and molecular dynamics studies. By the example of the Glu-specific V8 protease and the aromatic amino acid-specific chymotrypsin both the empirical and computer-aided design of specific substrate mimetics is described. The influence of the leaving group specifically recognized by the enzyme is also considered. The benefits of these artificial substrates over common acyl donor components are illustrated by selected synthesis reactions of small peptides, peptide isosteres, non-peptidic carboxylic acid amides, and the coupling of peptide fragments at non-specific ligation sites resulting in biologically active peptide products. Finally, this review focuses on critical syntheses that uses specific-amino acid-containing peptides as the reactants of ligation. Based on these, the restrictions of the substrate mimetics approach is critically discussed and techniques to their overcoming are presented.

Differences in the protein-kinase-A-dependent regulation of CFTR Cl- channels and Na+-K+ pumps in guinea-pig ventricular myocytes.

Protein-kinase-A- (PKA-) dependent regulation of cystic fibrosis transmembrane conductance regulator (CFTR) Cl- current (I(CFTR)) and Na+-K+ pump current (Ip) was studied in single guinea-pig ventricular myocytes. Both currents were measured simultaneously by means of whole-cell recording at 30 degrees C. The adenylyl cyclase activator forskolin was used to stimulate PKA activity. At -20 mV, forskolin (4 microM) induced a fast activation of I(CFTR) and a delayed stimulation of Ip. Despite the strikingly different time courses, however, the potency of the drug to regulate both currents was identical. Half-maximal activation of I(CFTR) and stimulation of Ip, respectively, were observed at 9.6 x 10(-8) M and 9.9 x 10(-8) M forskolin. Inclusion of a specific peptide inhibitor of PKA in the pipette solution (PKI, 20 microM) blocked forskolin's effect on Ip. However, regardless of the time allowed for cell dialysis, there still was a marked, transient activation of I(CFTR), which could be prevented by: (1) a short pre-activation of I(CFTR) with forskolin or (2) the additional inclusion in the pipette solution of a synthetic peptide (Ht31 peptide, 60 microM) that interferes with PKA binding to its anchoring proteins. Thus, there is a tight functional coupling between PKA and CFTR Cl- channels in guinea-pig ventricular myocytes. The coupling is probably due to the close physical proximity of channels and kinases mediated by PKA anchoring proteins. Na+-K+ pumps, on the other hand, though also regulated by PKA, appear to be loosely coupled to the kinases.

Enzymatic coupling of specific peptides at nonspecific ligation sites: effect of Asp189Glu mutation in trypsin on substrate mimetic-mediated reactions.

Two main drawbacks seriously restrict the synthetic value of proteases as reagents in peptide fragment coupling: (i) native proteolytic activity and, thus, risk of undesired peptide cleavage; (ii) limited enzyme specificities restricting the amino acid residues between which a peptide bond can be formed. While the latter can be overcome by the use of substrate mimetics achieving peptide bond formation at nonspecific ligation sites, the risk of proteolytic cleavage still remains and hinders the wide acceptance of this powerful strategy for peptide coupling. This paper reports on the effect of the trypsin point mutant Asp189Glu on substrate mimetic-mediated reactions. The effect of this mutation on the steady-state hydrolysis of substrate mimetics of the 4-guanidinophenyl ester type and on trypsin-specific Lys- and Arg-containing peptides was investigated. The results were confirmed by enzymatic coupling reactions using substrate mimetics as the acyl donor and specific amino acid-containing peptides as the acyl acceptor. The competition assay verifies the predicted shift in substrate preference from Lys and Arg to the substrate mimetics and, thus, from cleavage to synthesis of peptide bonds. The combination of results obtained qualifies the trypsin mutant D189E as the first substrate mimetic-specific peptide ligase.

Synthesising protease-stable isopeptides by proteases: an efficient biocatalytic approach on the basis of a new type of substrate mimetics.

A biocatalytic route to the 'post-synthesis' formation of Asp/Glu-derived isopeptides is illustrated on the basis of the Staphylococcus aureus V8 protease used as the biocatalyst, a new type of substrate mimetics as the donor peptides, and several acceptor peptides varying in length and sequence.

Peptide bond formation mediated by substrate mimetics. Structure-guidedoptimization of trypsin for synthesis.

Substrate mimetics are excellent tools for protease-mediated peptide synthesis that enable the coupling of peptides independently of the primary specificity of the enzyme without undesired cleavages of the newly formed peptide bonds. However, the synthetic utility of this beneficial approach is limited to reactions with nonspecific amino-acid-containing peptides while the coupling of specific ones leads to unwanted cleavages due to the native proteolytic activity of the biocatalyst. This paper reports on the use of site-directed mutagenesis to design trypsin variants with decreased cleavage activity. Starting from the variant D189S, which is known for its low proteolytic potential, Ser189 and Ser190 were exchanged for Ala to further repress the inherent amidase activity of trypsin D189S. The effect of mutations was analysed by model synthesis reactions using specific amino-acid-containing peptides and substrate mimetics as the reactants. Finally, computer-assisted protein-ligand docking studies were performed to get closer insight into the molecular basis of the experimental results.

Assay of diverse protease activities on the basis of a small synthetic substrate.

The available methods for assaying of protease activity of unknown or partially defined specificity utilize long peptides, mostly denatured proteins, comprehending at least all coded amino acids in cleavable positions. In contrast, here we report on an alternative approach which utilizes a small synthetic ester substrate containing only one amino acid. The approach equally detects endo- and carboxypeptidases with a wide variety of specificities including enzymes specific for basic, acidic, aromatic, and nonaromatic hydrophobic amino acid moieties. The results further revealed that most proteases could be detected in activities considerably less than 1 U. In contrast to the methods used thus far, the enzymatic hydrolysis of the small substrate can be easily and rapidly assayed by a shift in absorption resulting in a change in color of the assay mixture at visible wavelengths. Thus, no additional instrumental efforts are generally required. On the basis of these characteristics, the approach presented here could be particularly valuable for monitoring the purification of enzymes or as a rapid check for protease activity.

Engineering of substrate mimetics as novel-type substrates for glutamic acid-specific endopeptidases: design, synthesis, and application.

This account reports on the development and function of novel substrate mimetics as artificial substrates for Glu-specific endopeptidases. Firstly, in an empirical way, various aliphatic and aromatic analogs of the already established carboxymethyl thioester-substrate mimetics were designed from simple structure-function relationship studies. The specificity of the newly developed substrates for Staphylococcus aureus V8 protease-catalyzed reactions have been examined by steady-state hydrolysis kinetic studies. Additionally, these studies were expanded to the use of the equally Glu-specific endopeptidase from Bacillus licheniformis (BL-GSE) which can easily be purified from alcalase in high yields. Finally, the novel substrate mimetics were used as acyl donor components in BL-GSE- and V8 protease-catalyzed model acyl transfer reactions. The results clarify the newly developed substrate mimetics as efficient acyl donors as well as BL-GSE as an attractive alternative to V8 protease for enzymatic peptide synthesis.

Substrate mimetics and freezing strategy: a useful combination that broadens the scope of proteases for synthesis.

[reaction: see text] We present an irreversible and efficient protease-based method for peptide synthesis which occurs independently of the primary specificity of proteases and also without proteolytic side reactions. The key feature of this approach is the combination of the substrate mimetics strategy with frozen state enzymology. Model reactions catalyzed by several proteases qualify this approach as a powerful concept in the direction of a more universal application of proteases as biocatalysts for peptide ligation.

Trypsin-specific acyl-4-guanidinophenyl esters for alpha-chymotrypsin-catalysed reactions computational predictions, hydrolyses, and peptide bond formation.

The function of acyl-4-guanidinophenyl esters as substrate mimetics for the serine protease alpha-chymotrypsin was investigated by protein-ligand docking, hydrolysis, and acyl transfer experiments. On the basis of protein-ligand docking studies, the binding and hydrolysis properties of these artificial substrates were estimated. The predictions of the rational approach were confirmed by steady-state hydrolysis studies on 4-guanidinophenyl esters derived from coded amino acids (which alpha-chymotrypsin is not specific for), noncoded amino acids, and even simple carboxylic acid moieties. Enzymatic peptide syntheses qualify these esters as suitable acyl donors for the coupling of acyl components far from the natural enzyme specificity, thus considerably expanding the synthetic utility of alpha-chymotrypsin.

Protease-catalyzed fragment condensation via substrate mimetic strategy: a useful combination of solid-phase peptide synthesis with enzymatic methods.

The concept of substrate mimetic strategy represents a new powerful method in the field of enzymatic peptide synthesis. This strategy takes advantage of the shift in the site-specific amino acid moiety from the acyl residue to the ester-leaving group of the carboxyl component enabling acylation of the enzyme by nonspecific acyl residues. As a result, peptide bond formation occurs independently of the primary specificity of proteases. Moreover, because of the coupling of nonspecific acyl residues, the newly formed peptide bond is not subject to secondary hydrolysis achieving irreversible peptide synthesis. Here, we report the combination of solid-phase peptide synthesis with substrate mimetic-mediated enzymatic peptide fragment condensations. First, the utility of the oxime resin strategy for the synthesis of peptide fragments in the form of substrate mimetics esterified as 4-guanidinophenyl-, phenyl- and mercaptopropionic acid esters was investigated. The study was completed by using the resulting N(alpha)-protected peptide esters as acyl donors in trypsin-, alpha-chymotrypsin- and V8 protease-catalyzed fragment condensations.

Nonconventional amide bond formation catalysis: programming enzyme specificity with substrate mimetics.

This article reports on the design and characteristics of substrate mimetics in protease-catalyzed reactions. Firstly, the basis of protease-catalyzed peptide synthesis and the general advantages of substrate mimetics over common acyl donor components are described. The binding behavior of these artificial substrates and the mechanism of catalysis are further discussed on the basis of hydrolysis, acyl transfer, protein-ligand docking, and molecular dynamics studies on the trypsin model. The general validity of the substrate mimetic concept is illustrated by the expansion of this strategy to trypsin-like, glutamic acid-specific, and hydrophobic amino acid-specific proteases. Finally, opportunities for the combination of the substrate mimetic strategy with the chemical solid-phase peptide synthesis and the use of substrate mimetics for non-peptide organic amide synthesis are presented.

Investigations on the enzyme specificity of clostripain: a new efficient biocatalyst for the synthesis of peptide isosteres.

To explore the ability of the cysteine protease clostripain as a biocatalyst for the synthesis of peptide isosteres, the S'-subsite specificity of this enzyme toward unnatural substrates was investigated. First, the function of clostripain for acylating aliphatic noncyclic and cyclic amines varying in chain length and ring size was analyzed using a standard acyl donor. Additionally, this series was expanded by use of aromatic amines, amino alcohols, derivatives of non-alpha-amino carboxylic acids, and symmetric and asymmetric diamines, respectively. The results obtained give a detailed picture of the unique reactivity of clostripain toward synthetic substrates, allowing insights into the basic enzyme-substrate interactions. Furthermore, the data provide a guideline for the use of clostripain as a biocatalyst for synthesis of peptide isosteres. The study was completed by the utilization of a model substrate mimetic enabling clostripain to react with noncoded and non-amino acid-derived amines as well as nonspecific acyl moieties. The results of this study indicate that this approach may extend the application range of clostripain as a biocatalyst outside of peptide synthesis.

Protease catalysis mediated by a substrate mimetic: a novel enzymatic approach to the synthesis of carboxylic acid amides.

We present a protease-based method for the coupling of non-coded and non-amino-acid-derived amines with carboxy components. The key feature of this approach is the combination of the substrate-mimetic strategy with the ability of the cysteine protease clostripain to accept a wide spectrum of amines. Firstly, we tested the use of the 4-guanidinophenyl ester leaving group to mediate acceptance of non-coded and non-amino-acid-derived acyl residues. This employed beta-amino acid and simple carboxylic acid moieties as acyl donors, and several amino acid and peptide units as acyl acceptors. The study was completed by the use of non-amino-acid-derived acyl acceptors comprising simple amines, amino alcohols, and diamines. The results indicate that the approach presented is a useful strategy for the synthesis of peptide isosteres, peptide analogues, and organic amides. These last open a new range of synthetic applications of proteases completely beyond peptide synthesis, achieving efficient and selective acylations of non-amino-acid-derived amines under extraordinarily mild reaction conditions.

Protease-catalyzed hydrolysis of substrate mimetics (inverse substrates): A new approach reveals a new mechanism.

Contrary to common protease substrates, the hydrolysis of 4-guanidinophenyl esters of the Boc-Xaa-OGp type by trypsin and trypsin-like proteases performs easily and independently of the structure and chirality of the acyl moiety. The hydrolysis of this new class of substrate mimetics, previously called inverse substrates, is enabled by the highly specific leaving group. However, the mechanism cannot be explained on the basis of the conventional binding model which defines the interactions between the protease and its substrate. Hydrolysis and aminolysis kinetics, protein-ligand docking, and molecular dynamics studies have been carried out in order to get insight into the catalytic mechanism which holds for these substrate mimetics. The experimental and theoretical results obtained for the serine protease trypsin suggest a novel extended kinetic model. It explains the hydrolysis of these types of protease substrates and accounts for the structural consequences for their aminolysis.

Programming of enzyme specificity by substrate mimetics: investigations on the Glu-specific V8 protease reveals a novel general principle of biocatalysis.

In this paper the universal validity of the substrate mimetic concept in enzymatic C-N ligations was expanded to anionic leaving groups based on the specificity determinants of Glu-specific endopeptidase from Staphylococcus aureus (V8 protease). In an empirical way a specific mimetic moiety was designed from simple structure-function relationship studies. The general function of the newly developed substrate mimetics to serve as an artificial recognition site for V8 protease have been examined by hydrolysis kinetic studies. Enzymatic peptide syntheses qualify the strategy of substrate mimetics as a powerful concept for programming the enzyme specificity in the direction of a more universal application of enzymes in the general area of biocatalysis.

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. In contrast, no binding of P1' proline-containing peptides was observed. It could be demonstrated that the specificity of the S' subsite is not restricted to L-amino acids. Effective P'-S' interactions were also found for beta- and gamma-amino acids indicating that the enzyme does not form close contacts to the backbone of P1' and P2' amino acid residues.