RNase-stable RNA: conformational parameters of the nucleic acid backbone for binding to RNase T1.

An RNA sequence showing high stability with respect to digestion by ribonuclease T1 (RNase T1) was isolated by in vitro selection from an RNA library. Although ribonuclease T1 cleaves single-stranded RNA specifically after guanosine residues, secondary structure calculations predict several guanosines in single-stranded areas. Two of these guanosines are part of a GGCA-tetraloop, a recurring structure element in the secondary structure predictions. Molecular dynamics simulations of the conformation space of the nucleotides involved in this tetraloop show on the one hand that the nucleic acid backbone of the guanosines cannot realise the conformation required for cleavage by RNase T1. On the other hand, it could be shown that an RNA molecule not forced into a tetraloop occupies this conformation several times in the course of the simulation. The simulations confirm the GGCA-tetraloop as an RNase-stable secondary structure element. Our results show that, besides the known prerequisite of a single-stranded RNA, RNase T1 has additional demands on the substrate conformation.

Hydrazino peptides as foldamers: an extension of the beta-peptide concept.

Replacing the C(beta) atoms in the beta-amino acid constituents of beta-peptides by nitrogen atoms leads to hydrazino peptides. A systematic conformation analysis of blocked hydrazino peptide oligomers of the general type I at the HF/6-31G, MP2/6-31G, and DFT/B3LYP/6-31G levels of ab initio MO theory and on the basis of molecular mechanics reveals a wide variety of secondary structures, as for instance various helices and sheet- and turnlike conformers. Some of them are closely related to secondary structure types found in beta-peptides; others represent novel types. Thus, a very stable, novel helix with 14-membered hydrogen-bonded pseudocycles, which occupies a conformation space different from that of helices with 14-membered rings found among the most stable conformers in beta-peptides, is indicated. The most important secondary structure elements are characterized by interactions between peptidic NH and CO groups. The additional hydrazino N(alpha)H group takes part in special structuring effects but is of lesser importance for secondary structure formation. The influence of environmental effects on the existence and stability of the various structure types is discussed. Due to the wide variety of structural possibilities, hydrazino peptides might be a useful tool for peptide and protein design.

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.

A possible role of N-cadherin in thalidomide teratogenicity.

Several experimental findings indicate that the adhesion molecule N-cadherin participates in distinct processes of embryogenesis that spatiotemporarily correlate with high sensitivity to thalidomide. Therefore, we suppose that thalidomide might interfere with N-cadherin-mediated interactions. This hypothesis is supported by protein-ligand docking studies simulating and characterizing the binding of thalidomide to N-cadherin molecules. Thalidomide was found to bind at the N-terminal domain of N-cadherin mimicking a tryptophan residue which is critical for the homodimerization of the adhesion molecule. Based on these results, we suggest that thalidomide might disturb cellular recognition and migration processes in morphogenesis by interaction with N-cadherin.

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.

Molecular dynamics of a tetrasaccharide subunit of chondroitin 4-sulfate in water.

Molecular dynamics (MD) simulations on a tetrasaccharide subunit of chondroitin 4-sulfate (CS4) in aqueous solution were carried out to study its interactions with water. Pair distribution functions and diffusion coefficients were calculated from a 4 ns trajectory and the hydration of different molecular groups was analysed. The average values of the interglycosidic torsion angles found in the simulations are phi 13 = -10 degrees, psi 13 = -85 degrees and phi 13 = 80 degrees, psi 13 = 90 degrees for the beta-(1-->3) linkage, and phi 14 = -10 degrees, psi 14 = -70 degrees for the beta-(1-->4) linkage. Hydrophobic patches formed by sugar ring CH groups were found. The diffusion coefficients of the water molecules vary from 1.4 x 10(-9) to 2.3 x 10(-9) m2 s-1 depending on the distances between the water molecules and the atoms of the CS4 molecule and the type of CS4 atoms, respectively. Reorientation correlation times of the water molecules in the vicinity of different CS4 atoms were estimated to be about 1 ps at a polymer concentration of 4 wt.% CS4. The number of hydrogen bonds between the water molecules and the acceptor atoms of CS4 was determined to be about 20 per disaccharide unit, indicating a higher hydration ability of chondroitin sulfate in comparison with non-sulfated oligosaccharides. Substructures, where water molecules are involved in hydrogen bonds to different sugar rings, were found, which may be important for the stabilisation of the secondary structure of the CS4 molecule.

Basic conformers in beta-peptides.

The conformation of oligomers of beta-amino acids of the general type Ac-[beta-Xaa]n-NHMe (beta-Xaa = beta-Ala, beta-Aib, and beta-Abu; n = 1-4) was systematically examined at different levels of ab initio molecular orbital theory (HF/6-31G*, HF/3-21G). The solvent influence was considered employing two quantum-mechanical self-consistent reaction field models. The results show a wide variety of possibilities for the formation of characteristic elements of secondary structure in beta-peptides. Most of them can be derived from the monomer units of blocked beta-peptides with n = 1. The stability and geometries of the beta-peptide structures are considerably influenced by the side-chain positions, by the configurations at the C alpha- and C beta-atoms of the beta-amino acid constituents, and especially by environmental effects. Structure peculiarities of beta-peptides, in particular those of various helix alternatives, are discussed in relation to typical elements of secondary structure in alpha-peptides.

3-Amino-5-phenoxythiophenes: syntheses and structure-function studies of a novel class of inhibitors of cellular L-triiodothyronine uptake.

A series of substituted 3-amino-5-phenoxythiophenes was synthesized starting from malodinitrile and carbon disulfide. The resulting dicyanoketenedithiolate reacts via Thorpe-Dieckmann cyclization with halogen methanes bearing electron-withdrawing groups to give thiophene-2-thiolates, which can be transformed into 3-amino-5-(methylsulfonyl)thiophene-4-carbonitriles. Replacement of the methylsulfonyl groups by substituted phenolates provides the substituted 3-amino-5-phenoxythiophenes. Some of the derivatives show a considerable inhibitory potency for the L-T3 uptake in inhibition studies on human HepG2 hepatoma cells with maximum values of about 60% at a dose of 10(-5) M for the most potent 2-benzoyl derivatives. The structure of the phenoxythiophenes fits well into a general concept derived for other classes of L-T3 uptake inhibitors, which postulates an angular and perpendicular orientation of the ring systems in these compounds as a prerequisite for an inhibitory potency. Docking studies for the phenoxythiophenes with transthyretin as a receptor model show their preferred attack at the L-T4/L-T3 binding channel.

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.

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'. We replaced Lys60 with Glu and Asp to introduce a high specificity for basic residues into the S1' site of trypsin. Both mutations cause a dramatic increase in the S1' specificity for Arg and Lys as measured by acyl transfer reactions. In K60E, the preference for Arg increases 70-fold while the preference for P1'-Lys increases 12-fold. In contrast, the preferences for other P1' residues either decrease slightly or remain the same. Thus, K60E prefers P1'-Arg over most other P1' residues by 2 orders of magnitude. Similar results are obtained when P1' specificity is measured in peptide cleavage assays. K60D exhibits an S1' specificity profile very similar to that of K60E, although the P1'-Arg preference is reduced by a factor of 2.5. Molecular modeling studies suggest that the high S1' specificity for Arg in K60E may be due to the formation of a salt bridge between Glu60 and the P1'-Arg of the substrate.

Secondary structure formation in N-substituted peptides.

A systematic conformational analysis on several model peptides with N-substituted amino acids was performed on the basis of ab initio MO theory at the HF/6-31G* and HF/3-21G levels with inclusion of solvation effects to study the influence of N-substitution on the formation of typically secondary structural elements, e.g. beta sheets, helices and turns. The conformational flexibility of some structures was examined by means of molecular dynamics simulations in the gas phase and in solution. The results show a restriction of the conformational flexibility of the peptide chain after introduction of an N-substituted amino acid. N-substitution makes beta sheet formation more difficult. Several consecutive N-substituted amino acids in a sequence lead to conformers different from those found on the energy hypersurface of the corresponding N-unsubstituted peptides. There is a strong tendency to form periodically helical conformations, e.g. the polyglycine II or the alpha helix, which can be extended over several N-substituted amino acid residues. As long as 1<--4 hydrogen bond formation remains possible, the major types of beta turns can be formed with a distinct preference for the betaII and betaVIa turns. The betaI turn in particular is considerably destabilized.

Synthesis, anticonvulsant activity, and structure-activity relationships of sodium channel blocking 3-aminopyrroles.

Starting from the corresponding acetophenone and glycine derivatives, a series of new 3-aminopyrroles was synthesized in few steps. Using this procedure with hydrazine and hydroxylamine instead of the glycinates provides access to 3-aminopyrazoles and 5-amino 1,2-oxazoles. The various derivatives were tested for anticonvulsant activity in a variety of test models. Several compounds exhibit considerable activity with a remarkable lack of neurotoxicity. 4-(4-Bromophenyl)-3-morpholinopyrrole-2-carboxylic acid methyl ester, 3, proved to be the most active compound. It was protective in the maximal electroshock seizure (MES) test in rats with an oral ED50 of 2.5 mg/kg with no neurotoxicity noted at doses up to 500 mg/kg. Compound 3 blocks sodium channels in a frequency-dependent manner. The essential structural features which could be responsible for an interaction with an active site of the voltage-dependent sodium channel are established within a suggested pharmacophore model.

Inhibition of thyroid hormone uptake by calcium antagonists of the dihydropyridine class.

A series of substituted 4-phenyl-1,4-dihydropyridines 2a-m was tested for their inhibitory effects on L-triiodothyronine (L-T3) uptake by human HepG2 hepatoma cells. The most potent compounds were the nitro-substituted derivatives 2,6-dimethyl-4-(4'-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylic acid 3-ethyl ester 5-methyl ester (2m) and the well-known calcium antagonists nitrendipine (2k) and nifedipine (2j) with an uptake inhibition between 80.5 and 85.8% at an application dose of 10(-5) M. On the basis of a theoretical conformational analysis (ab initio MO theory, molecular mechanics, molecular dynamics) of the dihydropyridine derivatives, a unifying stereochemical concept was derived postulating an angular arrangement of the two rings where the phenyl ring of the calcium antagonists, which corresponds to the outer phenyl ring of the thyroid hormones, is bisecting the dihydropyridine ring as a prerequisite for inhibitory potency. This model includes also inhibitors of the N-phenylanthranilic acid type. The interaction of the calcium antagonists with transthyretin (TTR) is discussed in relation to thyroid hormones. The influence of hydrophobicity was estimated by the experimental determination of the 1-octanol/water partition coefficients.

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. Furthermore, the absolute configuration of the alpha-Tfm-substituted amino acid was found to exert considerable effects on the proteolytic stability, especially in P'1 substituted peptides. Investigations of this phenomenon using empirical force field calculations revealed that in the (S,R,S)-diasteromer the steric constraints exhibited by the alpha-Tfm group can be outweighed by an advantageous interaction of the flourine atoms with the serine side chain of the enzyme. In contrast, a favourable interaction between substrate and enzyme is impossible for the (S,S,S)-diastereomer.

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. Comparative studies in ice and at room temperature verify the importance of freeze-concentration which, however, is not sufficient for a complete understanding of the observed effects. Furthermore, the phase behaviour of frozen systems is discussed.

Solution conformation of [D-Pen2, D-Pen5] enkephalin in water: a NMR and molecular dynamics study.

The solution conformation of [D-Pen2, D-Pen5] enkephalin (DPDPE), a highly potent delta-selective opioid agonist, was examined by means of NMR, molecular mechanics and molecular dynamics methods. The structural information in the solvent water was obtained employing one- and two-dimensional methods of 1H and 13C-NMR spectroscopy. Based on the distance geometry technique using the ROE data as input, 400 conformers were obtained and considered in the structure analysis. Alternatively, about 2000 conformers were stochastically generated and related to the NMR data after energy minimization. The structure analysis provides one conformer in agreement with all NMR data, which belongs to the lowest energy conformation group. This structure may serve as a reference conformer for DPDPE analogues synthesized with the aim of activity increase.

Peptides and peptoids--a quantum chemical structure comparison.

Peptoids represent a very interesting structure alternative to peptides. Based on ab initio MO theory employing the 6-31G* and 3-21G basis sets and considering correlation energy, a systematic structure comparison between the basic structure units of peptoids and peptides is performed. The calculations show three minimum conformations denoted as C7 beta, alpha D, and alpha that do not correspond to conformers on the peptide potential energy hypersurface. The possibility of cis peptide bonds in the peptoids was examined. The solvent influence on the structure was estimated by means of various quantum chemical continuum models.

The specificity of chymotrypsin. A statistical analysis of hydrolysis data.

From the literature we collected all available quantitative data on the chymotrypsin-catalyzed hydrolysis of series of amino acid and peptide substrates. Utilizing this data base, we performed calculations on their quantitative structure/activity relationship (QSAR). The substrates were considered to be composed of fragments; log(kcat/Km) values for the substrates resulted from additive contributions of their fragments. Despite the fact that the kinetic constants in the data base were determined by different authors under various reaction conditions, the data are well described by the simple additivity model. Obviously, the intrinsic specificity of chymotrypsin dominates the influence of varying reaction conditions.

Protein-water interaction energies as predictor for antigenic determinants.

Goodford's GRIN/GRID method is used for the prediction of antigenic determinants of lysozyme by calculation of protein-water interaction energies. The comparison of the regions of high interaction energy with experimentally determined contact surfaces in antigen-antibody complexes and epitopes obtained by cross-reactivity measurements shows a noteworthy agreement. The model is proposed to enlarge the basis of theoretical models for epitope prediction. It may contribute to the increase of the prediction value when applied together with other methods.