Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Å resolution

Abstract

Improved refinement of the crystal structure of GroEL from Escherichia coli has resulted in a complete atomic model for the first 524 residues. A new torsion-angle dynamics method and non-crystallographic symmetry restraints were used in the refinement. The model indicates that conformational variability exists due to rigid-body movements between the apical and intermediate domains of GroEL, resulting in deviations from strict seven-fold symmetry. The regions of the protein involved in polypeptide and GroES binding show unusually high B factors; these values may indicate mobility or discrete disorder. The variability of these regions may play a role in the ability of GroEL to bind a wide variety of substrates.

GroEL‐Mediated protein folding

“…IA). The crystal structure of unliganded GroEL refined at 2.8 8, from an orthorhombic crystal form shows a cylindrical complex 145 8, in height and 135 8, in diameter, with a central channel or cavity at either terminus measuring 45 8, in diameter (Braig et al, 1994.…”

“…Because the amino acids forming the walls of the channel are hydrophobic in character (Fig. lB), and because their substitution with polar amino acids abolishes polypeptide binding (Braig et al, 1994;Fenton et al, 1994), it appears that hydrophobic contacts between the channel wall and the exposed hydrophobic surface of non-native folding intermediates mediate polypeptide binding (see below for further discussion). The GroEL subunit is composed of 547 amino acids folded into three domains.…”

“…The right panel is a diagrammatic representation of the middle one, with the domains designated A (apical), I (intermediate), and E (equatorial); also identified here are the central cavity (C) and one of the side openings (W). From Braig et al (1994). with permission.…”

“…1B). Moreover, the residues in these elements were poorly determined and appear highly mobile in the X-ray structures, with large B-factors, suggesting an ability to move to accommodate a variety of individual polypeptide ligands (Braig et al, 1994Boisvert et al, 1996). Finally, mutations changing hydrophobic residues in these regions to charged or hydrophilic ones resulted in mutant GroELs that were unable to bind polypeptide substrates .…”

“…This, in turn, dictates asymmetric GroES binding to the nucleotide-occupied ring. The structural bases for both positive and negative cooperativity remain unclear, although in the former case, contacts within a ring, between equatorial domains, and between intermediate domains and neighboring apical domains, appear to be important; in the latter case, presumably the two major sites of contact across the equatorial plane between each subunit and its neighbors in the opposite ring must provide the signaling pathway (Braig et al, 1994;Roseman et al, 1996).…”