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.

/pdf/the-amber-biomolecular-simulation-programs-e2nyq1ef44.pdf

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).

/pdf/cellulose-nanomaterials-review-structure-properties-and-2z8x922p3v.pdf

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.

/pdf/microbial-cellulose-utilization-fundamentals-and-4yec12qx1c.pdf

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

Computer modeling of the tetrasaccharide nystose

The conformational equilibria of the low-energy conformers of isomaltose have been studied in different solvents. The structure of each individual conformer was refined from the 18 distinct low-energy regions determined from potential energy function. Molecular geometry optimization was carried out using the quantum chemical method of perturbative configuration interaction with localized orbitals or PCILO and yielded to 15 distinct minima. Carbon-proton vicinal coupling constants 3JC-H have been calculated based on the finite perturbation theory formulation with the intermediate neglect of differential overlap for these minima. For evaluation of the influence of the environment on the conformational structure of isomaltose, the population of the low-energy conformers was estimated in four solvents by a method in which the total energy is divided into the energy of the isolated molecule and the solvation energy. The calculated abundances of conformers depend strongly on the solvents. Based on the determined abundance of conformers, thermodynamically averaged torsion angles and coupling constants 3JC-H describing the “average” conformation about glycosidic linkage have been calculated. Results obtained are compared with available experimental data from solution and solid state.

Solvent effect on the stability of isomaltose conformers

The neutral polysaccharide agarose is a linear polymer whose idealized structure is made up of alternating residues of a 1 3 linked β-D-galactopyranose and 1 4 linked 3,6-anhydro-α-L-galactopyranose. Apparently conflicting reports have been published about the nature of the helical structure of agarose in the condense phase. Recent developments in the field of molecular modeling of polysaccharides offer some new opportunities to reexamine the structural basis underlying the formation and stabilization of ordered structures.



The conformational spaces available for each disaccharide segments were investigated via molecular dynamics simulations. Then, making use of the available experimental information of the helical symmetry, axial advances, the optimal glycosidic torsion angles were assessed. The search for the lowest energy helix included both left- and right-handed, and both single- and double-helical, models. A further analysis considered all possible arrangements occurring between an agarose chain, in a given conformation, and another chain. Both parallel and antiparallel settings of the chains were evaluated. Unit-cell dimensions as well as lattice symmetry were derived from which intensities of x-ray reflections were calculated.



The calculations lead to the prediction of three single-helical structure and one parallel double-helical model; they are all left-handed and the chains pack in an antiparallel way. The predicted crystalline structures compare favorably with available experimental data. Water can occupy 30–45% of the space in the crystal structures, which is in accordance with the gel-forming behavior. The models obtained may reflect the relative arrangements of agarose helices in some of the main allomorphs. They provide some insights into the common structural features and into the differences that accompany the conformational transitions between these allomorphs. © 1998 John Wiley & Sons, Inc. Biopoly 46: 11–29, 1998

Molecular modeling of agarose helices, leading to the prediction of crystalline allomorphs

Modeling of Interactions of Polysaccharide Chains: Application to Crystalline Polymorphism of Starch Granules

Polyvalent carbohydrate-protein interactions play a key role in bio- and pathological processes, including cell-cell communication and pathogen invasion. In order to study, control and manipulate these interactions gold nanoparticles have been employed as a 3D scaffold, presenting carbohydrate ligands in a multivalent fashion for use as high affinity binding partners and a model system for oligosaccharide presentation at biomacromolecular surfaces. In this study, the binding of a series of mannose-functionalised gold nanoparticles to the dimeric BC2L-A lectin from Burkholderia cenocepacia has been evaluated. BC2L-A is known to exhibit a high specificity for (oligo)mannosides. Due to the unique structure and binding nature of this lectin, it provides a useful tool to study (oligo)saccharides presented on multivalent scaffolds. Surface plasmon resonance and isothermal titration calorimetric assays were used to investigate the effect of ligand presentation density towards binding to the bacterial lectin. We show how a combination of structural complementarities between ligand presentation and lectin architecture and statistical re-binding effects are important for increasing the avidity of multivalent ligands for recognition by their protein receptors; further demonstrating the application of glyconanotechnology towards fundamental glycobiology research as well as a potential towards biomedical diagnostics and therapeutic treatments.

Serge Pérez

Papers

Computer modeling of the tetrasaccharide nystose

Solvent effect on the stability of isomaltose conformers

Molecular modeling of agarose helices, leading to the prediction of crystalline allomorphs

Modeling of Interactions of Polysaccharide Chains: Application to Crystalline Polymorphism of Starch Granules

Influence of ligand presentation density on the molecular recognition of mannose-functionalised glyconanoparticles by bacterial lectin BC2L-A.