Computer simulations

Because of the complexity of plant cell wall structure in terms of its components and organi­zation, it is difficult to decipher cell wall imaging results without knowledge of its molecular and electronic structures. Even though recent experiments using synchrotron X-ray and neutron diffraction have elucidated the crystal structures of cellulose Ia and Ip from algae and tunicate respectively (15, 16), the cellulose structures in plant cell walls remain largely unclear. However, it is known that the cross-sectional diameter of an elementary cellulose fibril is only about 3-5 nm in size (9). It has been further proposed (9) that the cellulose elementary fibril consists of 6, 12, and 18 glucan chains in the center, middle, and interface respectively, with increasing disorder. Only the six center chains can be considered truly

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(d) CfCBM3-GFP

Cellulose elementary fibril

Подпись: pectinHemicelluloses

Figure3.10 Total internal reflection fluorescence micrograph of fresh maize parenchyma cell wall labeled by QCBM3-GFP and QCBM6-RFP. (Modified from Ding et al, 2006.) (Reproduced in color as Plate 3.) crystalline. This hypothesis is yet to be tested due to the lack of available experimental techniques. Combined ab initio and force-field molecular dynamics simulations provide a unique tool to investigate the plant cell wall structure at the molecular and electronic levels. Molecular modeling will help shed light on the true nature of biomass recalcitrance at the atomic and molecular levels, thus pointing out ways to overcome this resistance to its deconstruction. Even less is understood about the structures of hemicelluloses, and the mechanisms and energetics between hemicelluloses and cellulose interactions. Hemicellu­loses are polysaccharides consisting of mostly xylose and other minor sugars. Xylan and xyloglucan (XG) are the main hemicelluloses in plant cell walls. Xylan displays large struc­tural variation and complexity. The backbone of xylan is a linear polymer of xylose linked via the (3-(1-4) glycosidic bond. In higher plants, the linear backbone is substituted by a variety of side chains mainly a-L-arabinofuranosyl and a-D-glucopyranosyl uronic acid units (73). XG has a glucan backbone wherein up to 75% of the glucose (G) units are sub­stituted at O6 with a-D-xylose (X) (74). Some of the xylose residues are then substituted at O2 with (3-D-galactose (L), which can be further substituted at O2 with a-L-fucose (F). Previous molecular dynamics studies (75-79) of plant cell wall structure focused mainly on

crystalline cellulose structures with unrealistic sizes and dimensions. Furthermore, the ma­jority of these simulations relied only on force-field-based molecular dynamics simulations (73,74,76-78). It is known that the accuracy of the simulations of carbohydrates will depend on the quality of the force field used. Matthews and coworkers (75) used second-generation CHARMM force fields; however, their cellulose crystal size was significantly larger than the actual size in plant cell walls. It is known that surfaces and interfaces will dominate the prop­erties of nanostructured materials. It is thus possible that this diminished cellulose surface to volume ratio in Matthews’ initial work led to some unrealistic conformational and hydrogen bonding structures in cellulose. Because the properties of cellulose and hemicelluloses are dominated by hydrogen bonding interactions, the force field method is not ideal for describ­ing this type of interaction. In contrast, application of ab initio-based molecular dynamics simulations to investigate the atomic and electronic structures of crystalline cellulose Ip yielded very good agreement with X-ray and neutron diffraction results, particularly for the hydrogen bonding network (79). Ab initio molecular dynamics with CPMD (80, 81) is another promising method to investigate the structures of celluloses and hemicelluloses in regard to their interaction mechanisms and general energetics. CPMD is capable of simu­lating thousands of atoms with currently available computing power (82). Combined with classical MD, it is possible to investigate the structures of the plant cell wall with up to tens of thousands of atoms.