Localization of flexible sites in thread-like molecules from electron micrographs. Comparison of interstitial,...

A computer method for detecting kinks and flexible sites in thread-like molecules was developed. The method is based on the determination of the local curvature along the digitized electron micrographs of the molecules. The root-mean-square curvature provided a measure for the local flexibility, which is related to the persistence length. The influence of various error sources was assessed using computer-simulated thread molecules. "Flexibility profiles" showing the variation of flexibility along molecules were calculated for interstitial, basement membrane and intima collagens. Approximately uniform stiffness corresponding to a persistence length of 60 nm was found for the triple helices of interstitial and monomeric intima collagen. A highly flexible site in interstitial collagen could be assigned to a non-triple helical segment in the sequence surrounding the linkage site of the N-terminal propeptide. A flexible site in the triple helix of collagen I corresponds to a segment of the sequence lacking proline residues. Flexibility varies strongly along the collagen IV molecule. This is consistent with the fact that a series of non-triple helical interruptions have already been found in the not yet completed amino acid sequence of basement membrane collagen. Most of the detected flexible sites allow random bending about the mean zero, but in one case, at the border of the 7S domain of polymeric collagen IV, a flexible site with a preferential angle of 40 degrees was found.