Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis
© 2019 American Chemical Society. Lignin is an abundant biopolymer of phenylpropanoid monomers that is critical for plant structure and function. Based on the abundance of lignin in the biosphere and interest in lignin valorization, a more comprehensive understanding of lignin biosynthesis is impera...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Chemical Society (ACS)
2021
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| Online Access: | https://hdl.handle.net/1721.1/136531 |
| _version_ | 1811096198676742144 |
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| author | Orella, Michael J Gani, Terry ZH Vermaas, Josh V Stone, Michael L Anderson, Eric M Beckham, Gregg T Brushett, Fikile R Román-Leshkov, Yuriy |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Orella, Michael J Gani, Terry ZH Vermaas, Josh V Stone, Michael L Anderson, Eric M Beckham, Gregg T Brushett, Fikile R Román-Leshkov, Yuriy |
| author_sort | Orella, Michael J |
| collection | MIT |
| description | © 2019 American Chemical Society. Lignin is an abundant biopolymer of phenylpropanoid monomers that is critical for plant structure and function. Based on the abundance of lignin in the biosphere and interest in lignin valorization, a more comprehensive understanding of lignin biosynthesis is imperative. Here, we present an open-source software toolkit, Lignin-KMC, that combines kinetic Monte Carlo and first-principles calculations of radical coupling events to model lignin biosynthesis in silico. Lignification is simulated using the Gillespie algorithm with rates derived from density functional theory calculations of individual fragment couplings. Using this approach, we confirm experimental findings regarding the impact of lignification conditions on the polymer structure such as (1) the positive correlation between sinapyl alcohol fraction and depolymerization yield and (2) the primarily benzodioxane linked structure of C-lignin. Additionally, we identify the in planta monolignol supply rate as a possible control mechanism for lignin biosynthesis based on evolutionary stresses. These examples not only highlight the robustness of our modeling framework but also motivate future studies of new lignin types, unexplored monolignol chemistries, and lignin structure predictions, all with an overarching aim of developing a more comprehensive molecular understanding of native lignin, which, in turn, can advance the biological and chemistry communities interested in this important biopolymer. |
| first_indexed | 2024-09-23T16:40:09Z |
| format | Article |
| id | mit-1721.1/136531 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T16:40:09Z |
| publishDate | 2021 |
| publisher | American Chemical Society (ACS) |
| record_format | dspace |
| spelling | mit-1721.1/1365312023-12-06T18:15:57Z Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis Orella, Michael J Gani, Terry ZH Vermaas, Josh V Stone, Michael L Anderson, Eric M Beckham, Gregg T Brushett, Fikile R Román-Leshkov, Yuriy Massachusetts Institute of Technology. Department of Chemical Engineering © 2019 American Chemical Society. Lignin is an abundant biopolymer of phenylpropanoid monomers that is critical for plant structure and function. Based on the abundance of lignin in the biosphere and interest in lignin valorization, a more comprehensive understanding of lignin biosynthesis is imperative. Here, we present an open-source software toolkit, Lignin-KMC, that combines kinetic Monte Carlo and first-principles calculations of radical coupling events to model lignin biosynthesis in silico. Lignification is simulated using the Gillespie algorithm with rates derived from density functional theory calculations of individual fragment couplings. Using this approach, we confirm experimental findings regarding the impact of lignification conditions on the polymer structure such as (1) the positive correlation between sinapyl alcohol fraction and depolymerization yield and (2) the primarily benzodioxane linked structure of C-lignin. Additionally, we identify the in planta monolignol supply rate as a possible control mechanism for lignin biosynthesis based on evolutionary stresses. These examples not only highlight the robustness of our modeling framework but also motivate future studies of new lignin types, unexplored monolignol chemistries, and lignin structure predictions, all with an overarching aim of developing a more comprehensive molecular understanding of native lignin, which, in turn, can advance the biological and chemistry communities interested in this important biopolymer. 2021-10-27T20:35:48Z 2021-10-27T20:35:48Z 2019 2021-06-09T15:00:28Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/136531 en 10.1021/ACSSUSCHEMENG.9B03534 ACS Sustainable Chemistry & Engineering Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf American Chemical Society (ACS) Other repository |
| spellingShingle | Orella, Michael J Gani, Terry ZH Vermaas, Josh V Stone, Michael L Anderson, Eric M Beckham, Gregg T Brushett, Fikile R Román-Leshkov, Yuriy Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis |
| title | Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis |
| title_full | Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis |
| title_fullStr | Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis |
| title_full_unstemmed | Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis |
| title_short | Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis |
| title_sort | lignin kmc a toolkit for simulating lignin biosynthesis |
| url | https://hdl.handle.net/1721.1/136531 |
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