Topological frustration and the folding of interleukin-1 beta.
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.
Gosavi
Shachi
S
Center for Theoretical Biological Physics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA.
Chavez
Leslie L
LL
Jennings
Patricia A
PA
Onuchic
José N
JN
D003198:Computer Simulation; D004734:Energy Metabolism; D006801:Humans; D007375:Interleukin-1 / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism*; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
D007375:Interleukin-1; D010446:Peptide Fragments