title: Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables.
abstract: Numerically predicting rate constants of protein folding and other relevant biological events is still a significant challenge. We show that the combination of partial path transition interface sampling with the optimal interfaces and free-energy profiles provided by path collective variables makes the rate calculation for practical biological applications feasible and efficient. This methodology can reproduce the experimental rate constant of Trp-cage miniprotein folding with the same level of accuracy as transition path sampling at a fraction of the cost.
authors.affiliation: Spanish National Cancer Research Centre, CNIO, calle Melchor Fernandez Almagro 3, 28029 Madrid, Spain.
authors.forename: J
authors.initials: J
authors.lastname: Juraszek
authors.forename: G
authors.initials: G
authors.lastname: Saladino
authors.forename: T S
authors.initials: TS
authors.lastname: van Erp
authors.forename: F L
authors.initials: FL
authors.lastname: Gervasio
mesh_terms: D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D010455:Peptides; C508725:Trp-cage peptide