Computational design of 5-carboxyl-2-pentenoyl-CoA reductase from Thermobifida fusca to enhance adipic acid production
YANG Ju1, MAO Yin1, HUANG Xiaoqiang2, ZHOU Shenghu1, DENG Yu1*
1(School of Bioengineering,Jiangnan University,Wuxi 214122,China) 2(Department of Computational Medicine & Bioinformatics,University of Michigan,Ann Arbor 48109,USA)
Abstract: In order to enhance the biosynthesis of adipic acid, the active pocket of 5-carboxy-2-pentenoyl-CoA reductase was modified using computational enzyme design.Based on the substrate binding model,fourteen residues including Ser 88,Leu 89,Ile 90,Pro 91,Ala 92,Val 93,Lys 95,Leu 96,Thr 161,Thr 246,Thr 249,Ile 250,Gln 253 and Tyr 367 were designed to improve the combination between the enzyme and 5-carboxy-2-pentenoyl-CoA and the catalytic activity of 5-carboxy-2-pentenoyl-CoA reductase by introducing hydrogen bonds network.In the 10 designs (Des0-Des9), the carboxyl of 5-carboxy-2-pentenoyl-CoA could form hydrogen bonds with Gln253Arg and Ile250Gln in Des0, Des3, Des4 and Des9.And Gln253Arg could form hydrogen bonds with Leu89Ser (Des0 and Des9) or Leu89Thr (Des3 and Des4) with Thr364.In order to test these designs, the stability of hydrogen bonds were analyzed by molecular dynamics simulation.The results showed that the four hydrogen bonds designed in Des0 were stable during the process of 16 ns molecular dynamics simulation.It indicated that Des0 may have a strong binding effect with 5-carboxy-2-pentenoyl-CoA.Accordingly, we speculated that Des0 could improve the catalytic activity of 5-carboxy-2-pentenoyl-CoA reductase, which should be verified by subsequent experiments.
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2021, Vol. 47 
