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J Mol Biol. 2006 Mar 31;357(3):986-96. Epub 2005 Dec 9.

Topological frustration and the folding of interleukin-1 beta.

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Center for Theoretical Biological Physics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA.


The cytokine, interleukin-1beta (IL-1beta), adopts a beta-trefoil fold. It is known to be much slower folding than similarly sized proteins, despite having a low contact order. Proteins are sufficiently well designed that their folding is not dominated by local energetic traps. Therefore, protein models that encode only the folded structure and are energetically unfrustrated (Gō-type), can capture the essentials of the folding routes. We investigate the folding thermodynamics of IL-1beta using such a model and molecular dynamics (MD) simulations. We develop an enhanced sampling technique (a modified multicanonical method) to overcome the sampling problem caused by the slow folding. We find that IL-1beta has a broad and high free energy barrier. In addition, the protein fold causes intermediate unfolding and refolding of some native contacts within the protein along the folding trajectory. This "backtracking" occurs around the barrier region. Complex folds like the beta-trefoil fold and functional loops like the beta-bulge of IL-1beta can make some of the configuration space unavailable to the protein and cause topological frustration.

[Indexed for MEDLINE]

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