查看文章

A 100 ns molecular dynamics simulation of penta‐alanine in explicit water is performed to study the reversible folding and unfolding of the peptide. Employing a standard principal component analysis (PCA) using Cartesian coordinates, the resulting free‐energy landscape is found to have a single minimum, thus suggesting a simple, relatively smooth free‐energy landscape. Introducing a novel PCA based on a transformation of the peptide dihedral angles, it is found, however, that there are numerous free energy minima of comparable energy (≲ 1 kcal/mol), which correspond to well‐defined structures with characteristic hydrogen‐bonding patterns. That is, the true free‐energy landscape is actually quite rugged and its smooth appearance in the Cartesian PCA represents an artifact of the mixing of internal and overall motion. Well‐separated minima corresponding to specific conformational structures are also …