Extended Ensemble Molecular Dynamics Study of Ammonia-Cellulose I Complex Crystal Models: Free-Energy Landscape and Atomistic Pictures of Ammonia Diffusion in the Crystalline Phase.

Here, we report extended ensemble molecular dynamics simulations of ammonia-cellulose I complex crystal models to evaluate the diffusion behavior of the guest ammonia molecules and the potential of mean force (PMF), namely, the free energy change along the chosen reaction coordinate, for migration of an ammonia molecule in the crystal models. Accelerated molecular dynamics simulations confirmed that ammonia molecules almost exclusively diffused through the hydrophilic channel even when the crystal framework was retained. Adaptive steered molecular dynamics simulations detected distinct PMF peaks with heights of approximately 7 kcal/mol as the ammonia molecule passed through the cellulose-chain layers.

Molecular and Crystal Structure of a Chitosan-Zinc Chloride Complex.

We determined the molecular and packing structure of a chitosan-ZnCl complex by X-ray diffraction and linked-atom least-squares. Eight D-glucosamine residues-composed of four chitosan chains with two-fold helical symmetry, and four ZnCl molecules-were packed in a rectangular unit cell with dimensions = 1.1677 nm, = 1.

Molecular Dynamics Simulation of Cellulose Synthase Subunit D Octamer with Cellulose Chains from Acetic Acid Bacteria: Insight into Dynamic Behaviors and Thermodynamics on Substrate Recognition.

The present study reports the building of a computerized model and molecular dynamics (MD) simulation of cellulose synthase subunit D octamer (CesD) from . CesD was complexed with four cellulose chains having DP = 12 (G12) by model building, which revealed unexpected S-shaped pathways with bending regions. Combined conventional and accelerated MD simulations of CesD complex models were carried out, while the pyranose ring conformations of the glucose residues were restrained to avoid undesirable deviations of the ring conformation from the form.

Nanocellulose enriches enantiomers in asymmetric aldol reactions.

Cellulose nanofibers obtained from wood pulp by TEMPO-mediated oxidation acted as a chiral enhancer in direct aldol reactions of 4-nitrobenzaldehyde and cyclopentanone with ()-proline as an organocatalyst. Surprisingly, catalytically inactive TEMPO-oxidized cellulose nanofibers enriched the (,)-enantiomer in this reaction, affording 89% ee in the form with a very high yield (99%). Conversely, nanocellulose-free ()-proline catalysis resulted in poor selectivity (64% ee, form) with a low yield (18%).

Molecular Dynamics Simulation of Cellulose I-Ethylenediamine Complex Crystal Models.

Cellulose I fibrils swell on exposure to ethylenediamine (EDA), which forms the cellulose I-EDA complex. These are regarded as host materials with guest intercalation. The present study reports molecular dynamics (MD) simulations of cellulose I-EDA crystal models with finite fiber to reproduce desorption of EDA molecules.

DFT Optimization of Isolated Molecular Chain Sheet Models Constituting Native Cellulose Crystal Structures.

Because of high crystallinity and natural abundance, the crystal structures of the native cellulose allomorphs have been theoretically investigated to elucidate the cellulose chain packing schemes. Here, we report systematic structure optimization of cellulose chain sheet models isolated from the cellulose Iα and Iβ crystals by density functional theory (DFT). For each allomorph, the three-dimensional chain packing structure was partitioned along each of the three main crystal planes to construct either a flat chain sheet model or two stacked chain sheet models, each consisting of four cello-octamers.

Molecular dynamics simulations of theoretical cellulose nanotube models.

Nanotubes are remarkable nanoscale architectures for a wide range of potential applications. In the present paper, we report a molecular dynamics (MD) study of the theoretical cellulose nanotube (CelNT) models to evaluate their dynamic behavior in solution (either chloroform or benzene). Based on the one-quarter chain staggering relationship, we constructed six CelNT models by combining the two chain polarities (parallel (P) and antiparallel (AP)) and three symmetry operations (helical right (H), helical left (H), and rotation (R)) to generate a circular arrangement of molecular chains.

Double helix formation from non-natural amylose analog polysaccharides.

Double helix formation from the non-natural anionic and cationic amylose analog polysaccharides (amylouronic acid and amylosamine, respectively) was achieved through electrostatic interactions. A water-insoluble complex was obtained by simply mixing the two polysaccharides in water. The H NMR analysis indicated that the formation of the complexes with an approximately equimolar unit ratio from the two polysaccharides was resulted regardless of feed ratios for mixing.

Theoretical study of the structural stability of molecular chain sheet models of cellulose crystal allomorphs.

The structural stabilities of the molecular chain sheets constituting the crystal structures of the cellulose allomorphs Iα, Iβ, II, and IIII were investigated by density functional theory (DFT) optimization of the isolated chain sheet models with finite dimensions. The DFT-optimized chain sheet models of the two native cellulose crystals developed a right-handed twist with a similar amount of twisting. The DFT-optimized cellulose II (010) and (020) models twisted in opposite directions with right- and left-handed chirality, respectively.

Molecular dynamics study of carbohydrate binding module mutants of fungal cellobiohydrolases.

The present study reports the systematic survey of binding free energies at the interface between a carbohydrate-binding module (CBM) and a cellulose Iα crystal model using molecular dynamics' calculations. The two wild type CBMs (Cel7A CBM and Cel6A CBM) have been studied, as well as seven mutants of Cel7A CBM. A comparison of the experimental data for the two wild type and the four mutants CBMs (i.

Amylose's recognition of chirality in polylactides on formation of inclusion complexes in vine-twining polymerization.

Amylose selectively includes poly(L-lactide) (PLLA) among the poly(lactide)s (PLAs) to produce an inclusion complex when the phosphorylase-catalyzed polymerization of α-D-glucose 1-phosphate is performed in the presence of PLLA, poly(D-lactide) (PDLA), or poly(DL-lactide) (PDLLA) (vine-twining polymerization). This result indicates that amylose recognizes the chirality in PLAs on the formation of an inclusion complex in vine-twining polymerization. Modeling calculations support the amylose's chiral recognition in favor of PLLA and the atomistic details of the inclusion complex which involved the preferred orientation of the constituent molecular chains with respect to their fiber axis is proposed.

Molecular cloning and characterization of the nitric oxide synthase gene from kuruma shrimp, Marsupenaeus japonicus.

Nitric oxide (NO) signaling is involved in many physiological processes in vertebrates and invertebrates. In crustaceans, nitric oxide synthase (NOS) plays a significant role in the regulation of the nervous system and in innate immunity. Here, we describe the entire cDNA sequence (4616 bp) of the kuruma shrimp Marsupenaeus japonicus NOS (Mj NOS) generated using the reverse transcriptase-polymerase chain reaction (RT-PCR) and 5'- and 3'- rapid amplification PCRs of cDNA ends from brain and gill mRNAs.

Systematic docking study of the carbohydrate binding module protein of Cel7A with the cellulose Ialpha crystal model.

A computer docking study has been carried out on the crystal surfaces of cellulose Ialpha crystal models for the carbohydrate binding module (CBM) protein of the cellobiohydrolase Cel7A produced by Trichoderma reesei. Binding free energy maps between the CBM and the crystal surface were obtained by calculating the noncovalent interactions and the solvation free energy at grid points covering the area of the unit cell dimensions at the crystal surface. The potential maps obtained from grid searches of the hydrophobic (110) crystal surface exhibited two distinct potential wells.

Inhibition of RuBisCO cloned from Thermosynechococcus vulcanus and expressed in Escherichia coli with compounds predicted by Molecular Operation Environment (MOE).

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) of a thermophilic cyanobacterium, Thermosynechococcus vulcanus, was cloned and expressed in Escherichia coli. The purified enzyme had higher thermostability than RuBisCOs isolated from mesophilic cyanobacteria. Prediction of the tertiary structure was performed using the software Molecular Operating Environment (MOE).

Molecular dynamics simulations of solvated crystal models of cellulose I(alpha) and III(I).

Swelling behaviors of cellulose I(alpha) and III(I) crystals have been studied using molecular dynamics simulations of the solvated finite-crystal models. The typical crystal models consisted of 48 x 10-mer chains. For the cellulose I(alpha) crystal, models consisting of different numbers of chains and chain lengths were also studied.

Exhaustive crystal structure search and crystal modeling of beta-chitin.

An exhaustive search of the crystal structure of beta-chitin was carried out by simultaneously optimizing all the structural parameters based on published X-ray diffraction data and stereochemical criteria. The most probable structure was characterized by a parallel-up chain polarity, a gg orientation of hydroxymethyl groups and an intermolecular hydrogen bond along the a-axis, which essentially reproduced the original structure proposed by Gardner and Blackwell. The proposed crystal structure was subsequently subjected to crystal modeling using the AMBER force field.

Swelling behavior of the cellulose Ibeta crystal models by molecular dynamics.

The various crystal models of cellulose Ibeta, each differing in crystal size, have been studied by computer simulation using the amber molecular-dynamics package and the GLYCAM parameters. The four types of crystal model were constructed by a combination of two base-plane sizes, consisting of either 24 or 48 chains and two chain lengths having either 10 or 20 residues. The base planes of the crystal models were composed by the edges of the [1,1,0], [1,-1,0], and [1,0,0] crystal planes, where the [1,1,0] plane was assigned to the longest edge.

Three D structures of chitosan.

Crystal structures of two polymorphs of chitosan, tendon (hydrated) and annealed (anhydrous) polymorphs, have been reported. In both crystals, chitosan molecule takes up similar conformation (Type I form) to each other, an extended two-fold helix stabilized by intramolecular O3-O5 hydrogen bond, which is also similar to the conformation of chitin or cellulose. Three chitosan conformations other than Type I form have been found in the crystals of chitosan-acid salts.

Fourth 3D structure of the chitosan molecule: conformation of chitosan in its salts with medical organic acids having a phenyl group.

Chitosan salts with two medical organic acids having phenyl groups (salicylic and gentisic acids) exhibited fiber diffraction patterns of a new type of crystal which does not compare with known types I and II. The crystals, called type III salts, showed a fiber repeat of 2.550 nm and a meridional reflection at the 5th layer line.

The directionality of chitin biosynthesis: a revisit.

The molecular directionality of chitin biosynthesis was investigated by transmission electron microscopy (TEM) using electron crystallography methods applied to reducing-end-labelled beta-chitin microcrystals from vestimentiferan Lamellibrachia satsuma tubes and nascent beta-chitin microfibrils from the diatom Thalassiosira weissflogii. The data allowed confirmation that the microfibrils were extruded with their reducing end away from the biosynthetic loci, an orientation consistent only with elongation through polymerization at the non-reducing end of the growing chains. Such a chain-extension mechanism, which has also been demonstrated for cellulose and hyaluronan, appears to be general for glycosyltransferases that belong to the GT2 (glycosyl transferase 2) family.

Dependence of the mechanical properties of a pullulan film on the preparation temperature.

The mechanical properties of pullulan films prepared at various temperatures were investigated. The films prepared at high temperatures (40 degrees C and 60 degrees C; H-films) did not show any clear plastic deformation in tensile test, indicating that they were brittle. In contrast, those prepared at low temperatures (4 degrees C, 13 degrees C, and 25 degrees C; L-films) showed such deformation.

Directional degradation of beta-chitin by chitinase A1 revealed by a novel reducing end labelling technique.

A novel procedure for labelling the molecular ends of beta-chitin crystals has been established. By introducing a hydrazide derivative of biotin at the reducing end of a chitin chain, followed by a specific interaction between biotin and streptavidin coupled with a colloidal gold particle, the chain directionality of beta-chitin microcrystals could be directly visualized by transmission electron microscopy. This method allowed to certify the parallelism of the chitin chains in the beta-chitin microcrystals, and also to label the reducing tips of beta-chitin microcrystals degraded by Bacillus circulans chitinase A1.