Buckling transition in long α-helices.

The treatment of bending and buckling of stiff biopolymer filaments by the popular worm-like chain model does not provide adequate understanding of these processes at the microscopic level. Thus, we have used the atomistic molecular-dynamic simulations and the Amber03 force field to examine the compression buckling of α-helix (AH) filaments at room temperature. It was found that the buckling instability occurs in AHs at the critical force f(c) in the range of tens of pN depending on the AH length. The decrease of the force f(c) with the contour length follows the prediction of the classic thin rod theory. At the force f(c) the helical filament undergoes the swift and irreversible transition from the smoothly bent structure to the buckled one. A sharp kink in the AH contour arises at the transition, accompanied by the disruption of the hydrogen bonds in its vicinity. The kink defect brings in an effective softening of the AH molecule at buckling. Nonbonded interactions between helical branches drive the rearrangement of a kinked AH into the ultimate buckled structure of a compact helical hairpin described earlier in the literature.

A new two-state polymer folding model and its application to α-helical polyalanine.

A new two-state polymer folding model is proposed, in which the folding of a stiff helical polymer is enabled by allowing for short sequences of coils connecting shorter and separated helices. The folding is driven by short-range attraction energy among stacked helices and is opposed by the free-energy cost of forming coils from helical monomers. Principal outcomes of the model are equilibrium distribution of the number of helices and their length in helical polymers. The proposed model is applied to α-helical polyalanine. The distribution of the number of α-helices as a function of number of alanine residues is fitted to the corresponding result from molecular dynamics simulation employing an all-atom potential model with very good agreement. The influence and significance of the fitting parameters and possible use of the two-state folding model are discussed.

Molecular dynamics simulations of the folding of poly(alanine) peptides.

The secondary structures and the shapes of long-chain polyalanine (PA) molecules were investigated by all-atom molecular dynamics simulations using a modified Amber force field. Homopolymers of polyaminoacids such as PA are convenient models to study the mechanism of protein folding. It was found that the conformational structures of PA peptides are highly sensitive to the chain length. In the absence of solvent, straight α-helices dominate in short (n ∼ 20) peptides at room temperature. A shape transition occurs at a chain length n of 40-45; the compact helix-turn-helix structure (the double-leg hairpin) becomes favored over a straight α-helix. For n=60, double-leg and the triple-leg hairpins are the only structures present in PA molecules. An exploration of a chain organization in a cubic cavity revealed a clear predisposition of PA molecules for additional breaks in α-helices and the formation of multifolded hairpins. Furthermore, under confinement the hairpin structure becomes much looser, the antiparallel positions of helical stems are disturbed, and a sizeable proportion of the helical stems are transformed from α-helices into 3(10)-helices.

The effects of light-induced reduction of the photosystem II reaction center.

Accumulation of reduced pheophytin a (Pheo-D1) in photosystem II reaction center (PSII RC) under illumination at low redox potential is accompanied by changes in absorbance and circular dichroism spectra. The temperature dependences of these spectral changes have the potential to distinguish between changes caused by the excitonic interaction and temperature-dependent processes. We observed a conformational change in the PSII RC protein part and changes in the spatial positions of the PSII RC pigments of the active D1 branch upon reduction of Pheo-D1 only in the case of high temperature (298 K) dynamics. The resulting absorption difference spectra of PSII RC models equilibrated at temperatures of 77 K and 298 K were highly consistent with our previous experiments in which light-induced bleaching of the PSII RC absorbance spectrum was observable only at 298 K. These results support our previous hypothesis that Pheo-D1 does not interact excitonically with the other chlorins of the PSII RC, since the reduced form of Pheo-D1 causes absorption spectra bleaching only due to temperature-dependent processes.