Search for folding nuclei in the spatial structure of proteins
Skugarev, A.V.; Galzitskaia, O.V.; Finkel'shteĭn, A.V.
Molekuliarnaia Biologiia 33(6): 1016-1026
1999
ISSN/ISBN: 0026-8984 PMID: 10624693 Document Number: 507274
The results of three new approaches to the search for folding nuclei in a given spatial protein structure are described. The first, the simplest, phenomenological approach is based on the assessment of the level of the incorporation of various protein chain residues into hydrophobic nucleus and secondary protein structure. It was shown that the results of this approach did not have sufficient experimental verification. The other two, more complicated but physically more correct approaches, using the branch and border method and dynamic programming, respectively, are based on a search for the saddle points of the free energy landscape in the network of protein folding/unfolding pathways. The results of these approaches are in better agreement with experimental data.