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Molecular basis of P450 OleTJE: an investigation of substrate binding mechanism and major pathways

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Abstract

Cytochrome P450 OleTJE has attracted much attention for its ability to catalyze the decarboxylation of long chain fatty acids to generate alkenes, which are not only biofuel molecule, but also can be used broadly for making lubricants, polymers and detergents. In this study, the molecular basis of the binding mechanism of P450 OleTJE for arachidic acid, myristic acid, and caprylic acid was investigated by utilizing conventional molecular dynamics simulation and binding free energy calculations. Moreover, random acceleration molecular dynamics (RAMD) simulations were performed to uncover the most probable access/egress channels for different fatty acids. The predicted binding free energy shows an order of arachidic acid < myristic acid < caprylic acid. Key residues interacting with three substrates and residues specifically binding to one of them were identified. The RAMD results suggest the most likely channel for arachidic acid, myristic acid, and caprylic acid are 2e/2b, 2a and 2f/2a, respectively. It is suggested that the reaction is easier to carry out in myristic acid bound system than those in arachidic acid and caprylic acid bound system based on the distance of Hβ atom of substrate relative to P450 OleTJE Compound I states. This study provided novel insight to understand the substrate preference mechanism of P450 OleTJE and valuable information for rational enzyme design for short chain fatty acid decarboxylation.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (Grant Nos. 31300599, 21572242), the Talents of High Level Scientific Research Foundation (Grant Nos. 6631113318, 6631113326) and Initial Foundation for Doctors (Grant No. 6631112308) of Qingdao Agricultural University and the Natural Science Foundation of Shandong Province, China (Grant No. ZR2015BM021).

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Authors and Affiliations

  1. Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China

    Juan Du, Lin Liu, Li Zhong Guo & Jian Ming Yang

  2. College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China

    Xiao Jun Yao

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  1. Juan Du
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Correspondence to Jian Ming Yang.

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Du, J., Liu, L., Guo, L.Z. et al. Molecular basis of P450 OleTJE: an investigation of substrate binding mechanism and major pathways. J Comput Aided Mol Des 31, 483–495 (2017). https://doi.org/10.1007/s10822-017-0013-x

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