COMPUTATION OF LOW-FREQUENCY NORMAL-MODES IN MACROMOLECULES - IMPROVEMENTS TO THE METHOD OF DIAGONALIZATION IN A MIXED BASIS AND APPLICATION TO HEMOGLOBIN

The method of diagonalization in a mixed basis (DIMB) that was publish ed previously (Mouawad.), L. and Perahia D., Biopolymers 33, 599, 1993 ), allows the computation of the low-frequency vibrational modes for l arge macromolecules. Improvements to this method are presented here, n amely the single and double truncation window techniques. The best con vergence rate is obtained with the double truncation windows, which co uple most efficiently the parts of the macromolecule which are far in sequence but close in space. Both methods were applied to the T-state of hemoglobin, to compare their efficiency. The resulting modes are an alyzed in order to study the pathways between T- and R-states of this protein. They show that the quaternary conformational changes are main ly due to one mode at 2 cm(-1).