How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?
The molecular dynamics trajectories of protein folding or unfolding, generated with the coarse-grained united-residue force field for the B domain of staphylococcal protein A, were analyzed by principal component analysis (PCA). The folding or unfolding process was examined by using free-energy landscapes (FELs) in PC space. By introducing a novel multidimensional FEL, it was shown that the low-dimensional FELs are not always sufficient for the description of folding or unfolding processes. Similarities between the topographies of FELs along low- and high-indexed principal components were observed.
Maisuradze
Gia G
GG
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
Liwo
Adam
A
Scheraga
Harold A
HA
D008956:Models, Chemical; D025341:Principal Component Analysis; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D013205:Staphylococcal Protein A / Q000737:chemistry*; D013816:Thermodynamics
D013205:Staphylococcal Protein A