Critical nucleation size in the folding of small apparently two-state proteins.
For apparently two-state proteins, we found that the size (number of folded residues) of a transition state is mostly encoded by the topology, defined by total contact distance (TCD) of the native state, and correlates with its folding rate. This is demonstrated by using a simple procedure to reduce the native structures of the 41 two-state proteins with native TCD as a constraint, and is further supported by analyzing the results of eight proteins from protein engineering studies. These results support the hypothesis that the major rate-limiting process in the folding of small apparently two-state proteins is the search for a critical number of residues with the topology close to that of the native state.
Bai
Yawen
Y
Laboratory of Biochemistry, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA. yawen@helix.nih.gov
Zhou
Hongyi
H
Zhou
Yaoqi
Y
D007700:Kinetics; D008962:Models, Theoretical; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
D011506:Proteins