Low frequency motions in phosphoglycerate kinase. A normal mode analysis Original Research Article

This paper presents a normal mode analysis of yeast Phosphoglycerate kinase, whose goal is to study the large amplitude collective motions of this protein. It is constituted of two globular domains, and many authors have proposed that domains have a relative movement between them in order to allow the phosphoryl transfer reaction. Our results show that the lowest frequency modes, below 5 cm−1, contribute the most to the hinge bending motions of the N- and C-terminal domains. We found three types of movements, which are a twist propeller motion, a scissors type hinge motion, and a shear motion between the domains. We present the local conformational variations which are coupled to the domain motions. The thermal atomic fluctuation at 300 K and the correlations between them, are also analyzed.