Resolving Free-Energy Contributions of Substrate Delivery to Desaturase by Atomistic Simulations

Abstract

The plant acyl-acyl carrier protein (ACP) desaturases are a family of soluble enzymes that convert saturated fatty-acyl ACPs into their cis-monounsaturated equivalents in an oxygen-dependent reaction. These enzymes play a key role in biosynthesis of mono-unsaturated fatty acids in plants. The archetype of this group is the ▵9-18:0-ACP desaturase that introduces a cis double bond between carbons 9 and 10 to produce oleoyl-ACP. ACPs are central proteins in the fatty acid biosynthesis that deliver the substrate to the desaturase. They have been reported to show a varying degree of local dynamics and structural variability depending on the substrate length. It has been suggested that the substrate specific change in structure and dynamics is crucial for the decreasing enzymatic activity in the case of the ▵9-desaturase for chains length shorter than 18. We investigated the solution structure and dynamics of ACP with four different substrate lengths (10, 14, 16, and 18) based on published NMR solution structures using extensive all atom molecular dynamics simulations. Umbrella sampling and replica exchange dynamics simulations highlight the chain length depend free energy of substrate binding and chain length depended binding motifs. This suggests that longer substrates have a lower binding energy, but also a much larger ensemble of structures that are accessible. Thereby estimating the effect on changes in the binding affinity of the substrate bound Acyl carrier protein to the ▵9-desaturase will not be able without taking into account the Enzyme itself.