Using chemical thermodynamics on networks to understand the universality of biological sugar-phosphate metabolism

利用网络化学热力学来理解生物糖磷酸代谢的普遍性

• 批准号: 22K03792
• 负责人: スミス エリック
• 金额: $ 1万
• 依托单位: Tokyo Institute of Technology
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2022
• 资助国家: 日本
• 起止时间: 2022-04-01 至 2025-03-31
• 项目状态: 未结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22K03792/
• 关键词: Chemical networks; Rule-based systems; Chemical graph grammars; Systems chemistry; Thermochemical databases; Sugar metabolism; Evolution optimization; Natural selection cost; computational chemistry

We demonstrated a partly-automated computational model that converts five simple reaction mechanisms for sugar-phosphate molecules into a list of all possible chemical solutions to the conversion problem of the Pentose Phosphate Pathway. We coupled the automatically-generated list of compounds to extraction of thermochemical data using the SMILES molecules representation as input to the eQuilibrator 3.0 Application Programming Interface. The output data are group-contribution estimates for molecular free energy, and are also automated and can be arbitrarily large. Only our transfer of SMILES representation from the output of the graph-chemistry language MOD to eQuilibrator has been done manually.We analyzed the topology of the chemical reaction network and proved that all possible pathways for the same transformation are constructed from a finite basis of circulations that can be constructed from symmetry rules. We used the thermochemical data on this network to study the transduction of chemical work, and to define an evolutionary cost function for any pathway. Results were reported by the PI in two invited presentations: "Combinatorics in evolution: From rule-based systems to the thermodynamics of selectivities" at the American Physical Society March meeting in Chicago (https://meetings.aps.org/Meeting/MAR22/Session/K04.1 ), and "Combinatorial Chemistry with Rule-Based Systems and its Associated Information Theory" in Sofia Bulgaria (http://physicsoflivingsystems.org/events/workshop-life-in-the-universe/ ), partly sponsored by the U.S. National Science Foundation.

我们演示了一个半自动化的计算模型，该模型将糖磷酸分子的五种简单反应机制转换为戊糖磷酸途径转换问题的所有可能化学解决方案的列表。 我们使用 SMILES 分子表示作为 eQuilibrator 3.0 应用程序编程接口的输入，将自动生成的化合物列表与热化学数据的提取相结合。 输出数据是分子自由能的群体贡献估计，并且也是自动化的并且可以任意大。 只是我们将 SMILES 表示从图形化学语言 MOD 的输出转移到 eQuilibrator 是手动完成的。我们分析了化学反应网络的拓扑结构，并证明同一转换的所有可能路径都是从有限的循环基础构建的，而循环的有限基础可以根据对称规则构建。 我们使用该网络上的热化学数据来研究化学功的转导，并定义任何途径的进化成本函数。 PI 在两场受邀演讲中报告了结果：在芝加哥举行的美国物理学会 3 月会议上的“进化中的组合学：从基于规则的系统到选择性热力学”(https://meetings.aps.org/Meeting/MAR22/Session/K04.1)，以及在保加利亚索非亚举行的“基于规则的系统的组合化学及其相关信息理论” (http://physicalsoflivingsystems.org/events/workshop-life-in-the-universe/)，部分由美国国家科学基金会赞助。