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bioRxiv · 10.1101/2023.08.17.553759

Data-Driven Modeling and Analysis of Fatty Acid Desaturase in Plants

McNaughton, A. D.·Shanklin, J.·Raugei, S.·Kumar, N.
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Abstract

Fatty acids and their derivatives continue to garner attention as sustainable alternatives to petrochemically derived materials. Towards this goal, we examine the plant membrane-bound fatty acid desaturases (FADs) and develop an overview of their 3D structure and phylogenic relationships. Through this effort we developed two plant fatty acid desaturase homology models that we analyzed with substrate docking and molecular dynamics simulations to better understand the diiron binding pocket that is characteristic of these proteins. The comparison between the Omega6 and Delta12 homology models specifically in regards to the binding affinity as a function of carbon chain length indicates that there is a dip in binding affinity near the 18:2 carbon chain length but the rest maintain a rather consistent binding affinity throughout. Furthermore, MD analysis highlights the importance of regions within the cytosolic cap domain on the binding pocket. PACS: 0000, 1111 2000 MSC: 0000, 1111 Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/553759v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1674c18org.highwire.dtl.DTLVardef@b4e775org.highwire.dtl.DTLVardef@c7ec21org.highwire.dtl.DTLVardef@15fa66c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDeveloped pipeline to predict function from protein sequence C_LIO_LIModeled two fatty acid desaturases and predicted their structure and functions C_LIO_LILeveraged docking simulations and molecular dynamics to confirm protein function C_LI

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McNaughton, A. D., Shanklin, J., Raugei, S., Kumar, N.. 2023-08-17. Data-Driven Modeling and Analysis of Fatty Acid Desaturase in Plants. https://doi.org/10.1101/2023.08.17.553759

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