Correlation between amino acid hydrophobicity scales and stain exclusion capacity of type I native collagen fibrils

The relationship between the negative staining band pattern of type 1 native collagen fibrils and the amino acid distribution along the fibril axis was studied by comparing averaged microdensitograms with theoretical traces calculated on the basis of different amino acid parameters. As well as the spatial parameter "bulkiness" (volume/length, ratio), various literature-reported scales of "hydrophobicity" were tested. Two "hydrophobicity" sets allowed a better fit with the actual patterns than "bulkiness" values. However, a general improvement in simulations was achieved by associating most "hydrophobicity" sets with the "bulkiness" set. These results suggest that amino acid "hydrophobicity" plays a key role in the appearance of negative staining patterns but a composite mechanism would seem to occur: the accessibility of available intermolecular interstices may be conditioned by molecular hindrance, corresponding to amino acid "bulkiness" as well as by water-repulsion effect, which correlates with amino acid "hydrophobicity." Moreover, a detailed comparison of actual and simulated patterns suggests that a modulation exists in the effectiveness of these two factors along each D-period according to the different molecular packing and concentration of hydrophobic amino acid clusters within overlap regions and gap regions, respectively.