Claus-W. von der Lieth

LINUCS: linear notation for unique description of carbohydrate sequences.

The use of proteomics databases has become indispensable for daily work of molecular biologists, but this situation has not yet been achieved for carbohydrate applications. One obvious reason is that existing data collections are only rarely annotated and no cross-linking to other resources exists. The existence of a generally accepted linear, canonical description for carbohydrates which can be readily processed by computers will enable efficient automatic cross-linking of distributed carbohydrate data collections by serving as a unique and unambiguous database access key. Various possibilities to derive a canonical notation are discussed. They can be divided into attempts that require structure description alone and alternatives that profit from the fact that a preferred graph direction (non-reducing to reducing end) exists within the structure. To open a fruitful discussion among glycoscientists a possible solution is presented where the reducing monosaccharide unit is selected as graph root and linkage information is used to define the priority of the various branches. A Web interface (http://www.dkfz.de/spec/linucs/) has been created that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form.

Identification and characterization of riproximin, a new type II ribosome-inactivating protein with antineoplastic activity from Ximenia americana

The aim of this study was to identify and characterize the active component(s) of Ximenia americana plant material used to treat cancer in African traditional medicine. By a combination of preextraction, extraction, ion exchange and affinity chromatography, a mixture of two cytotoxic proteins was isolated. Using degenerated primers designed on the de novo sequence of two tryptic peptides from one of these proteins, a DNA fragment was amplified and the sequence obtained was used to determine the complete cDNA sequence by the RACE method. Sequence analysis and molecular modeling showed that the new protein, riproximin, belongs to the family of type II ribosome inactivating proteins. These results are in good agreement with the ability of riproximin to inhibit protein synthesis in a cell‐free system, as well as with the cytotoxicity of riproximin, as demonstrated by its IC50 value of 0.5 pM in MCF7, 1.1 pM in HELA and 0.6 pM in CC531‐lacZ cells. To assess the antineoplastic efficacy of the purified riproximin in vivo, the CC531‐lacZ colorectal cancer rat metastasis model was used. Significant anticancer activity was found after administration of total dosages of 100 (perorally) and 10 (intraperitoneally) pmol riproximin/kg. These results suggest that riproximin has distinct potential for cancer treatment. —Voss, C., Eyol, E., Frank, M., von der Lieth, C.‐W., Berger, M. R. Identification and characterization of riproximin, a new type II ribosome‐inactivating protein with antineoplastic activity from Ximenia americana. FASEB J. 20, E334–E345 (2006)

Molecular dynamics simulations of glycoclusters and glycodendrimers

Protein-carbohydrate recognition plays a crucial role in a wide range of biological processes, required both for normal physiological functions and the onset of disease. Nature uses multivalency in carbohydrate-protein interactions as a strategy to overcome the low affinity found for singular binding of an individual saccharide epitope to a single carbohydrate recognition domain of a lectin. To mimic the complex multi-branched oligosaccharides found in glycoconjugates, which form the structural basis of multivalent carbohydrate-protein interactions, so-called glycoclusters and glycodendrimers have been designed to serve as high-affinity ligands of the respective receptor proteins. To allow a rational design of glycodendrimer-type molecules with regard to the receptor structures involved in carbohydrate recognition, a deeper knowledge of the dynamics of such molecules is desirable. Most glycodendrimers have to be considered highly flexible molecules with their conformational preferences most difficult to elucidate by experimental methods. Longtime molecular dynamics (MD) simulations with inclusion of explicit solvent molecules are suited to explore the conformational space accessible to glycodendrimers. Here, a detailed geometric and conformational analysis of 15 glycodendrimers and glycoclusters has been accomplished, which differ with regard to their core moieties, spacer characteristics and the type of terminal carbohydrate units. It is shown that the accessible conformational space depends strongly on the structural features of the core and spacer moieties and even on the type of terminating sugars. The obtained knowledge about possible spatial distributions of the sugar epitopes exposed on the investigated hyperbranched neoglycoconjugates is detailed for all examples and forms important information for the interpretation and prediction of affinity data, which can be deduced from biological testing of these multivalent neoglycoconjugates.

An endorsement to create open access databases for analytical data of complex carbohydrates

Abstract One of the aims of the emerging glycomics projects is to create a cell‐by‐cell catalogue of detected glycan structures. Mass spectrometry (MS) and NMR in combination with separation techniques are the most intensively applied experimental methods for the analysis of carbohydrates. Unlike genome and proteome databases, development of carbohydrate databases has gained a broader attention only recently. However, no spectral libraries of suitable pure and homogeneous standards have been compiled so far. The difficulties to describe complex carbohydrate structures are discussed and an overview of currently available data collections and applications is given. The current situation in glycobiology is characterized by a nearly complete loss of all primary analytical data. The Internet has fundamentally changed the practical and economic realities to collect and distribute scientific data. Four suitable approaches how to organize the updating process for analytical data collections in the field of glycosciences are discussed. It is anticipated that open access data collections provide a better dissemination of scientific data, quicken scientific findings, guarantee better quality of data and initiate a number of new initiatives to explore the available experimental data under various scientific questions. Therefore, any new initiative in glycosciences should be established under the open access philosophy.Abstract One of the aims of the emerging glycomics projects is to create a cell‐by‐cell catalogue of detected glycan structures. Mass spectrometry (MS) and NMR in combination with separation techniques are the most intensively applied experimental methods for the analysis of carbohydrates. Unlike genome and proteome databases, development of carbohydrate databases has gained a broader attention only recently. However, no spectral libraries of suitable pure and homogeneous standards have been compiled so far. The difficulties to describe complex carbohydrate structures are discussed and an overview of currently available data collections and applications is given. The current situation in glycobiology is characterized by a nearly complete loss of all primary analytical data. The Internet has fundamentally changed the practical and economic realities to collect and distribute scientific data. Four suitable approaches how to organize the updating process for analytical data collections in the field of glycos...

The protein data bank (PDB) as a versatile resource for glycobiology and glycomics

The compilation of data collections for carbohydrates has only recently gained momentum. The availability of such comprehensive databases, however, will be a prerequisite to successfully perform large-scale glycomics projects aiming to decipher new biological functions of glycans. With the carbohydrate structure suite (CSS), the carbohydrate-related data contained in the protein data bank (PDB) are now accessible through the Internet. It turned out that the PDB is a versatile resource for structural aspects in glycobiology. It provides reliable data about glycosylation sites, the conformational preferences of glycans and the specificity of protein carbohydrate recognition. A detailed comparison between the carbohydrate assignment reported in the PDB files and the nomenclature derived from atom coordinates guarantees that only consistent data will be evaluated. The automatic assignment of a unique structural description (LINUCS notation) enables easy cross-linking and referencing with other carbohydrate-related resources like NMR and MS-spectra. Exemplified for α- and β-N-acetylglucosamine it is shown that a particular distribution of amino acids is required to establish specific recognition for both anomers. The unrestricted use of primary data enables an online linkage of carbohydrate-related databases with other bioinformatics and biomedical resources and will thus provide maximal synergism.