FP6 priority

1.1.1   Genomics and Biotechnology for Health

1.1.1

Title of the proposal

Protein bioinformatics of starch-degrading enzymes and other glycoside hydrolases

Institute

Slovak Academy of Sciences, Institute of Molecular Biology
Dubravska cesta 21, 84251 Bratislava, Slovak Republic

Contact

Research subject for a potential FP6 project

The department of evolutionary biology performs the basic research in the field of protein bioinformatics. It is focused on theoretical studying the proteins at molecular level, i.e. to compare the primary and tertiary structures of proteins and to derive the relationships between the sequence and structure on one side and the function, specificity and stability on the other side. The enzymes hydrolysing starch and related oligo- and polysaccharides, especially from the alpha-amylase family (about 30 different enzyme specificities), are in the center of the attention. In a wider sense, also other families of glycoside hydrolases (e.g., pectin degrading enzymes, glucoamylases, xylanases, etc.) as well as other enzyme families (e.g., catalases, catalase-peroxidases, hemagglutinins) are of interest. Generally the department is oriented on the proteins and enzymes adopting the most frequently used protein-folding motifs, such as TIM-barrel and parallel beta-helix. Currently the enzymes from important metabolic pathways (e.g., glycolysis) have been taken into account with regard to available sequence information from completely sequenced genomes.

Recent international cooperation of the research team

Department of Chemistry, Carlsberg Laboratory, Copenhagen, Denmark;
Department of Chemistry, University of Manitoba, Winnipeg, Canada;
Oral Biology, Dental School, University of Newcastle, Newcastle upon Type, U.K.;
Departament de Bioquimica i Biotecnologia, Universitat Rovira i Virgili, Tarragona, Spain

Proposer´s relevant publications related to the research subject

Janecek, S., Svensson, B., Henrissat, B. 1997. Domain evolution in the alpha-amylase family. J. Mol. Evol. 45: 322-331.
Janecek, S., Leveque, E., Belarbi, A., Haye, B. 1999. Close evolutionary relatedness of alpha-amylases from Archaea and plants. J. Mol. Evol. 48: 421-426.
Janecek, S., Sevcik, J. 1999. The evolution of starch-binding domain. FEBS Lett. 456: 119-125.
Janecek, S., Svensson, B., Russell, R.R.B. 2000. Location of repeat elements in glucansucrases of Leuconostoc and Streptococcus species. FEMS Microbiol. Lett. 192: 53-57.
MacGregor, E.A., Janecek, S., Svensson, B. 2001. Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes. Biochim. Biophys. Acta 1546: 1-20.