Dominant reaction pathways in protein folding: A direct validation against molecular dynamics simulations.
The dominant reaction pathway (DRP) is an algorithm to microscopically compute the most probable reaction pathways in the overdamped Langevin dynamics without investing computational time in simulating the local thermal motion in the metastable configurations. In order to test the accuracy of such a method, we investigate the dynamics of the folding of a beta hairpin within a model that accounts for both native and non-native interactions. We compare the most probable folding pathways calculated with the DRP method with the folding trajectories obtained directly from molecular dynamics simulations. We find that the two approaches give consistent results.
Faccioli
Pietro
P
Dipartimento di Fisica, Universitá degli Studi di Trento, Via Sommarive 14, Povo (Trento) I-38100, Italy. faccioli@science.unitn.it
Lonardi
Alice
A
Orland
Henri
H
D000465:Algorithms; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012996:Solutions / Q000737:chemistry; D013816:Thermodynamics
D010455:Peptides; D011506:Proteins; D012996:Solutions