Paper Citing NAMD - Abstract
Liu, Yanxin; Struempfer, Johan; Freddolino, Peter L.; Gruebele, Martin; Schulten, Klaus
Structural Characterization of lambda-Repressor Folding from All-Atom Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:1117-1123, MAY 3 2012
The five-helix bundle lambda-repressor fragment is a fast-folding protein. A length of 80 amino acid residues puts it on the large end among all known microsecond folders, and its size poses a computational challenge for molecular dynamics (MD) studies. We simulated the folding of a novel lambda-repressor fast-folding mutant (lambda-HG) in explicit solvent using an all-atom description. By means of a recently developed tempering method, we observed reversible folding and unfolding of lambda-repressor in a 10 mu s trajectory. The folding kinetics was also investigated through a set of MD simulations run at different temperatures that together covered more than 125 mu s. The protein was seen to fold into a native-like topology at intermediate temperature, and a slow-folding pathway was identified. The simulations suggest new experimental observables for better monitoring of the folding process, and a novel mutation is expected to accelerate lambda-repressor folding.
