A method to explore transition paths in macromolecules. Applications to hemoglobin and phosphoglycerate kinase Original Research Article

A method to find low energy paths in macromolecules is described. It can be applied either to determine paths between two given energy minimum conformations, or to explore low energy paths departing from one energy minimized conformation. The principle of the method consists in carrying out energy minimizations or molecular dynamics simulations with root mean square distance constraints with respect to a reference structure. The method is illustrated by applications to N-methyl-alanyl-acetamide, hemoglobin and phosphoglycerate kinase.