By using principal component analysis (PCA) to examine the molecular dynamics (MD) of protein folding trajectories, generated with the coarse-grained UNRES force field, for the B-domain of staphylococcal protein A and the triple β-strand WW domain from the formin binding protein 28 (FBP), we demonstrate how different free energy landscapes (FELs) and folding pathways of trajectories can be, even though they appear to be very similar by visual inspection of the time dependence of the root-mean-square deviation (rmsd). Approaches to determine the minimal dimensionality of FELs for a correct description of protein folding dynamics are discussed. The correlation between the amplitude of the fluctuations of proteins and the dimensionality of the FELs is shown. The advantage of internal-coordinate PCA over Cartesian PCA for small proteins is also illustrated.
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