Summary: The interaction between xylan and cellulose microfibrils is important for secondary cell wall properties in vascular plants; however, the molecular arrangement of xylan in the cell wall and the nature of the molecular bonding between the polysaccharides are unknown. In dicots, the xylan backbone of β‐(1,4)‐linked xylosyl residues is decorated by occasional glucuronic acid, and approximately one‐half of the xylosyl residues are O‐acetylated at C‐2 or C‐3. We recently proposed that the even, periodic spacing of GlcA residues in the major domain of dicot xylan might allow the xylan backbone to fold as a twofold helical screw to facilitate alignment along, and stable interaction with, cellulose fibrils; however, such an interaction might be adversely impacted by random acetylation of the xylan backbone. Here, we investigated the arrangement of acetyl residues in Arabidopsis xylan using mass spectrometry and NMR. Alternate xylosyl residues along the backbone are acetylated. Using molecular dynamics simulation, we found that a twofold helical screw conformation of xylan is stable in interactions with both hydrophilic and hydrophobic cellulose faces. Tight docking of xylan on the hydrophilic faces is feasible only for xylan decorated on alternate residues and folded as a twofold helical screw. The findings suggest an explanation for the importance of acetylation for xylan–cellulose interactions, and also have implications for our understanding of cell wall molecular architecture and properties, and biological degradation by pathogens and fungi. They will also impact strategies to improve lignocellulose processing for biorefining and bioenergy.

Cellulose‐builder is a user‐friendly program that builds crystalline structures of cellulose of different sizes and geometries. The program generates Cartesian coordinates for all atoms of the specified structure in the Protein Data Bank format, suitable for using as starting configurations in molecular dynamics simulations and other calculations. Crystalline structures of cellulose polymorphs Iα, Iβ, II, and III_I of practically any size are readily constructed which includes parallelepipeds, plant cell wall cellulose elementary fibrils of any length, and monolayers. Periodic boundary conditions along the crystallographic directions are easily imposed. The program also generates atom connectivity file in PSF format, required by well‐known simulation packages such as NAMD, CHARMM, and others. Cellulose‐builder is based on the Bash programming language and should run on practically any Unix‐like platform, demands very modest hardware, and is freely available for download from ftp://ftp.iqm.unicamp.br/pub/cellulose‐builder.

Microbial aromatic catabolism offers a promising approach to convert lignin, a vast source of renewable carbon, into useful products. Aryl-O-demethylation is an essential biochemical reaction to ultimately catabolize coniferyl and sinapyl lignin-derived aromatic compounds, and is often a key bottleneck for both native and engineered bioconversion pathways. Here, we report the comprehensive characterization of a promiscuous P450 aryl-O-demethylase, consisting of a cytochrome P450 protein from the family CYP255A (GcoA) and a three-domain reductase (GcoB) that together represent a new two-component P450 class. Though originally described as converting guaiacol to catechol, we show that this system efficiently demethylates both guaiacol and an unexpectedly wide variety of lignin-relevant monomers. Structural, biochemical, and computational studies of this novel two-component system elucidate the mechanism of its broad substrate specificity, presenting it as a new tool for a critical step in biological lignin conversion.

Thiazolidinediones (TZDs) act through peroxisome proliferator activated receptor (PPAR) γ to increase insulin sensitivity in type 2 diabetes (T2DM), but deleterious effects of these ligands mean that selective modulators with improved clinical profiles are needed. We obtained a crystal structure of PPARγ ligand binding domain (LBD) and found that the ligand binding pocket (LBP) is occupied by bacterial medium chain fatty acids (MCFAs). We verified that MCFAs (C8–C10) bind the PPARγ LBD in vitro and showed that they are low-potency partial agonists that display assay-specific actions relative to TZDs; they act as very weak partial agonists in transfections with PPARγ LBD, stronger partial agonists with full length PPARγ and exhibit full blockade of PPARγ phosphorylation by cyclin-dependent kinase 5 (cdk5), linked to reversal of adipose tissue insulin resistance. MCFAs that bind PPARγ also antagonize TZD-dependent adipogenesis in vitro. X-ray structure B-factor analysis and molecular dynamics (MD) simulations suggest that MCFAs weakly stabilize C-terminal activation helix (H) 12 relative to TZDs and this effect is highly dependent on chain length. By contrast, MCFAs preferentially stabilize the H2-H3/β-sheet region and the helix (H) 11-H12 loop relative to TZDs and we propose that MCFA assay-specific actions are linked to their unique binding mode and suggest that it may be possible to identify selective PPARγ modulators with useful clinical profiles among natural products.

A molecular dynamics simulation study of the local structures and H-bond distribution for water–dimethyl sulfoxide (DMSO) mixtures over the entire composition range is presented. Analysis of several site-site pair distribution functions reveals that two well-defined kinds of aggregates characterize the molecular association between water and DMSO in solution. One of them, already identified through recent neutron diffraction experiments and computer simulations, consists of two water molecules H-bonded to the oxygen atom of a DMSO molecule, such that the angle between the two H-bonds is nearly tetrahedral. The other complex features a central water molecule and two DMSO, making H-bonds to water hydrogens. According to the simulation data, these molecular aggregates coexist with each other in the mixture, but their proportions change with composition. 1DMSO-2water complexes predominate over 2DMSO-1water aggregates for water-rich mixtures (water mole fractions >50%), whereas the opposite is true for DMSO-rich mixtures. The present simulations also seem to indicate that an association between a pair of DMSO molecules through their oxygen atoms is made possible by the formation of the 2DMSO-1water complexes. Implications of the existence of these aggregates to the mobility and other dynamic properties of these mixtures are briefly discussed.

The xylan decoration pattern in all lineages of gymnosperms permits hydrogen bonding of xylan to cellulose.