The staining pattern of collagen fibrils. Improved correlation with sequence data

The periodic banding pattern of stained collagen fibrils observed in the electron microscopic can be correlated with the charge distribution deduced from the amino acid sequence. Earlier work used alpha 1 chain sequence data only. The present study incorporates alpha 2 as well as alpha 1 sequence data, so that the complete distribution of charged residues is used. Correlation is improved if it is supposed that the extrahelical terminal regions are contracted. The optimal value of the periodicity, D, (previously 232.3 +/- 0.5 residues using alpha 1 data only), is now 234.2 +/- 0.5 residues, assuming uniform spacing of residues in the helical body of the molecule. This value agrees better with values obtained by others from analyses of interactions between molecules, using sequence data alone. Using the improved value of D, the relative axial locations of the charged residues in the fibril are displayed. In this way, the charged residues contributing to each band in the fibril staining pattern can be identified.