Master Thesis Defense: Onur Yükselen
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  • Master Thesis Defense: Onur Yükselen

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COMBINING IN SILICO DOCKING AND MOLECULAR DYNAMICS SIMULATIONS TO PREDICT THE IMPACT OF MUTATIONS ON THE SUBSTRATE SPECIFICITY OF BTL2 LIPASE

 

Onur Yükselen

 

Biological Sciences and Bioengineering, MSc Program, 2012

 

Thesis Jury

Assoc. Prof. Uğur Osman Sezerman (Thesis Supervisor), Assoc. Prof. Batu Erman, Assoc. Prof. Devrim Gözüaçık, Assoc. Prof. Levent Öztürk, Prof. Dr. Canan Atılgan

Date &Time: July 24th, 2012 – 14:30

Place: FENS G029

 

 

Keywords: Molecular dynamics, docking, scoring function, BTL2, Bacillus thermocatenulatus, lipase, specific activity, mutation, specificity, triglycerides

 

Abstract

 

Lipases are enzymes that hydrolyze the ester bond between acyl groups and glycerol in triacylglycerides which gives the products of glycerol and fatty acids. Bacillus thermocatenulatus lipase (BTL2) has shown highest activity toward tributyrin (C4) as substrate. Whilebroad selectivity on the chain length of the fatty acids has a key role in waste water treatment, and laundry formulations; short chain length specificity can be used in the food and cosmetic industry. In order to predict its chain length substrate specificity (tributyrin (C4)/tricaprylin (C8)) upon mutation, we developed a scoring function which combines in silico docking and molecular dynamics tools. After calibration on experimentally validated mutants, our scoring function is able to discriminate substrates specificities and predict the impact of a mutation (whether it enhances or reduces) in a rapid and accurate manner (overall correlation r=0.7930, p=0.0007). Also ranking of substrate specificities within the mutants were 100% correct. This method can be powerfully adapted to other protein families to predict the effect of a mutation for the one specific substrate or multiple substrates.