We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

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The Amber biomolecular simulation programs

Chitin and chitosan: Properties and applications

This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).

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Cellulose nanomaterials review: structure, properties and nanocomposites

Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.

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Microbial cellulose utilization: fundamentals and biotechnology.

A general all-atom force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers was developed using state-of-the-art ab initio and empirical parametrization techniques. The valence parameters and atomic partial charges were derived by fitting to ab initio data, and the van der Waals (vdW) parameters were derived by conducting MD simulations of molecular liquids and fitting the simulated cohesive energies and equilibrium densities to experimental data. The combined parametrization procedure significantly improves the quality of a general force field. Validation studies based on large number of isolated molecules, molecular liquids and molecular crystals, representing 28 molecular classes, show that the present force field enables accurate and simultaneous prediction of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases. Detailed results of the parametrization and validation f...

COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds

A unified representation of helical parameters (n,h) based on a polar mapping is proposed. Its application to the case of polysaccharides allows a straightforward comparison of all secondary structures displayed by this class of biopolymers in the solid state. Based on the concept that a disordered state of a polymer may be described by a succession of local helical parameters, the application of this unified representation has been extended to the simulation of chain behavior in solution.

Unified representation of helical parameters: Application to polysaccharides

Some mannose-binding legume lectins show higher affinity for fucosylated glycans than for glycans without fucose. These lectins possess a secondary binding site. Owing to the possibility of additional fucose binding, oligosaccharides adopt different conformations depending on whether they contain fucose or not. To study these conformational differences, complexes of fucosylated and unfucosylated glycans with Lens culinaris lectin have been modeled. Starting points were X-ray structures of lentil lectin and complexes of the homologous Lathyrus ochrus lectin. The SYBYL molecular modeling package with the TRIPOS force field was used. Two different models were built, displaying in both a network of hydrogen bonds between the saccharide and the binding site. Furthermore, to compare the free and bound ligand, conformational analysis in the free state has been performed. A complete analysis of all possible disaccharide fragments has been performed using the MM3 force field. A CICADA analysis employing the same force field was carried out to study the complete oligosaccharide. Low-energy conformers found by CICADA were clustered in conformational families and analyzed in terms of flexibility and rotational barriers. All values of glycosidic torsion angles are in the range as calculated by MM3 for the disaccharides.

Conformational analysis of biantennary glycans and molecular modeling of their complexes with lentil lectin.

Ethylene glycol di(para-chlorobenzoate) crystals are monoclinic, space group C2/c, with a = 12.733(9), b = 9.522(8), c = 12.762(8) A, β = 79.63(10)°, and Z = 4. The structure was solved by direct m...

Etudes conformationnelles de dérivés d'oligométhylène glycols et de composés apparentés. Partie II. Structure cristalline et moléculaire du di(parachlorobenzoate) d'éthylène glycol, C16H12O4Cl2

Polysaccharides form the most abundant and diverse family of biopolymers. With several hundreds of known examples they offer a great diversity of chemical structures, ranging from simple linear homopolymers to branched heteropolymers, having repeating units of up to octasaccharides. Simple polysaccharides, with a repeating structure composed of monosaccharides, are used to store energy, as in starch, glycogen, locust bean gum and guar gum. Carbohydrate functions are not limited to the storage or production of energy. Cellulose, a simple polymer of glucose, is an essential constituent of plant cell walls. It generates hard and solid elements in the form of tough fibers. The plasticity of the cell wall is further regulated via hydrated cross-linked three-dimensional networks where polysaccharides such as pectins play a key function. In marine species, carbohydrate polymers such as agar, alginates and carrageenans play a similar role. Other polysaccharides create viscous extracellular layers around bacteria. In the animal kingdom, the family of glycosaminoglycans (hyaluronate, chondroitin sulfate, derma-tan sulfate etc.) plays a key role in governing the solution properties of some physiological fluids as well as participating in the structural buildup of the intercellular matrix.

Shapes and interactions of polysaccharide chains

The conformational behaviour of Me-5-deoxy-α- d -ribofuranoside (1) and Me-5-deoxy-β- d -ribofuranoside (2) has been assessed through computations performed with the molecular mechanics programs MM3 using the flexible residue method and AMBER using the algorithm for conformational searches of the program CICADA. Both AMBER's native force field and all the known parameter sets for carbohydrates of the AMBER's force field were utilized. The results gained were completed and compared with ring shapes of d -ribofuranosides from ab initio calculations and from X-ray studies of d-ribofuranoside containing structures. While the production of apparently correct furanose models, which are thought to be even more flexible than pyranose rings, is a stringent test of the force fields in the modelling software, one can appreciate these results as a test of mean sugar parameter sets of program AMBER.

Serge Pérez

Papers

Unified representation of helical parameters: Application to polysaccharides

Conformational analysis of biantennary glycans and molecular modeling of their complexes with lentil lectin.

Etudes conformationnelles de dérivés d'oligométhylène glycols et de composés apparentés. Partie II. Structure cristalline et moléculaire du di(parachlorobenzoate) d'éthylène glycol, C16H12O4Cl2

Shapes and interactions of polysaccharide chains

Comparison of force-fields parametrizations as applied to conformational analysis of ribofuranosides