title: How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?
abstract: 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.
authors: Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
authors: Gia G
authors: GG
authors: Maisuradze
authors: Adam
authors: A
authors: Liwo
authors: Harold A
authors: HA
authors: Scheraga
mesh_terms: D008956:Models, Chemical; D025341:Principal Component Analysis; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D013205:Staphylococcal Protein A / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D013205:Staphylococcal Protein A