title: Simulating temperature jumps for protein folding.
abstract: We present a new computational methodology aimed to calculate the thermodynamics and kinetics of peptide folding. We focus in particular on temperature jump experiments of folding rates and show how a combination of replica exchange molecular dynamics (REMD) followed by multiplexed molecular dynamics starting from structures taken from the REMD runs can be used to extract properties in line with experiments. A model system, alanine20, is studied in this article as a proof of principle and used to describe the methodology.
authors.affiliation: Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA.
authors.forename: Seonah
authors.initials: S
authors.lastname: Kim
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Roitberg
mesh_terms: D000409:Alanine / Q000737:chemistry; D002942:Circular Dichroism; D007700:Kinetics; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D010455:Peptides; D011506:Proteins; D000409:Alanine