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 thermophilic xylanase from Bacillusstrain D3 suitable for use as a bleach booster in the paper pulping industry has been identified and characterized. The enzyme is suited to the high temperature and alkaline conditions needed for using xylanases in the pulp industry. The xylanase is stable at 60°C and relatively stable at high temperatures, with a temperature optimum of 75°C. The pH optimum is 6, but the enzyme is active over a broad pH range. The xylanase has been cloned and sequenced, and the crystal structure has been determined. The structure of BacillusD3 xylanase reveals an unusual feature of surface aromatic residues, which form clusters or “sticky patches” between pairs of molecules. These “sticky patches” on the surface of the enzyme are responsible for the tendency of the protein to aggregate at high concentrations in the absence of reagents such as ethylene glycol. The formation of dimers and higher order polymers via these hydrophobic contacts may also contribute to the thermostability of this xylanase. Proteins 29:77–86, 1997. © 1997 Wiley-Liss, Inc.

Structural basis of the properties of an industrially relevant thermophilic xylanase.

A new procedure (POLYS) for producing three-dimensional structures of polysaccharides and complex carbohydrates is described. This employs a builder concept combining a database of monosaccharide structures with a database containing information on populations of independent neighboring glycosidic linkages in disaccharide fragments. The computer program is written in C, and it can cope with both the complexity and the diversity of carbohydrates and the unique topological features arising from multiple branching. A simple ASCII syntax was developed for describing the primary structures in accordance with IUPAC nomenclature. The translation of the primary structure is made through the combined use of a lexical analyzer and a command interpreter. In this way the program can be considered as a compiler of primary structures of carbohydrates. However, it also generates secondary and tertiary structures in the form of Cartesian coordinates in formats used by most molecular mechanics programs and packages. In our laboratory POLYS was exhaustively tested on standard homopolysaccharide systems such as cellulose and mannan and found to work very well. We now report the ease of use and the efficiency of the molecular builder in applications to more complex carbohydrate systems. These include the structural exploration of a pentaantennary oligosaccharide having 135 residues, the complex family of pectic polysaccharides including the organization and distribution of side chains (arabinan, arabinogalactan, and galactan) on the rhamnogalacturonan backbone.

Serge Pérez

Papers

Structural basis of the properties of an industrially relevant thermophilic xylanase.

A molecular builder for carbohydrates: Application to polysaccharides and complex carbohydrates

Molecular relaxation of sucrose in aqueous solutions: how a nanosecond molecular dynamics simulation helps to reconcile NMR data

Aspects of the conformation of polyguluronate in the solid state and in solution

New three-dimensional structure for A-type starch