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A computational enzymatic optimization for fixing carbon dioxide to starch
- 1 Shanghai Pinghe Bilingual School
* Author to whom correspondence should be addressed.
Abstract
Carbon dioxide is fixed and processed into starch by the plants’ photosynthesis through complicated molecular pathways. While planting and cultivating crops are the major ways to harvest starch, an artificial anabolic pathway has recently been realized in China. Traditional crop production demands extended harvest periods, extensive land, and substantial water use. In contrast, the artificial pathway enhances starch synthesis efficiently, using fewer resources for a more sustainable approach. In 2021, Chinese researchers reported the anabolic starch artificial pathway (ASAP) to synthesize starch in vitro. Although the previous research established a milestone, steps need to be optimized. In this work, enzymatic starch synthesis is chosen to be further engineered, building mutants with similar catalytic functions. Computational tools are used to build an iterative docking-mutating simulation (IDMS). It can automatically finish the cycle of protein mutations and docking. Autodock and Rosetta are used in the coding. 445 different protein mutants are generated and analyzed in silico, among which the best five were chosen for experimental investigation. In the experimental analysis, mutant E shows nearly the same catalytic efficiency as the wild-type in the first hour, with a 2.5-fold expression rate.
Keywords
Protein engineering, Computational biology, Starch synthesis
[1]. IPCC. IPCC, 2022: Summary for Policy Makers.; 2022.
[2]. The State of Food Security and Nutrition in the World 2022.; 2022. doi:10.4060/cc0639en
[3]. Worldbank. Climate Explainer: Food Security and Climate Change. worldbank.org.
[4]. Schwander T, Von Borzyskowski LS, Burgener S, Cortina NS, Erb TJ. A synthetic pathway for the fixation of carbon dioxide in vitro. Science (1979). 2016;354(6314). doi:10.1126/science.aah5237
[5]. Korman TP, Opgenorth PH, Bowie JU. A synthetic biochemistry platform for cell free production of monoterpenes from glucose. Nat Commun. 2017;8. doi:10.1038/ncomms15526
[6]. Miller TE, Beneyton T, Schwander T, et al. Light-powered CO2 fixation in a chloroplast mimic with natural and synthetic parts. Science (1979). 2020;368(6491). doi:10.1126/science.aaz6802
[7]. Satanowski A, Dronsella B, Noor E, et al. Awakening a latent carbon fixation cycle in Escherichia coli. Nat Commun. 2020;11(1). doi:10.1038/s41467-020-19564-5
[8]. Cai T, Sun H, Qiao J, et al. Cell-free chemoenzymatic starch synthesis from carbon dioxide. Science (1979). 2021;373(6562). doi:10.1126/science.abh4049
[9]. Sheng F, Jia X, Yep A, Preiss J, Geiger JH. The crystal structures of the open and catalytically competent closed conformation of Escherichia coli glycogen synthase. Journal of Biological Chemistry. 2009;284(26). doi:10.1074/jbc.M809804200
[10]. Steiner K, Schwab H. Recent advances in rational approaches for enzyme engineering. Comput Struct Biotechnol J. 2012;2(3). doi:10.5936/csbj.201209010
[11]. DeLano WL. The PyMOL Molecular Graphics System, Version 2.3. Schrödinger LLC. Published online 2020.
[12]. Pettersen EF, Goddard TD, Huang CC, et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Science. 2021;30(1). doi:10.1002/pro.3943
[13]. Adasme MF, Linnemann KL, Bolz SN, et al. PLIP 2021: Expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucleic Acids Res. 2021;49(W1). doi:10.1093/nar/gkab294
[14]. Stourac J, Vavra O, Kokkonen P, et al. Caver Web 1.0: Identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic Acids Res. 2019;47(W1). doi:10.1093/nar/gkz378
[15]. Ashkenazy H, Abadi S, Martz E, et al. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res. 2016;44(W1). doi:10.1093/NAR/GKW408
[16]. Eberhardt J, Santos-Martins D, Tillack AF, Forli S. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. J Chem Inf Model. 2021;61(8). doi:10.1021/acs.jcim.1c00203
[17]. Trott O, Olson AJ. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. Published online 2009. doi:10.1002/jcc.21334
[18]. Chowdhury R, Grisewood MJ, Boorla VS, Yan Q, Pfleger BF, Maranas CD. IPRO+/−: Computational Protein Design Tool Allowing for Insertions and Deletions. Structure. 2020;28(12). doi:10.1016/j.str.2020.08.003
[19]. Podgornaia AI, Laub MT. Pervasive degeneracy and epistasis in a protein-protein interface. Science (1979). 2015;347(6222). doi:10.1126/science.1257360 t and unwavering guidance on the underlying theories that formed the foundation of this research.
Cite this article
Gao,R. (2024). A computational enzymatic optimization for fixing carbon dioxide to starch. Applied and Computational Engineering,63,90-99.
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The datasets used and/or analyzed during the current study will be available from the authors upon reasonable request.
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Volume title: Proceedings of the 4th International Conference on Materials Chemistry and Environmental Engineering
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