Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis
Name
LIGNIN-KMC__A_Toolkit_for_Simulating_Lignin_Biosynthesis_v1.pdf
Description
Submitted version
Size
1.05 MB
Format
Adobe PDF
Checksum (MD5)
97b1f6315ce5bd0d328ef8166b15f856
Author(s)
Orella, Michael J
Gani, Terry ZH
Vermaas, Josh V
Stone, Michael L
Anderson, Eric M
Beckham, Gregg T
Brushett, Fikile R
Román-Leshkov, Yuriy
Date Issued
2019
Journal
ACS Sustainable Chemistry & Engineering
Publisher
American Chemical Society (ACS)
Version
Original manuscript
Abstract
© 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.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
Terms of Use
Creative Commons Attribution-Noncommercial-Share Alike
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1021/ACSSUSCHEMENG.9B03534
