Using chemical thermodynamics on networks to understand the universality of biological sugar-phosphate metabolism
| Project/Area Number |
22K03792
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Review Section |
Basic Section 17050:Biogeosciences-related
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| Research Institution | Tokyo Institute of Technology |
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Principal Investigator |
スミス エリック 東京工業大学, 地球生命研究所, 特任教授 (50770468)
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| Co-Investigator(Kenkyū-buntansha) |
Smith Harrison 東京工業大学, 地球生命研究所, 研究員 (50843934)
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| Project Period (FY) |
2022-04-01 – 2025-03-31
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| Project Status |
Granted (Fiscal Year 2022)
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| Budget Amount *help |
¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2024: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2023: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2022: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
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| Keywords | Chemical networks / Rule-based systems / Chemical graph grammars / Systems chemistry / Thermochemical databases / Sugar metabolism / Evolution optimization / Natural selection cost / computational chemistry |
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| Outline of Research at the Start |
The most basic features of life are conserved across all living systems. Many are pathways of core metabolism, which all other living processes require. We will use computational chemistry to understand how uncontrolled chemical networks arise in nature and the way pathways are selected from them.
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| Outline of Annual Research Achievements |
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.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
In January 2023, the architects of the MOD software platform for
graph-grammar computational chemistry, Jakob Andersen (U. Southern
Denmark) and Christoph Flamm (U. Vienna), were hosted for 10 days at
the Earth-Life Science Institute at Tokyo Institute of Technology to
work with PI Smith and Co-I Smith to design the fully-automated computational pipeline from graphical rules to thermochemical landscapes and kinetic models. The essential modules to interface the software MOD and eQuilibrator 3.0, and other thermochemical network packages including CHNOSZ, were specified as a process map. The four researchers now maintain monthly conference calls to implement these interface components in Python scripts that connect to the MOD, eQuilibrator 3.0, and CHNOSZ Application Programming Interfaces. All required software runs native on the researchers' personal computers.
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| Strategy for Future Research Activity |
Three publications are planned for submission in 2023. The first summarizes presents a theory of the dissipation and work relations on chemical networks derived from the topological properties of the networks, based on our automatically-generated sugar-phosphate chemistries. These relations are the input to understanding biological optimization of observed pathways under evolution. The second paper will analyze the universality of biological sugar-phosphate chemistry using the dissipation and work results currently derived. The third paper will be for computational chemists, presenting the high-throughput pipeline that combines graph-grammar and thermochemical database methods in high-throughput fashion.
As part of a collaboration with a PhD student of PI Smith in the US, we have also modeled the set of all autocatalytic cores in the sugar-phosphate system. In 2023 we will relate the subnetworks capable of autocatalytic self-amplification to our existing topological analysis of the basis of all cycles in that network.
Work has also begun with current colleagues in France and Austria to develop rules sets describing their experimental results on mechanisms of prebiotic carbon fixation, which was promised as the third, high-risk part of our project. We plan in 2023 to assemble those rules into networks like our existing network for sugar phosphate chemistry, and to compare energy flow paths in prebiotic chemistry and extant biochemistry. Those works will be compared with new results obtained within ELSI and JAMSTEC on carbon fixation through electrochemical mechanisms.
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Report
(1 results)
Research Products
(4 results)
