Simulating temperature jumps for protein folding.
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.
Kim
Seonah
S
Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA.
Roitberg
Adrian E
AE
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
D010455:Peptides; D011506:Proteins; D000409:Alanine