Molecular modeling of substrate selectivity of Candida antarctica lipase B and Candida rugosa lipase towards c9, t11- and t10, c12-conjugated linoleic acid

Molecular modeling was used to clarify the mechanism of the selectivity of Candida antarctica lipase B and Candida rugosa lipase towards cis9, trans11 (c9, t11-) and trans10, cis12 (t10, c12-) conjugated linoleic acid. Hydrogen bonds network, substrate conformation, binding affinity and water molecules in the binding site were analyzed. Substrate conformation and binding affinity were not correlated with the experimental results of the substrate selectivity. On the contrary, better enzyme preference towards a substrate was correlated with two stronger hydrogen bonds (His-NɛH-Oa and His-NɛH-Ser-Oγ) and less water molecules between the substrate the binding pocket. Possible explanation of these was discussed.