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 published previously (Mouawad.), L. and Perahia D., Biopolymers 33, 599, 1993), allows the computation of the low-frequency vibrational modes for large macromolecules. Improvements to this method are presented here, namely the single and double truncation window techniques. The best convergence rate is obtained with the double truncation windows, which couple 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 analyzed in order to study the pathways between T- and R-states of this protein. They show that the quaternary conformational are mainly due to one mode at 2 cm-1.
Perahia
D
D
Laboratoire d'Enzymologie Physico-Chimique et Moléculaire, Université Paris-Sud, Orsay, France.
Mouawad
L
L
D006454:Hemoglobins / Q000737:chemistry*; D008956:Models, Chemical; D011487:Protein Conformation; D012984:Software
D006454:Hemoglobins; C100003:deoxyhemoglobin