Passive membrane transport of lignin-related compounds.
Josh V. Vermaas,Richard A. Dixon,Fang Chen,Shawn D. Mansfield,Wout Boerjan,John Ralph,Michael F. Crowley,Gregg T. Beckham +7 more
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It is predicted that passive transport processes in plants and bacteria for uncharged aromatic compounds are likely sufficient for lignin biosynthesis and catabolism, thus implying that membrane translocation rates are controlled by compound delivery and utilization rates and membrane concentration gradients.Citations
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The Plant Cell Wall: Biosynthesis, construction, and functions.
TL;DR: The use of cutting-edge technologies such as single-molecule imaging, nuclear magnetic resonance spectroscopy, and atomic force microscopy has provided much insight into the plant cell wall as an intricate nanoscale network, opening up unprecedented possibilities for cell wall research.
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A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion.
Sam J. B. Mallinson,Melodie M. Machovina,Melodie M. Machovina,Rodrigo L. Silveira,Rodrigo L. Silveira,Marc Garcia-Borràs,Nathan M. Gallup,Nathan M. Gallup,Christopher W. Johnson,Mark D. Allen,Munir S. Skaf,Michael F. Crowley,Ellen L. Neidle,Kendall N. Houk,Gregg T. Beckham,Jennifer L. DuBois,John McGeehan +16 more
TL;DR: The authors present the structures of GcoA and GcoB, a cytochrome P450-reductase pair that catalyzes aryl-O-demethylations and show that G coA displays broad substrate specificity, which is of interest for biotechnology applications.
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Lignin biosynthesis: old roads revisited and new roads explored
TL;DR: Several hypothetical models are presented based primarily on studies in model systems, which may or may not reflect the major lignification process in forest trees.
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Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440
Davinia Salvachúa,Davinia Salvachúa,Allison Z. Werner,Allison Z. Werner,Isabel Pardo,Martyna Michalska,Brenna A. Black,Bryon S. Donohoe,Stefan J. Haugen,Rui Katahira,Sandra Notonier,Sandra Notonier,Kelsey J. Ramirez,Antonella Amore,Samuel O. Purvine,Erika M. Zink,Paul E. Abraham,Richard J. Giannone,Suresh Poudel,Philip D. Laible,Robert L. Hettich,Gregg T. Beckham,Gregg T. Beckham +22 more
TL;DR: This work proposes a mechanism for extracellular nutrient acquisition from aromatic compounds by soil bacteria, which holds promise for improving the efficiency of microbial lignin conversion and suggests that OMVs could potentially be useful tools for synthetic biology and biotechnological applications.
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Distribution, mobility, and anchoring of lignin-related oxidative enzymes in Arabidopsis secondary cell walls.
Eva Yi Chou,Mathias Schuetz,Natalie Hoffmann,Yoichiro Watanabe,Richard Sibout,Richard Sibout,A. Lacey Samuels +6 more
TL;DR: Laccases and peroxidases localize to different wall domains in Arabidopsis stems, providing a mechanism for spatial control of lignification.
References
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Scalable molecular dynamics with NAMD
James C. Phillips,Rosemary Braun,Wei Wang,James C. Gumbart,Emad Tajkhorshid,Elizabeth Villa,Christophe Chipot,Robert D. Skeel,Laxmikant V. Kale,Klaus Schulten +9 more
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Journal ArticleDOI
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
Mark Abraham,Teemu Murtola,Roland Schulz,Roland Schulz,Szilárd Páll,Jeremy C. Smith,Jeremy C. Smith,Berk Hess,Erik Lindahl,Erik Lindahl +9 more
TL;DR: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules, and provides a rich set of calculation types.
Journal ArticleDOI
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.
Kenno Vanommeslaeghe,Elizabeth Hatcher,Chayan Acharya,Sibsankar Kundu,Shijun Zhong,Jihyun Shim,Eva Darian,Olgun Guvench,Pedro E. M. Lopes,Igor Vorobyov,Alexander D. MacKerell +10 more
TL;DR: An extension of the CHARMM force field to drug‐like molecules is presented, making it possible to perform “all‐CHARMM” simulations on drug‐target interactions thereby extending the utility ofCHARMM force fields to medicinally relevant systems.
Journal ArticleDOI
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
Jeffery B. Klauda,Richard M. Venable,J. Alfredo Freites,Joseph W. O’Connor,Douglas J. Tobias,Carlos Mondragon-Ramirez,Igor Vorobyov,Alexander D. MacKerell,Richard W. Pastor +8 more
TL;DR: The presented lipid FF is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains and is anticipated to be of utility for simulations of pure lipid systems as well as heterogeneous systems including membrane proteins.