Development of a systematic methodology to identify enzyme candidates to synthesize carbon monomers = 대사 네트워크에서의 탄소 모노머 합성을 위한 새로운 효소 가능 후보군을 제안하는 시스템 방법론 개발

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There have been several methods developed for the prediction of synthetic metabolic pathways leading to the production of desired chemicals. In these approaches, novel pathways were predicted based on chemical structure changes, enzymatic information, and/or reaction mechanisms, but the approaches generating a huge number of predicted results are difficult to be applied to real experiments. Also, some of these methods focus on specific pathways, and thus are limited to expansion to the whole metabolism. In the present study, we propose a system framework employing a retrosynthesis model with a prioritization scoring algorithm. This new strategy allows deducing the novel promising pathways for the synthesis of a desired chemical together with information on enzymes involved based on structural changes and reaction mechanisms present in the system database. The prioritization scoring algorithm employing Tanimoto coefficient and group contribution method allows examination of structurally qualified pathways to recognize which pathway is more appropriate. In addition, new concepts of binding site covalence, estimation of pathway distance and organism specificity were taken into account to identify the best synthetic pathway. Parameters of these factors are evolutionarily optimized when a newly proven synthetic pathway is registered. In order to show the applicability of the proposed system framework, the novel synthetic pathways for the production of isobutanol, 3-hydroxypropionate, and butyryl-CoA were predicted. The prediction results show that experimentally verified synthetic pathways were listed within the top 0.089% of the identified pathway candidates in all three test cases. It is expected that the systematical approach and framework developed in this study would be useful for the $\It{in silico}$ design of novel metabolic pathways to be employed for the efficient production of chemicals, fuels, and materials.
Park, Sun-Wonresearcher박선원researcher
한국과학기술원 : 생명화학공학과,
Issue Date
455377/325007  / 020057576

학위논문(박사) - 한국과학기술원 : 생명화학공학과, 2010.08, [ viii, 86 p. ]


대사 공학; 합성 생물학; 시스템 생물학; 대사 경로 합성; Pathway Synthesis; Metabolic Engineering; Synthetic Biology; Systems Biology

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