COMPUTER MODELING AND OTHER THEORETICAL STUDIES OF BIOPO

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ABSTRACT: Molecular dynamics computer simulations of octylglucoside (OG) micelles over a range of aggregation number from 5 to 100 indicated that clusters of 10 and above were stable on the 3 ns time scale. The stable clusters showed large undulations in shape, clear networks of hydrogen bonded headgroups, large exposed hydrophobic patches, and occasional exchange lipids with solvent. Preliminary simulations of a 27-mer with an added peptide suggest that the preceding features enhance the stability of micelle/peptide and micelle/peptide complexes. This work initiates the Laboratory's simulation study of the structure of surfactant based adjuvants. Langevin dynamics simulations were carried out on segments of several bacterial coat polysaccharides in an effort to understand their cross reactivity on the basis of distances between common functional groups. It was deduced that either explicit solvent or a well tuned potential of mean force (pmf) is required to avoid polymer collapse in simulations using CHARMM2 force field; efforts to develop a pmf using results from light scattering underway. Hydrodynamic calculations were used to estimate rotational diffusion tensors for the pentassaccharide lacto-N-fucopentaose-1 and the protein lysozyme. In both cases the results resolved ambiguities in the interpretation of order parameters and isomerization rates obtained from NMR relaxation measurements.