Name
Abstract | ||
|---|---|---|
We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native beta-sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting. |
Year | DOI | Venue |
|---|---|---|
2013 | 10.1371/journal.pcbi.1003002 | PLOS COMPUTATIONAL BIOLOGY |
Keywords | Field | DocType |
monte carlo method,protein sequencing,protein conformation,molecular dynamics simulation,chaperone proteins,computational biology,crystal structure,algorithms,protein folding,thermodynamics,protein interactions | Force field (physics),Protein folding,Protein–protein interaction,Protein sequencing,Biology,Threading (manufacturing),Molecular dynamics,Chaperone (protein),Bioinformatics,Protein structure | Journal |
Volume | Issue | Citations |
9 | 3 | 2 |
PageRank | References | Authors |
0.44 | 6 | 5 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Silvio a Beccara | 1 | 2 | 0.44 |
| Tatjana Skrbić | 2 | 5 | 0.91 |
| Roberto Covino | 3 | 3 | 0.80 |
| Cristian Micheletti | 4 | 41 | 6.08 |
| Pietro Faccioli | 5 | 5 | 1.24 |