POLYS 2.0: An open source software package for building three-dimensional structures of polysaccharides.

This article describes an update of POLYS, the POLYSaccharide builder, for generating three-dimensional structures of polysaccharides and complex carbohydrates (Engelsen et al., Biopolymers 1996, 39, 417-433). POLYS is written in portable ANSI C and is now released under an open source license.

A combined nuclear magnetic resonance and molecular dynamics study of the two structural motifs for mixed-linkage beta-glucans: methyl beta-cellobioside and methyl beta-laminarabioside.

The conformational and hydration properties of the two disaccharides methyl beta-cellobioside and methyl beta-laminarabioside were investigated by NMR spectroscopy and explicit solvation molecular dynamics simulations using the carbohydrate solution force field (CSFF). Adiabatic maps produced with this force field displayed 4 minima A: (Phi=300 degrees , Psi=280 degrees), B: (Phi=280 degrees , Psi=210 degrees), C: (Phi=260 degrees , Psi=60 degrees), and D: (Phi=60 degrees , Psi=260 degrees) for methyl beta-cellobioside and 3 minima A: (Phi=290 degrees , Psi=130 degrees), B: (Phi=270 degrees , Psi=290 degrees), and C: (Phi=60 degrees , Psi=120 degrees) for methyl beta-laminarabioside. Molecular dynamics simulations were initiated from all minima.

Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose Ibeta: the enzyme-substrate complex.

Cellobiohydrolases are the dominant components of the commercially relevant Trichoderma reesei cellulase system. Although natural cellulases can totally hydrolyze crystalline cellulose to soluble sugars, the current enzyme loadings and long digestion times required render these enzymes less than cost effective for biomass conversion processes. It is clear that cellobiohydrolases must be improved via protein engineering to reduce processing costs.

Starch phosphorylation--maltosidic restrains upon 3'- and 6'-phosphorylation investigated by chemical synthesis, molecular dynamics and NMR spectroscopy.

Phosphorylation is the only known in vivo substitution of starch, yet no structural evidence has been provided to explain its implications of the amylosidic backbone and its stimulating effects on starch degradation in plants. In this study, we provide evidence for a major influence on the glucosidic bond in starch specifically induced by the 3-O-phosphate. Two phosphorylated maltose model compounds were synthesized and subjected to combined molecular dynamics (MD) studies and 950 MHz NMR studies.

Structure and hydration of the amylopectin trisaccharide building blocks--Synthesis, NMR, and molecular dynamics.

To gain insight into the molecular details and hydration of amylopectin, the five constituting trisaccharides have been chemically synthesized as their methyl alpha-glycosides. All five trisaccharides were subjected to 950 MHz NMR spectroscopy for complete assignment and nanosecond molecular dynamics trajectories were calculated to study the structure and dynamics of the trisaccharides in aqueous solution. Systematic analysis of the simulation data revealed several examples of bridging water molecules playing an important role in the stabilization of specific amylopectin conformations, which was also supported by the experimental NMR data such as interresidue NOE's and heteronuclear scalar couplings between nuclei from neighboring residues.