Local Transition Gradients Indicating the Global Attributes of Protein Energy Landscapes

The relationship between local atomic fluctuations and global protein rearrangements is elusive. Here, molecular dynamics simulations of a peptide concerted with complex network analysis show that local transition gradients provide a quantitative description of the free energy landscape in terms of its valleys. The latter, compared with established methods, are found with the correct populations. Moreover, the iterative analysis of the fastest intervalley relaxations provides an intuitive tree like representation of the system dynamics. These results indicate that knowledge of the fast, local relaxations is sufficient to identify the general properties of free-energy surfaces in terms of basins of attraction and the hierarchy of transitions.