PDBsum entry 1ss8

Chaperone

PDB id: 1ss8

Contents

Protein chains

(+ 1 more) 524 a.a.

Waters ×107

References listed in PDB file

Key reference

Title

Exploring the structural dynamics of the e.Coli chaperonin groel using translation-Libration-Screw crystallographic refinement of intermediate states.

Authors

C.Chaudhry, A.L.Horwich, A.T.Brunger, P.D.Adams.

Ref.

J Mol Biol, 2004, 342, 229-245. [DOI no: 10.1016/j.jmb.2004.07.015]

PubMed id

15313620

Abstract

Large rigid-body domain movements are critical to GroEL-mediated protein folding, especially apical domain elevation and twist associated with the formation of a folding chamber upon binding ATP and co-chaperonin GroES. Here, we have modeled the anisotropic displacements of GroEL domains from various crystallized states, unliganded GroEL, ATPgammaS-bound, ADP-AlFx/GroES-bound, and ADP/GroES bound, using translation-libration-screw (TLS) analysis. Remarkably, the TLS results show that the inherent motions of unliganded GroEL, a polypeptide-accepting state, are biased along the transition pathway that leads to the folding-active state. In the ADP-AlFx/GroES-bound folding-active state the dynamic modes of the apical domains become reoriented and coupled to the motions of bound GroES. The ADP/GroES complex exhibits these same motions, but they are increased in magnitude, potentially reflecting the decreased stability of the complex after nucleotide hydrolysis. Our results have allowed the visualization of the anisotropic molecular motions that link the static conformations previously observed by X-ray crystallography. Application of the same analyses to other macromolecules where rigid body motions occur may give insight into the large scale dynamics critical for function and thus has the potential to extend our fundamental understanding of molecular machines.

Figure 4.
Figure 4. Effect of intermediate domain motion on apical domain in unliganded GroEL. For illustrative purposes, we have performed 25° clockwise and 25° counterclockwise rotations about the predominant libration axis of the intermediate domain (I1, see Figure 3). Two orthogonal views (top and bottom) of the resultant coordinates, related by a 90° vertical rotation are shown to capture the complex motion. The top views are looking approximately from a neighboring subunit in the ring, while the bottom views are from outside the ring looking towards the central 7-fold axis.

Figure 7.
Figure 7. Intermediate domain motion in the cis GroEL subunit leads to increased coupling with the equatorial domain. For illustrative purpose, we have performed 25° clockwise and 25° counterclockwise rotations about the predominant libration axis of the intermediate domain (I1, see Figure 6).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 229-245) copyright 2004.