Dynamic Monte Carlo simulations of globular protein folding. Model studies of in vivo assembly of four helix bundles and four member beta-barrels.
As part of an ongoing series of dynamic Monte Carlo simulations of globular protein folding, the nature of the folding pathway, of model four-member beta-barrels and four-helix bundles, under highly idealized conditions in vivo, has been examined. The ribosome is crudely modeled as an inert hard wall on to which the model protein chain is attached. Three cases are considered in detail. The first corresponds to post-translational assembly in which the fully synthesized chain is tethered to the wall and starts out under strongly denaturing conditions. The system is cooled down, and the chain is allowed to fold. Interestingly, the helical motif prefers to assemble parallel to the wall, whereas the beta-barrel, predominantly assembles with its principal axis perpendicular to the wall. In the former case, the dominant intermediate, the helical hairpin, is different from that in free solution, a three-helix bundle. The wall acts to reduce the expanse of configuration space that must be searched and aids in folding. Two situations that might lead to co-translational folding are also simulated. In the first case, to eliminate wall effects, the chain is slowly synthesized in free solution, and in the second case, it is slowly synthesized from the wall. In all cases, the chains are observed to fold post-translationally. While partially folded intermediates are observed during synthesis, they lack the stability to survive until chain synthesis is complete. The implications of these results for the folding in vivo of real protein chains is discussed, and a model of multiple domain protein folding is proposed.
Sikorski
A
A
Department of Chemistry, University of Warsaw, Poland.
Skolnick
J
J
D008961:Models, Structural; D008962:Models, Theoretical; D009010:Monte Carlo Method; D014176:Protein Biosynthesis; D011487:Protein Conformation; D011489:Protein Denaturation; D011506:Proteins / Q000235:genetics; D012270:Ribosomes / Q000378:metabolism
D011506:Proteins