Folding energy landscape and network dynamics of small globular proteins.
The folding energy landscape of proteins has been suggested to be funnel-like with some degree of ruggedness on the slope. How complex the landscape, however, is still rather unclear. Many experiments for globular proteins suggested relative simplicity, whereas molecular simulations of shorter peptides implied more complexity. Here, by using complete conformational sampling of 2 globular proteins, protein G and src SH3 domain and 2 related random peptides, we investigated their energy landscapes, topological properties of folding networks, and folding dynamics. The projected energy surfaces of globular proteins were funneled in the vicinity of the native but also have other quite deep, accessible minima, whereas the randomized peptides have many local basins, including some leading to seriously misfolded forms. Dynamics in the denatured part of the network exhibited basin-hopping itinerancy among many conformations, whereas the protein reached relatively well-defined final stages that led to their native states. We also found that the folding network has the hierarchic nature characterized by the scale-free and the small-world properties.
Hori
Naoto
N
Graduate School of Science and Technology, Kobe University, Rokkodai Nada Kobe 657-8501, Japan.
Chikenji
George
G
Berry
R Stephen
RS
Takada
Shoji
S
D003198:Computer Simulation; D007700:Kinetics; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D013816:Thermodynamics; D018909:src Homology Domains
C029152:G-substrate; D009419:Nerve Tissue Proteins