Genomics | Biocatalysis | Bioinformatics | Theory & Simulation
Automated analysis of enzyme reaction mechanisms
Syed Asad Rahman*, Gillleain Torrence, Franz Fenninger, Lorenzo Baldacci, Nimish Gopal, Gemma L Holliday, Janet M Thornton
*Corresponding author: Syed Asad Rahman
EMBL-EBI, Cambridge, UK
F1000Posters 2011, 2: 1349 (poster) [ENGLISH]
Poster [1.54 MB]
19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology 2011 (ISMB/ECCB), 17 - 19 Jul 2011, C07
Enzymes can be classified by the kind of chemical reactions they catalyze (e.g. The International Union of Biochemistry and Molecular Biology (IUBMB) enzyme classification). We present a novel method called “EC-BLAST” to search and compare enzymes based on chemical reactions.
This robust and efficient tool is based on an in-house algorithm. It computes atom-atom mapping between the reactant(s) and product(s) of a reaction and marks bond changes. A user can search similar enzymes based on the reactions’ substrate specificity, reaction centers and bond changes, or even a combination of these queries. The results are ranked based on a scoring function, highlighting the degree of conserved/variable regions between reactions. This information complements knowledge obtained from protein sequence/structure based studies. The knowledge of annotated reaction centers from the processed reactions can be used to predict the enzymes that can potentially transform or act on a query metabolite(s).
This tool will find application in various life science fields, and can be used to find alternate/missing enzymes in metabolic pathways, in drug discovery and toxicity based studies that not only require alternate pathways but also seek enzyme re-engineering. Additionally, it will help shed light on the evolutionary aspects of enzyme mechanisms. It can potentially provide a basic framework for both academic and industrial research and may eventually lead to a new classification system for enzymes.
No relevant conflicts of interest declared.
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