Paper Citing NAMD - Abstract
Martinez, Anna Victoria; DeSensi, Susan C.; Dominguez, Laura; Rivera, Eva; Straub, John E.
Protein folding in a reverse micelle environment: The role of confinement and dehydration
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 055107, FEB 7 2011
Characterization of the molecular interactions that stabilize the folded state of proteins including hydrogen bond formation, solvation, molecular crowding, and interaction with membrane environments is a fundamental goal of theoretical biophysics. Inspired by recent experimental studies by Gai and co-workers, we have used molecular dynamics simulations to explore the structure and dynamics of the alanine-rich AKA(2) peptide in bulk solution and in a reverse micelle environment. The simulated structure of the reverse micelle shows substantial deviations from a spherical geometry. The AKA(2) peptide is observed to (1) remain in a helical conformation within a spherically constrained reverse micelle and (2) partially unfold when simulated in an unconstrained reverse micelle environment, in agreement with experiment. While aqueous solvation is found to stabilize the N- and C-termini random coil portions of the peptide, the helical core region is stabilized by significant interaction between the nonpolar surface of the helix and the aliphatic chains of the AOT surfactant. The results suggest an important role for nonpolar peptide-surfactant and peptide-lipid interactions in stabilizing helical geometries of peptides in reverse micelle environments. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3545982]
