Analysis of shape transitions using molecular size descriptors associated with inner and outer regions of a polymer chain

In random polymers, all descriptors of average chain size have the same scaling behaviour with the number of monomers. However, the situation can be different in polymers with non-random structures, e.g. biopolymers with secondary structure. In this case, descriptors of molecular size associated with inner and outer regions of the polymer chain (where 'inner' and 'outer' are defined with respect to the center of mass) are not necessarily equivalent. Indeed, differences in behaviour between size descriptors can provide useful information on structure and conformation. In this work, we use the ratio of two distinct molecular size descriptors to classify polymer configurations in terms of local compactness. When applied to protein dynamics, the new size-ratio descriptor rho is able to distinguish between unfolding transitions leading to configurations with uniform and non-uniform monomer distributions. (C) 2003 Elsevier Science B.V. All rights reserved.