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Nonequilibrium dynamics of helix reorganization observed by transient 2D IR spectroscopy.

ABSTRACT: 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 ?-helix is released to evolve into the equilibrium distribution of ?-helix conformations. The bridge constrains the structure to be slightly displaced from the full ?-helix equilibrium near these residues, yet the peptide is not unfolded completely. The release is accomplished by a subpicosecond pulse of UV irradiation. The resulting 2D IR signals are used to obtain snapshots of the ?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.

SUBMITTER: Tucker MJ

PROVIDER: S-EPMC3808647 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

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Nonequilibrium dynamics of helix reorganization observed by transient 2D IR spectroscopy.

Tucker Matthew J MJ Abdo Mohannad M Courter Joel R JR Chen Jianxin J Brown Stephen P SP Smith Amos B AB Hochstrasser Robin M RM

Proceedings of the National Academy of Sciences of the United States of America 20131008 43

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 α-helix is released to evolve into the equilibrium distribution of α-helix conformations. The bridge constrains the structure to be slightly displaced from the full α-helix equilibrium near these residues, yet the peptide is not unfolded completely. T ...[more]

PMID: 24106309

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Project description:Dynamic and structural properties of carbonmonoxy (CO)-coordinated cytochrome c(552) from Hydrogenobacter thermophilus (Ht-M61A) at different temperatures under thermal equilibrium conditions were studied with infrared absorption spectroscopy and ultrafast two-dimensional infrared (2D IR) vibrational echo experiments using the heme-bound CO as the vibrational probe. Depending on the temperature, the stretching mode of CO shows two distinct bands corresponding to the native and unfolded proteins. As the temperature is increased from low temperature, a new absorption band for the unfolded protein grows in and the native band decreases in amplitude. Both the temperature-dependent circular dichroism and the IR absorption area ratio R(A)(T), defined as the ratio of the area under the unfolded band to the sum of the areas of the native and unfolded bands, suggest a two-state transition from the native to the unfolded protein. However, it is found that the absorption spectrum of the unfolded protein increases its inhomogeneous line width and the center frequency shifts as the temperature is increased. The changes in line width and center frequency demonstrate that the unfolding does not follow simple two-state behavior. The temperature-dependent 2D IR vibrational echo experiments show that the fast dynamics of the native protein are virtually temperature independent. In contrast, the fast dynamics of the unfolded protein are slower than those of the native protein, and the unfolded protein fast dynamics and at least a portion of the slower dynamics of the unfolded protein change significantly, becoming faster as the temperature is raised. The temperature dependence of the absorption spectrum and the changes in dynamics measured with the 2D IR experiments confirm that the unfolded ensemble of conformers continuously changes its nature as unfolding proceeds, in contrast to the native state, which displays a temperature-independent distribution of structures.

Dataset Information

Nonequilibrium dynamics of helix reorganization observed by transient 2D IR spectroscopy.

Publications

Nonequilibrium dynamics of helix reorganization observed by transient 2D IR spectroscopy.

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