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United States Department of Agriculture

Agricultural Research Service

Lignin Models
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Downloadables:
Annual Reviews in Plant Biology Supplimentary material for "Lignin Biosythesis" review, Annual Reviews in Plant Biology 54, 519-546 (2003).

The structures were constructed based loosely on data from NMR spectra (the HMQC experiment of which is available from the sidebar) described in the following references.
• Marita JM, Ralph J, Lapierre C, Jouanin L, Boerjan W. 2001. NMR characterization of lignins from transgenic poplars with suppressed caffeic acid O-methyltransferase activity. J. Chem. Soc., Perkin Trans. 1: 2939-45.
• Ralph J, Lapierre C, Marita J, Kim H, Lu F, Hatfield RD, Ralph SA, Chapple C, Franke R, Hemm MR, Van Doorsselaere J, Sederoff RR, O'Malley DM, Scott JT, MacKay JJ, Yahiaoui N, Boudet A-M, Pean M, Pilate G, Jouanin L, Boerjan W. 2001. Elucidation of new structures in lignins of CAD- and COMT-deficient plants by NMR. Phytochem. 57: 993-1003.

For details on interunit frequencies and 2D structures of each of these lignins, please download the .pdf file from the sidebar.

Notes
1. The colors of contours in the NMR spectra and of the groups in the jpeg stills and the 3D ViewerLite (.msv) files are similar. This way it is readily seen in the NMR spectra and in the models that, for example, the beta-ether units A (cyan) are prevalent in the wild-type lignins, but less prevalent in the COMT-deficient lignin. Since it is only these units that cleave by thioacidolysis, DFRC, or in pulping reactions, it is clear why the COMT-deficient lignin is less easily degraded. The new benzodioxane units J in the COMT-deficient lignin are colored red (in the NMR and in the models). The branch points (4-O-5 units E, orange; dibenzodioxocin units D2, dark blue) are also easily identified in the Models.
2. The wild type has only a single branchpoint (4-O-5); the COMT-deficient has two (a 4-O-5 again, and now a dibenzodioxocin, due to its higher guaiacyl content, as revealed by the NMR). Branchpoints provide the only deviation from “linear” structures.
3. The structures represent only 1 of many millions of isomers. For the wild type, there are 38 optical centers leading to 238 potential optical isomers and one half that number of physically distinct isomers. However, the relative stereochemistries of 3 pairs of centers are fixed (e.g. trans-ring junctions in phenylcoumarans). We calculate that there are 235 optical isomers and therefore 234 (17,179,869,184) real viable isomers for the structure shown. Similarly, the COMT-deficient model has 228 (constrained) optical isomers and therefore 227 (134,217,728) physically distinct isomers. Note that providing more rings with stereochemical constraints dramatically reduces the number of isomers, but that this simple 20-mer still has over 134 million possible isomers, only one of which is modeled here. {This is provided to emphasize that their racemic nature alone confers incredible complexity and variability on polymeric lignins}.
4. The structures have been minimized in place, but it must be emphasized that each unit is probably just a local minimum – full optimization over all conformational space in a molecule of this size is impractical. It is ONLY A MODEL!

Acknowledgements:
These models are derived from data in the papers mentioned above, and based on Brunow's softwood lignin model (in Biopolymers. 2001, Vol 1, pp 89-116). In addition, special thanks to Jane Marita for determining this data, to Tom Elder (Auburn University) and Ray Fort (U. Maine) for discussion and for alerting us to the Accelrys ViewLite program – the only one we currently know of that will allow us to color-code the lignin units, and to Bill Lindmeier for arranging this web page. This webpage was to accompany a review article for Annual Reviews in Plant Biology "Lignin Biosynthesis" by Marie Baucher, John Ralph and Wont Boerjan, 2002, in preperation

Models

All Viewers:
WT Poplar MWL.pdb
Poplar sense-COMT MWL.pdb
ViewerLite Models:
WT Poplar MWL color.msv
Poplar sense-COMT MWL color.msv

Windows Users:
Download Accelrys' free ViewerLite to view the any of the models.*

Macintosh:
Download the RasMol Viewer, or if you are using Virtual PC, ViewerLite is Higly reccomended.*

Images
Click on the thumbnail for large scale images (~100k)


Poplar-WT-surface

Poplar-WT-stick

Poplar-COMT-surface

Poplar-COMT-stick

Acrobat Files

2D NMR Spectra


Poplar Lignin Models
This file contains the images and data contained on this page.

*Other viewers will display the PDB files correctly, but only ViewerLite will have the lignin subunits color coded.


Last Modified: 12/6/2011