A 3-D Model of a Perennial Ryegrass Primary Cell Wall and Its Enzymatic Degradation

Abstract

Abstract:We have developed a novel 3-D, agent-based model of cell-wall digestion to improve our understanding of ruminal cell-wall digestion. It offers a capability to study cell walls and their enzymatic modification, by providing a representation of cellulose microfibrils and non-cellulosic polysaccharides and by simulating their spatial and catalytic interactions with enzymes. One can vary cell-wall composition and the types and numbers of enzyme molecules, allowing the model to be applied to a range of systems where cell walls are degraded and to the modification of cell walls by endogenous enzymes. As a proof of principle, we have modelled the wall of a mesophyll cell from the leaf of perennial ryegrass and then simulated its enzymatic degradation. This is a primary, non-lignified cell wall and the model includes cellulose, hemicelluloses (glucuronoarabinoxylans, 1,3;1,4-β-glucans, and xyloglucans) and pectin. These polymers are represented at the level of constituent monosaccharides, and assembled to form a 3-D, meso-scale representation of the molecular structure of the cell wall. The composition of the cell wall can be parameterised to represent different walls in different cell types and taxa. The model can contain arbitrary combinations of different enzymes. It simulates their random diffusion through the polymer networks taking collisions into account, allowing steric hindrance from cell-wall polymers to be modelled. Steric considerations are included when target bonds are encountered, and breakdown products resulting from enzymatic activity are predicted. OPEN ACCESSComputation 2014, 2 24

In Silico Comparison of the Hemicelluloses Xyloglucan and Glucuronoarabinoxylan in Protecting Cellulose from Degradation

“…Although not evident in Figure 2, this was also the case for the Low XG wall, as can be seen by viewing the Supplementary S1. Cel51A has a diameter of 20.4 rg (7.5 nm) and Cel9D a diameter of 17.7 rg (6.5 nm) [16]. This puts an upper limit of 6.5 nm for pore size in the centres of the walls, but no lower limit.…”

“…In our model, the average step size of an enzyme is about 0.5 rg in an iteration [16]. Taking a value for rg of 3.65 Å [17], an iteration of our model corresponds to about 0.365 ms of elapsed time, and each simulation corresponds to a duration of about 5 h. We have no data available on the enzymatic degradation of composite walls of the type we have modelled.…”

“…We modelled the four composite cell walls by adapting a previously published 3-D model of a perennial ryegrass cell wall (RGCW) and its enzymatic degradation [16]. All four cell walls had several elements in common with RGCW, namely nine CMFs arranged in parallel (with the cellulose molecules 60 glucosyl residues long) with 35 (1,3;1,4)-β-glucans attached, all in their original configurations.…”

“…The first model cell wall (Low XG) was created as a control, and contained 93 XGs, which were in the RGCW model [16]. The second model cell wall (Low GAX) had no XGs, but contained 93 GAXs from the RGCW in their original configurations.…”

“…We populated the four cell walls with Cel51A (an endo-1,4-β-glucanase) and Cel9D (an exo-1, 4-β-glucanase that cleaves glucosyl residues from the nonreducing end of cellulose) which have been characterised from the rumen bacterium Fibrobacter succinogenes S85 and shown to act synergistically [18,19], and which we have previously modelled [16].…”