Kevin J. Naidoo

Learn More
The puckered conformations of furanose and pyranose carbohydrate rings are central to analyzing the action of enzymes on carbohydrates. Enzyme reaction mechanisms are generally inaccessible to experiments and so have become the focus of QM(semiempirical)/MM simulations. We show that the complete free energy of puckering is required to evaluate the accuracy(More)
Several blood-feeding organisms, including the malaria parasite detoxify haem released from host haemoglobin by conversion to the insoluble crystalline ferriprotoporphyrin IX dimer known as haemozoin. To date the mechanism of haemozoin formation has remained unknown, although lipids or proteins have been suggested to catalyse its formation. We have found(More)
We present a CHARMM Carbohydrate Solution Force Field (CSFF) suitable for nanosecond molecular dynamics computer simulations. The force field was derived from a recently published sugar parameter set.1 Dihedral angle parameters for the primary alcohol as well as the secondary hydroxyl groups were adjusted. Free energy profiles of the hydroxymethyl group for(More)
Molecular dynamics simulations have been used to model the flexibility of the seven-sugar oligosaccharide of the lectin from Erythrina corallodendron in three separate simulations: one of the isolated oligosaccharide in vacuo, one of the oligosaccharide in solution and one of the oligosaccharide linked to the protein in solution. Adiabatic conformational(More)
The primary mechanism for relieving tensile strain in alpha-linked polysaccharides (e.g., [alpha-d-Glc-(1-->4)alpha-d-Glc]n) is achieved by complex rotations of the glycosidic linkages. This is shown through computer simulations of atomic force microscopy stretching experiments in combination with free energy calculations of the unfolding pattern for(More)
We investigated link atom approaches for treating the polar C-O bond with particular reference to the glycosidic bond found in complex carbohydrates. We show that cutting this bond after the oxygen in the QM region and saturating the QM system with a hydrogen link atom leads to greater conformational and configurational accuracy at the boundary compared(More)
The conformations of several β1→β1' diglycosyl disulfides were investigated by NMR and computational methods. Experimental data, such as NOEs, proton-proton and proton-carbon-13 coupling constants, measured for solutions in DMSO, are in good agreement with values obtained by MD simulations in explicit DMSO. The disulfide torsion angles (C1-S-S-C1')(More)
The approach used to calculate the two-electron integral by many electronic structure packages including generalized atomic and molecular electronic structure system-UK has been designed for CPU-based compute units. We redesigned the two-electron compute algorithm for acceleration on a graphical processing unit (GPU). We report the acceleration strategy and(More)
Glycosylation of cellobiose hydrolase I (CBHI), is a key step in the processing and degradation of cellulose. Here the pathways and barriers of the reaction are explored using the free energy from adaptive reaction coordinate forces (FEARCF) reaction dynamics method coupled with SCC-DFTB/MM. In many respects CBHI follows the expected general GH7 family(More)
Understanding carbohydrate ring pucker is critical to rational design in materials and pharmaceuticals. Recently we have generalized our adaptive reaction coordinate force biasing method to perform calculations on multidimensional reaction coordinates. We termed this the Free Energies from Adaptive Reaction Coordinate Forces (FEARCF) method. Using FEARCF in(More)