Unraveling proteins: A molecular mechanics study

An internal coordinate molecular mechanics study of unfolding peptide chain s by external stretching has been carried out to predict the type of force spectra that may be expected from single-molecule manipulation experiments currently being prepared. Rather than modeling the stretching of a given pr otein, we have looked at the behavior of simple secondary structure element s (alpha-helix, beta-ribbon, and interacting alpha-helices) to estimate the magnitude of the forces involved in their unfolding or separation and the dependence of these forces on the way pulling is carried out as well as on the length of the structural elements. The results point to a hierarchy of forces covering a surprisingly large range and to important orientational e ffects in the response to external stress.