Study of GroEL Conformational Mobility by Cryo-Electron Microscopy and Molecular Dynamics

Abstract

Bacterial chaperonin GroEL is a complex ring-shaped protein oligomer that promotes the folding of other proteins by encapsulating them in the cavity. There is very little structural information about the disordered C-terminal fragment of the GroEL subunits, which is involved in the folding of the substrate protein. A 3D reconstruction of the GroEL apo-form was obtained by cryo-electron microscopy (cryo-EM) with a resolution of 3.02 Å and supplemented by molecular dynamics (MD) calculations. The results of cryo-EM and MD are in good agreement and demonstrate a diverse mobility of the protein subunit domains. The MD results predict the dynamics and the network of intramolecular contacts of the C-terminal sections of the protein. These results are of great importance for the subsequent study of the mechanism of protein folding in the GroEL cavity.

Structural and Computational Study of the GroEL–Prion Protein Complex

“…Since the MD approach allows us to simulate the time evolution of the GroEL–PrP system, the validity of the result is determined by whether the simulation time is sufficient for the system to exhibit equilibrium behavior. To determine the sufficiency, we compared the cryo-EM local resolution map ( Figure S9 ) with the probability distribution map (described in [ 30 ]) obtained from MD by averaging the coordinates through the time steps ( Figure S10 ). These maps exhibit the same features.…”

“…Starting conformations of GroEL and PrP were chosen from a molecular dynamics simulation of two separated proteins, conducted by our group earlier [ 29 , 30 ]. The GroEL–PrP complex was assembled in two variants: GroEL–PrP(N) with the N-domain in the GroEL cavity and GroEL–PrP(C) with the C-domain in the GroEL cavity.…”