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  • Title: Conformational stability of the full-atom hexameric model of the ClpB chaperone from Escherichia coli.
    Author: Zietkiewicz S, Slusarz MJ, Slusarz R, Liberek K, Rodziewicz-Motowidło S.
    Journal: Biopolymers; 2010 Jan; 93(1):47-60. PubMed ID: 19714768.
    Abstract:
    The Escherichia coli heat shock protein ClpB, a member of the Hsp100 family, plays a crucial role in cellular thermotolerance. In co-operation with the Hsp70 chaperone system, it is able to solubilize proteins aggregated by heat shock conditions and refold them into the native state in an ATP-dependent way. It was established that the mechanism of ClpB action depends on the formation of a ring-shaped hexameric structure and the translocation of a protein substrate through an axial channel. The structural aspects of this process are not fully known. By means of homology modeling and protein-protein docking, we obtained a model of the hexameric arrangement of the full-length ClpB protein complexed with ATP. A molecular dynamics simulation of this model was performed to assess its flexibility and conformational stability. The high mobility of the "linker" M-domain, essential for the renaturing activity of ClpB, was demonstrated, and the size and shape of central channel were analyzed. In this model, we propose the coordinates for a loop between b4 and B6 structural elements, not defined in previous structural research, which faces the inside of the channel and may therefore play a role in substrate translocation.
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