Sandra V. Bennun

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Effective representation and characterization of biosynthetic pathways of glycosylation can be facilitated by mathematical modeling. This paper describes the expansion of a previously developed detailed model for N-linked glycosylation with the further application of the model to analyze MALDI-TOF mass spectra of human N-glycans in terms of underlying(More)
Phase and mixing behavior of dilauroylphosphatidylcholine (DLPC)/distearoylphosphatidylcholine (DSPC) lipid mixtures are studied by molecular dynamics simulations with use of a coarse-grained model over a wide range of concentrations. The results reveal that phase transformations from the fluid to the gel state can be followed over a microsecond time scale.(More)
Abnormalities in glycan biosynthesis have been conclusively linked to many diseases but the complexity of glycosylation has hindered the analysis of glycan data in order to identify glycoforms contributing to disease. To overcome this limitation, we developed a quantitative N-glycosylation model that interprets and integrates mass spectral and(More)
This work characterizes the impact of lipid symmetry/asymmetry on drying/rehydration reorganization in phase-separated dilauroylphosphatidylcholine (DLPC)/distearoylphosphatidylcholine (DSPC) supported lipid bilayers (SLBs) at the submicron and micron-scale. In addition the prevention of major drying/rehydration reorganization by the use of trehalose is(More)
Molecular modeling of phospholipids on many scales has progressed significantly over the last years. Here we review several membrane models on intermediate to large length scales restricting ourselves to particle based coarse-grained models with implicit and explicit solvent. We explain similarities and differences as well as their connection to experiments(More)
The Chinese hamster ovary (CHO) cell is the gold standard for manufacturing of glycosylated recombinant proteins for production of biotherapeutics. The similarity of its glycosylation patterns to the human versions enable the products of this cell line favorable pharmacokinetic properties and lower likelihood of causing immunogenic responses. Because glycan(More)
Variations in two-dimensional membrane structures on the molecular length scale are considered to have an effect on the mechanisms by which living cell membranes maintain their functionality. We created a molecular model of a patterned bilayer to asses the static and dynamic variations of membrane lateral and transbilayer distribution in two-component lipid(More)
Karhunen-Loeve analysis, a special variant of principal component analysis, is used to describe and analyze the dynamics of self-assembled pattern formation in a mixed phospholipid bilayer. The dominant modes of the evolving heterogeneities in density and dynamics are elucidated. At low temperatures the evolution of patterns can be followed by the principal(More)
In this contribution, we discuss several important technical aspects which are relevant for the molecular modeling of biomembranes in aqueous environments. We study the effect of coarse-grained water models on free and supported systems and show that the choice of water model has dramatic repercussions on the phase behavior. We characterize the phase(More)
Despite some recent successes in deciphering new cancer molecular makers, there is still a clear and continual need to develop new technologies that help characterizing existing biomarkers or facilitate discovery of new biomarkers. An important systems biology opportunity on this respect is provided by understanding the glycosylation changes associated with(More)