Abstract
Structural elements inserted in proteins are essential to define folding/unfolding 1 mechanisms and partner recognition events governing signaling processes in living organisms. 2 Here, we present an original approach to model the folding mechanism of these structural elements. 3 Our approach is based on the exploitation of local, sequence-dependent structural information 4 encoded in a database of three-residue fragments extracted from a large set of high-resolution 5 experimentally determined protein structures. The computation of conformational transitions leading 6 to the formation of the structural elements is formulated as a discrete path search problem using this 7 database. To solve this problem, we propose a heuristically-guided depth-first search algorithm. The 8 domain-dependent heuristic function aims at minimizing the length of the path in terms of angular 9 distances, while maximizing the local density of the intermediate states, which is related to their 10 probability of existence. We have applied the strategy to two small synthetic polypeptides mimicking 11 two common structural motifs in proteins. The folding mechanisms extracted are very similar to 12 those obtained when using traditional, computationally expensive approaches. These results show 13 that the proposed approach, thanks to its simplicity and computational efficiency, is a promising 14 research direction. 15