Detection of breaking points in helices linking separate domains

Abstract

A novel method is proposed to predict whether two domains connected by a helical link can mutually reorient themselves, as well as where the helix can be distorted to allow the domain-domain movements. The method, based on analysis of the variation of the a.d.p. values along the helix link, is applied to three proteins--calmodulin, lysozyme, and hemagglutinin--for which both the domain-domain flexibility and the helix fragment responsible for it are well documented. The helix regions that are variously distorted to permit domain-domain reorientation are well predicted. The method is also applied to colicin Ia and shows that an inter-domain rearrangement can take place as previously postulated. The prediction of the helix breaking point should prove useful in interpreting structural data and in defining the domain borders automatically for proteins built by domains connected by helical links.