Institute of Molecular Biology
Topic
Amylolytic enzymes – in silico approaches to study their sequences, structures, specificities and evolution
PhD. program
Molecular Biology, Biochemistry
Name of the supervisor
prof. Ing. Štefan Janeček, DrSc.
Contact:
Receiving school
Commenius University, Faculty of Natural Sciences
Annotation
PhD-study will be focused on amylolytic enzymes using bioinformatics, i.e. in silico approaches. The subject of study will be represented by amylolytic enzymes from alpha-amylase families classified in the sequence-based server CAZy (Carbohydrate-Active enZymes; http://www.cazy.org/) into several glycoside hydrolase (GH) families: (i) clan GH-H – families GH13, GH70 and GH77; (ii) families GH57 and GH119; and (iii) family GH126. For example, the main alpha-amylase family GH13 – part of the clan GH-H and simultaneously consisting of 47 subfamilies – contains more than 175 thousand protein sequences covering cca 30 different enzyme specificities (January 2024). Amylolytic enzymes from individual families differ from each other by their sequences and structures, domain arrangement of their protein molecules as well as their catalytic machineries. All this reflects their evolutionary history in relation to enzyme specificity and taxonomy. To contribute to the knowledge of unique sequence-structural features responsible for specific properties of amylolytic enzymes, especially with regard to their substrate preference and product profile, as well as to elucidating their evolution, will belong to the main goals of the PhD study. The results should also lead to establishing new enzyme subfamilies and assigning enzyme specificities for hypothetical proteins obtained from complete genomes sequencing. Protein design of amylolytic enzymes represents an additional possible use of achieved knowledge. The dissertation will be
carried out in the Laboratory of Protein Evolution (http://imb.savba.sk/~janecek/), which belongs to the world's leading workplaces involved in the study of amylolytic enzymes in the broadest sense. The PhD-study program also includes participation in a wide international co-operation with the possibility to travel for both short- and long-term stays to renowned laboratories abroad – in Europe and overseas, where it is possible to undertake the PhD-student's own experimental work in an effort to confirm the hypotheses from bioinformatics approaches to the study of amylolytic enzymes performed in the home Laboratory.
carried out in the Laboratory of Protein Evolution (http://imb.savba.sk/~janecek/), which belongs to the world's leading workplaces involved in the study of amylolytic enzymes in the broadest sense. The PhD-study program also includes participation in a wide international co-operation with the possibility to travel for both short- and long-term stays to renowned laboratories abroad – in Europe and overseas, where it is possible to undertake the PhD-student's own experimental work in an effort to confirm the hypotheses from bioinformatics approaches to the study of amylolytic enzymes performed in the home Laboratory.