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Biomedical subjects

G Barnickel

Publications and source records attributed to G Barnickel.

16 recordsLinked to original sources
PubMed2001

Discriminating between drugs and nondrugs by prediction of activity spectra for substances (PASS).

Using the computer system PASS (prediction of activity spectra for substances), which predicts simultaneously several hundreds of biological activities, a training set for discriminating between drugs and nondrugs is created. For the training set, two subsets of databases of drugs and nondrugs (a subset of the World Drug Index, WDI, vs the Available Chemicals Directory, ACD) are used. The high value of prediction accuracy shows that the chemical descriptors and algorithms used in PASS provide highly robust structure-activity relationships and reliable predictions. Compared to other methods applied in this field, the direct benchmark undertaken with this paper showed that the results obtained with PASS are in good accordance with these approaches. In addition, it has been shown that the more specific drug information used in the training set of PASS, the more specific discrimination between drug and nondrug can be obtained.

Computer Simulation↗
PubMed1997

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins.

LIGSITE is a new program for the automatic and time-efficient detection of pockets on the surface of proteins that may act as binding sites for small molecule ligands. Pockets are identified with a series of simple operations on a cubic grid. Using a set of receptor-ligand complexes we show that LIGSITE is able to identify the binding sites of small molecule ligands with high precision. The main advantage of LIGSITE is its speed. Typical search times are in the range of 5 to 20 s for medium-sized proteins. LIGSITE is therefore well suited for identification of pockets in large sets of proteins (e.g., protein families) for comparative studies. For graphical display LIGSITE produces VRML representations of the protein-ligand complex and the binding site for display with a VRML viewer such as WebSpace from SGI.

Algorithms↗
PubMed1996

The comparison of geometric and electronic properties of molecular surfaces by neural networks: application to the analysis of corticosteroid-binding globulin activity of steroids.

It is shown how a self-organizing neural network such as the one introduced by Kohonen can be used to analyze features of molecular surfaces, such as shape and the molecular electrostatic potential. On the one hand, two-dimensional maps of molecular surface properties can be generated and used for the comparison of a set of molecules. On the other hand, the surface geometry of one molecule can be stored in a network and this network can be used as a template for the analysis of the shape of various other molecules. The application of these techniques to a series of steroids exhibiting a range of binding activities to the corticosteroid-binding globulin receptor allows one to pinpoint the essential features necessary for biological activity.

Drug Design↗
PubMed1992

Synthesis and dopaminergic activity of some 3-(1,2,3,6-tetrahydro-1-pyridylalkyl)indoles. A novel conformational model to explain structure-activity relationships.

The synthesis and dopaminergic properties of a novel type of dopamine agonist is described. The number and kind of essential structural elements differ significantly from that of the rigid apomorphine-type dopamine agonists. Using standard molecular modeling techniques, a conformational model is developed proposing a U-shaped conformation which might be energetically preferred through aromatic pi-pi-interactions between both of the electron rich aromatic structural elements of this class of compounds. Superimposition of conformations of the lead compound 28 with apomorphine yields a novel model explaining the atypical structure-activity relationships found in this class of indolealkylamines.

Animals↗
PubMed1991

Conformation-based design of two cyclic physalaemin analogues.

Two new cyclic analogues of physalaemin were designed on the basis of the conformation found in DMSO solution. Glp-Ala-cyclo(-Asp-Pro-Asn-Lys-)-Phe-Tyr-Gly-Leu-Met-NH2 (1) was synthesized by cyclization of physalaemin. In 2 the Asp residue was replaced by Glu. The linear analogue of 2 was synthesized by the solid phase method and subsequently cyclized. Two-dimensional nmr methods were employed to assign the proton and carbon resonances. Proton-proton distances were extracted from rotating frame nuclear Overhauser effect spectra and used as restraints in the molecular dynamics calculations. Analogue 1 was found to have a similar conformation as physalaemin, whereas 2 did not form intramolecular hydrogen bonds. The pharmacological evaluation revealed that both peptides have similar potencies as physalaemin in the dog carotid artery (NK-1 receptor). Therefore, the charged side chains of physalaemin appear not essential for NK-1 activation. However, the other tachykinin receptors show good sensitivity to the cyclic peptides. It is concluded that the replacement of a salt bridge by an amide bond connecting the side chains of natural residues might provide useful information about the biological significance of some charged side chains of neurokinins.

Amino Acid Sequence↗
PubMed1991

Synthesis, conformational studies, and molecular dynamics calculations of two cyclic tetrapeptides with 17- and 18-membered rings.

Two cyclic tetrapeptides [Boc-cyclo(-Xxx-Pro-Asn-Lys-)OMe (Xxx = Asp or Glu)] were synthesized and investigated by NMR spectroscopy. They were designed in order to mimic the salt bridge found in physalaemin. Isomers of the urethane bond were observed in DMSO solution. The ROESY spectrum allowed the assignment of many signals of the minor isomer of both compounds. Conformational studies based on the temperature gradients of the NH chemical shifts, coupling constants, and ROEs revealed a similar conformation for the Asp analogue as proposed for physalaemin. A beta I turn with Pro and Asn in the corner positions was found for the major isomer. No hydrogen bonds were detected for the major isomer of the cyclic Glu analogue. Molecular dynamics calculations, using the NMR based initial structures, yielded sets of conformations in agreement with the experimental data. It is concluded that the salt bridge in physalaemin is best approximated by a lactam formed from the original amino acids.

Amino Acid Sequence↗
PubMed1985

High state of order of isolated bacterial lipopolysaccharide and its possible contribution to the permeation barrier property of the outer membrane.

The conformational properties of the isolated S form of Salmonella sp. lipopolysaccharide (LPS), of Re mutant LPS, and of free lipid A were investigated by using X-ray diffraction and conformational energy calculations. The data obtained showed that LPS in a dried, in a hydrated, and probably also in an aqueous dispersion state is capable of forming bilayered lamellar arrangements similar to phospholipids. From the bilayer packing periodicities, a geometrical model of the extensions of the LPS regions lipid A, 2-keto-3-deoxyoctulosonic acid, and O-specific chain along the membrane normal could be calculated. Furthermore, the lipid A component was found to assume a remarkably high ordered conformation: its fatty acid chains were tightly packed in a dense hexagonal lattice with a center-to-center distance of 0.49 nm. The hydrophilic backbone of lipid A showed a strong tendency to form domains in the membrane, resulting in a more or less parallel arrangement of lipid A units. According to model calculations, the hydrophilic backbone of lipid A appears to be oriented approximately 45 degrees to the membrane surface, which would lead to a shed roof-like appearance of the surface structure in the indentations of which the 2-keto-3-deoxyoctulosonic acid moiety would fit. In contrast, the O-specific chains assume a low ordered, heavily coiled conformation. Comparison of these structural properties with those known for natural phospholipids in biological membranes indicates that the high state of order of the lipid A portion of LPS might be an important factor in the structural role and permeation barrier functions of LPS in the outer membrane of gram-negative bacteria.

Bacteria↗
PubMed1984

A new proposal for the primary and secondary structure of the glycan moiety of pseudomurein. Conformational energy calculations on the glycan strands with talosaminuronic acid in 1C conformation and comparison with murein.

Using the method of conformational energy calculations, favoured conformations of a pseudomurein sugar strand built up from beta 1,3-linked N-acetyl-D-glucosamine and N-acetyl-L-talosaminuronic acid were obtained. Such a completely beta 1,3-linked polysaccharide primary structure, although contrasting with the originally proposed alternating beta 1,3-alpha 1,3-linked structure [König, H., Kandler, O., Jensen, M. and Rietschel, E. Th. (1983) Hoppe-Seyler's Z. Physiol. Chem. 364, 627-636] would be in agreement with all experimental data hitherto known. Starting from an analysis of favoured conformations of the monosaccharide building blocks and those obtained for disaccharide parts, the favoured helical conformations of the complete polysaccharide chains could be explored. Our completely beta 1,3-linked chain could adopt two types of conformation: extended and hollow; the latter was discarded as unsuitable for cell wall assembly. The extended conformation type was shown to exhibit a remarkable similarity if compared to the secondary structures accessible to murein-type polysaccharide chains. In contrast to the conformations accessible for the beta 1,3-alpha 1,3-linked primary structure, the new hypothetical pseudomurein structure was found to be more extended, possessed a flexible peptide attachment site at every second sugar residue and led to an orientation of consecutive peptide attachment sites analogous to the data known for murein-type chains. From the two possibilities compatible with the experimental data available, the completely beta 1,3-linked sugar strand structure could well be realized in the native pseudomurein network of methanobacteria. In this case the hypothesis for a similar three-dimensional architecture for murein and pseudomurein would be supported.

Carbohydrate Conformation↗
PubMed1984

Structural studies on the bacterial cell wall peptidoglycan pseudomurein. I. Conformational energy calculations on the glycan strands in C1 conformation and comparison with murein.

Conformational energy calculations have been used to explore the conformations which may be realized for the sugar moiety of murein and pseudomurein. For the building blocks of the pseudomurein sugar strands, i.e. for the monosaccharides beta-D-N-acetylglucosamine (NAG) and alpha-L-N-acetyltalosaminuronic acid (NAT), both in C1 ring conformation, as well as for their 1,3 and 1,4 linked disaccharides, the favoured conformations were obtained. The helical parameters of sugar strands of both linkage types, which describe the regular structure of the corresponding polysaccharides, poly-(1,3-NAT-NAG) and poly-(1,4-NAT-NAG), were calculated. Both types of polysaccharides poly-(NAG-NAT) considered in this study favoured extended conformations, which in the case of 1,3 linked polymers showed less gain of length per saccharide unit compared to 1,4 linked poly-(NAG-NAT) residues. For a 1,3 linked sugar moiety of pseudomurein every pair of neighbouring peptides attached to glycan chain pointed in favoured conformations approximately to opposite sides of the strands, whereas in a 1,4 linked poly-(NAG-NAT) the peptides protruded approximately to the same side of the glycan moiety. A comparison between pseudomurein and murein revealed that the sugar moieties of both peptidoglycans have similar features in respect to their overall structure, i.e. both favoured more or less extended structures. In contrast to these data the shapes of the resulting polysaccharide moieties were remarkably different. In poly-(1,3-NAG-NAT) the glycan chains possessed a zig-zag-like arrangement, whereas for glycan chains of the murein type relatively flat structures were preferred. These remaining differences in the conformational arrangement between both peptidoglycans depend strongly on the C1 chair conformation of NAT. It is, therefore, attractive to speculate about an hypothetical pseudomurein sugar chain configuration comprising beta-L-N-acetyltalosaminuronic acid in its 1C conformation.

Acetylglucosamine↗
PubMed1984

Study of the Zn-containing DD-carboxypeptidase of Streptomyces albus G by small-angle X-ray scattering in solution.

Study of the Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase of Streptomyces albus G by small-angle X-ray scattering in solution yielded the following molecular parameters: radius of gyration R = 1.82 +/- 0.05 nm; largest diameter D = 5.9 +/- 0.2 nm; relative molecular mass Mr = 17000 +/- 2000; volume V approximately equal to 35 +/- 2 nm3; degree of hydration: 0.25 +/- 0.02 g water/g protein. By reference to theoretical scattering curves of rigid triaxial homogeneous bodies, a model which fits all experimental data is an elliptical cylinder. Such a model is compatible with that observed in the crystal structure. At those high concentrations necessary to form inactive enzyme-ligand associations the non-competitive beta-lactam inhibitors, cephalothin and cephalosporin C, drastically altered the scattering behaviour of the protein.

Carboxypeptidases↗
PubMed1982

Infrared spectroscopy, a tool for probing bacterial peptidoglycan. Potentialities of infrared spectroscopy for cell wall analytical studies and rejection of models based on crystalline chitin.

Infrared spectroscopic measurements are used to obtain insights into the three-dimensional architecture of peptidoglycan (murein), the rigid component of almost all bacterial cell walls. The infrared spectra of various types of peptidoglycans (including all chemotypes and examples of the so called A and B groups) were compared to each other and to those obtained from crystalline chitin. All peptidoglycans investigated exhibited very similar infrared spectra. In particular the conformationally sensitive amide A, I and II absorption bands were found to be constantly centered around 3300 cm-1, 1657 cm-1 and 1534 cm-1 respectively; furthermore, the spectral region between 1200 cm-1 and 800 cm-1, characterized by several strong absorption bands connected to complex sugar ring modes, proved to be remarkably uniform. Additionally the infrared spectra remained significantly constant between -175 degrees C and + 75 degrees C and turned out to be rather independent of sample preparation (solvent replacement, freeze-drying and film producing). An analysis of band half-widths revealed no high crystalline state of order of peptidoglycan. On the basis of band positions and half-widths of amide bands, regular conformations like alpha helices of beta pleated sheets could be excluded. Several distinctive, fingerprint-like spectral features of the various murein samples permitted a facile identification of individual peptidoglycans. Moreover, infrared spectroscopy seems to be very promising as an analytical tool, e.g. for tracing variations of cell wall structure, detecting conformational changes and estimating crosslinking indices in a quick and simple way. The comparative analysis of amide band positions and band half-widths yielded substantial differences between infrared spectra of chitin and murein, thus rejecting previous models based on the assumption of a nearly crystalline chitin-like structure of the glycan chains of murein.

Bacteria↗
PubMed1979

Conformational energy calculation on the peptide part of murein.

Conformational energy calculations have been carried out on N-acetyl-L-alanyl-D-gamma-glutamyl-L-lysyl-D-alanyl-D-alanine as a model of the peptide moiety of peptidoglycan. Although many conformations were of comparable energy, particular favoured conformations were selected by assuming conformational similarity between the pentapeptide and the tetrapeptide found during biosynthesis subsequent to the cross-linking of the peptide chains in murein. The common feature of these conformations, which include the global minimum of the pentapeptide, is a ring-shaped backbone. The global minimum is stabilised by a hydrogen bond between the -NH group of L-alanine and the -CO group of the penultimate D-alanine. The distance between the D-lactyl group and the side-chain of the diamino acid is about 1.5 nm. The ring-like structures will accomodate chemical modifications that have been observed in peptidoglycan. The present ring-like structure differs considerably from the models proposed as yet. Energetically beta-pleated sheet conformations and a flat 2.2(7) helical structure are not favoured. Furthermore, an alpha helix cannot occur. The suggested new model exhibits no significant relationship to the solid state conformation of beta-lactam antibiotics.

Amino Acid Sequence↗
PubMedDate not supplied

Conformational and topological aspects of the three-dimensional architecture of bacterial peptidoglycan.

An atomic model of the conformation of peptidoglycan was taken as the basis for an analysis of packing patterns of the peptidoglycan strands in two- and three-dimensional arrangements. For the sake of clarity, glycan strands were approximated by cylindrical rods around which a continuous helix of possible peptide cross-linkage sites was arranged. Using the packing patterns obtained, several important properties of the murein network could be explained. These include variations in the degree of cross-linking in Gram-negative and Gram-positive bacteria and an estimation of the number of peptide monomers, di/trimers and oligomers present. Furthermore, our model is compatible with the well known flexibility of the murein fabric and the distinct elastic properties of the cell wall in gram-positive cocci and rod-shaped bacteria.

Bacteria↗