Figure 2.

Effect of synthase affinity for inner chains on the homogeneity of the glycogen molecule. (A) In the absence of constraints on the preferential sites of enzyme work, the molecule of glycogen results highly inhomogeneous. In particular, the molecule shows two types of structural irregularities. First, there is excessive branching up to tier ∼30 and hence many incomplete chains. Second, the branching is asymmetric because left branch is created before right branch (at fifth and tenth residues, respectively). (B) When synthase is assumed to operate on inner chains, the glycogen molecule displays the homogeneity reported in the literature for cellular glycogen (see Table 2). The affinity of synthase for inner chains represents the minimal assumption to fulfill almost complete homogeneity. The phosphorylase is not required to exhibit affinity for inner or outer chains, although the homogeneity of glycogen slightly increases if phosphorylase is assumed to have preference for outer chains (not shown). Nonetheless, in the simulations there are no imposed constraints on phosphorylase. It should be realized that both the inhomogeneous (A) and the homogeneous (B) molecules contain the same number of glucose residues and that the time courses of total glucose content during the growth process for the two molecules are nearly identical (not shown). Note that the images are bidimensional representations (not projections of the tridimensional structure) of the actual glycogen structure, and the visualization parameters (e.g., the variation of the angle between branches as a function of the distance from the center) have been chosen only for illustration purposes. The filled circle in the middle of the molecule represents glycogenin.