A NEW METHOD TO CALCULATE REACTION PATHS FOR CONFORMATIONAL TRANSITIONS OF LARGE MOLECULES

Path energy minimization (PEM), a novel method for the generation of a reaction path linking two known conformers of a molecule, is presente d. The technique is based on optimizing a function which closely appro ximates the peak potential energy of a quasi-continuous path between t he fixed end points. A transition involving the change in the pucker a ngle of alpha-D-xylulofuranose is used as a test case. The method is s hown to be capable of identifying transition state structures and ener gy barriers. The utility of the method is demonstrated by an applicati on to substantial conformational transition of the ion-channel forming polypeptide gramicidin A.