Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

Molecular Dynamics Simulations of Protein Unfolding and Translocation Resulting from Allosteric Motions of ClpY

Clp ATPases are macromolecular machines which use the energy released from ATP hydrolysis to unfold, translocate and degrade misfolded proteins. ClpY, a bacterial unfoldase within this family, assembles into a homohexameric ring structure with a narrow central pore. Flexible diaphragm forming loops within this channel undergo large scale conformational changes driven by ATP binding and hydrolysis. The result is unfolding and translocation of a tagged substrate protein. We employ coarse grained molecular dynamics simulations to probe coupling between the allosteric motions of the central pore loops and the unfolding and translocation of a four helix bundle protein (Fig 1). We determine that minimal unfolding of the SP into an obligatory non-native intermediate, a three helix bundle, is required for translocation. The pathway for unfolding is unraveling from the C-terminus, which is in agreement with experiments1. Multiple translocation pathways are observed following the initial unfolding event. Weak mechanical forces exerted by the pore loops accompanied by transient SP binding to the I domain effect translocation2. We also investigate the ordering of allosteric transitions within individual subunits of the ClpY ring. Experiments suggest non-concerted allostery (3); however, the preference between sequential and random allostery remains unclear. To determine the efficacy of the possible allosteric mechanisms, we perform simulations of concerted, random, and sequential (clockwise and counterclockwise, viewed proximal to the I domain) mechanisms. The concerted simulations do not result in translocation, in accord with experiments1. Our results indicate that sequential clockwise simulations are the most efficient in the handling and translocation of the substrate protein.

Figure 1: Unfolding and translocation of a substrate protein formed from the four helix bundle protein (magenta) and ssrA degradation tag (yellow). Two subunits of ClpY (green) have been removed.


  1. C. Lee, M. Schwartz, S. Prakash, M. Iwakura, A. Matouschek Mol Cell 7, 627-637 (2001).
  2. A. Kravats, M. Jayasinghe, G. Stan Proc. Natl. Acad. Sci. USA 108, 2234-2239 (2011).
  3. A. Martin, T. A. Baker, R. T. Sauer Nature 437, 1115—1120 (2005).

Andrea Kravats1
Manori Jayasinghe2
George Stan1

1Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221
2Department of Chemistry, Northern Kentucky University, Highland Heights, KY 41099