Folding with downhill behavior and low cooperativity of proteins.
The downhill folding observed experimentally for a small protein BBL is studied using off-lattice Gō-like model. Our simulations show that the downhill folding has low cooperativity and is barrierless, which is consistent with the experimental findings. As an example of comparison in detail, the two-state folding behavior of proteins, for example, protein CI2, is also simulated. By observing the formation of contacts between the residues for these two proteins, it is found that the physical origin of the downhill folding is due to the deficiency of nonlocal contacts which determine the folding cooperatively. From a statistics on contacts of the native structures of 17 well-studied proteins and the calculation of their cooperativity factors kappa2 based on folding simulations, a strong correlation between the number of nonlocal contacts per residue NN and the factors kappa2 is obtained. Protein BBL with a value of NN = 0.73 has the lowest cooperativity factor kappa2 = 0.34 among all 17 proteins. A crossover around NNc approximately 0.9 could be defined to separate the two-state folders and the downhill folder roughly. A protein would behave downhill folding when its NN = NNc. For proteins with their NN values are about (or slightly larger than) NNc, the folding behaves with low cooperativity and the barriers are small, showing a weak two-state behavior or a downhill-like behavior. Furthermore, simulations on mutants of a two-state folder show that a mutant becomes a downhill folder when its NN is reduced to a value smaller than NNc. These could enable us to identify the downhill folding or the cooperative two-state folding behavior solely from the native structures of proteins.
Zuo
Guanghong
G
Department of Physics, Nanjing University, China.
Wang
Jun
J
Wang
Wei
W
D055592:Biophysical Phenomena; D001703:Biophysics; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D019277:Entropy; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009154:Mutation; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D025941:Protein Interaction Mapping; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D013816:Thermodynamics
D011506:Proteins