Paper Citing NAMD - Abstract
Tucker, Matthew J.; Abdo, Mohannad; Courter, Joel R.; Chen, Jianxin; Brown, Stephen P.; Smith, Amos B., I.I.I.; Hochstrasser, Robin M.
Nonequilibrium dynamics of helix reorganization observed by transient 2D IR spectroscopy
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:17314-17319, OCT 22 2013
The relaxation of helical structures very close to equilibrium is observed via transient 2D IR spectroscopy. An initial distribution of synthetically distorted helices having an unnatural bridge linking the 10th and 12th residues of an alanine-rich a-helix is released to evolve into the equilibrium distribution of a-helix conformations. The bridge constrains the structure to be slightly displaced from the full a-helix equilibrium near these residues, yet the peptide is not unfolded completely. The release is accomplished by a subpico-second pulse of UV irradiation. The resulting 2D IR signals are used to obtain snapshots of the similar to 100-ps helical conformational reorganization of the distorted dihedral angle and distance between amide units at chemical bond length-scale resolution. The decay rates of the angle between the dipoles, dihedral angles, and distance autocorrelations obtained from molecular dynamics simulations support the experiments, providing evidence that the final helix collapse conforms to linear response theory.
