Biomedical subjects

W Heiden

Publications and source records attributed to W Heiden.

4 recordsLinked to original sources

PubMed1994

Segmentation of protein surfaces using fuzzy logic.

An algorithm has been developed that can be used to divide triangulated molecular surfaces into distinct domains on the basis of physical and topographical molecular properties. Domains are defined by a certain degree of homogeneity concerning one of these properties. The method is based on fuzzy logic strategies, thus taking into consideration the smooth changes of the properties considered along complex macromolecular surfaces. Scalar qualities assigned to every node point on a triangulated surface are translated into linguistic variables, which can then be processed using a special fuzzy dissimilarity operator. Possible applications are demonstrated using surface segmentation for properties like electrostatic potential, lipophilicity and shape for the analysis of serine proteinase substrate/inhibitor specificity.

Algorithms↗

PubMed1993

A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces.

A new method for display and analysis of lipophilic/hydrophilic properties on molecular surfaces is presented. The present approach is based on the concept of Crippen and coworkers that the overall hydrophobicity of a molecule (measured as the logarithm of the partition coefficient in an octanol/water system) can be obtained as a superposition of single atom contributions. It is also based on the concept of molecular lipophilicity potentials (MLP) first introduced by Audry and coworkers in order to establish a 3D lipophilicity potential profile in the molecular environment. Instead of using a l/r- or an exponential distance law between the atomic coordinates and a point on the molecular surface, a new distance dependency is introduced for the calculation of an MLP-value on the solvent-accessible surface of the molecule. In the present formalism the Crippen values (introduced for atoms in their characteristic structural environment) are 'projected' onto the van der Waals surface of the molecule by a special weighting procedure. This guarantees that only those atomic fragments contribute significantly to the surface values that are in the close neighbourhood of the surface point. This procedure not only works for small molecules but also allows the characterization of the surfaces of biological macromolecules by means of local lipophilicity. Lipophilic and hydrophilic domains can be recognized by visual inspection of computer-generated images or by computational procedures using fuzzy logic strategies. Local hydrophobicities on different molecular surfaces can be quantitatively compared on the basis of the present approach.

Alcohols↗

PubMed1990

Triangulation algorithms for the representation of molecular surface properties.

A triangulation algorithm for a dotted surface (i.e. a surface defined by point coordinates in three dimensions) is given. The individual triangles are generated on the basis of a hierarchy of strategies according to increasing surface complexity. While for small molecules an elementary algorithm is sufficient to triangulate the surface, large molecules-like proteins-generally need all steps of the hierarchy. Although this program has been developed with the aim of triangulating molecular surfaces, it can in principle be applied to any surface defined by 3D point coordinates.

Algorithms↗

PubMed1988

The influence of tetraphenylborates (hydrophobic anions) on yeast cell electro-rotation.

The action of a series of tetraphenylborate ion (TPB) derivatives on yeast cells was studied by electro-rotation of the pre-treated cells. TPB derivatives in which all four phenyl groups were substituted with fluorine, chlorine or trifluoromethyl were much more toxic than the unsubstituted compound, the effect increasing dramatically with increasing size of substituents. These observations suggest that the toxicity of these hydrophobic ions is determined mainly by their size and possibly also by the chemical inductivity of their substituent groups. The order of the toxicities of these ions was in fair agreement with literature values for their translocation rates across artificial bilayers. Incubation times of 3 h were used as standard, longer incubations (up to 48 h) showed that the number of cells affected by low doses of TPB increased with the logarithm of time after the first hour of incubation. Although measurements of the percentage of cells showing co-field rotation showed that controls were not adversely affected by incubations as long as 9 h, rotation spectra showed that some cells suffer loss of internal conductivity during extended incubations. Decrease of the pH of the incubation medium, or inclusion of high concentrations of NaCl or KCl, potentiated the effects of these hydrophobic ions. The toxicity developed slowly, and the sensitivity of the assay was only very weakly dependent on the cell suspension density.

Boron Compounds↗