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.
Polymer Institute, Slovak Academy of Sciences, 845 41 Bratislava, Slovakia.
Peter
P
Palenčár
Polymer Institute, Slovak Academy of Sciences, 845 41 Bratislava, Slovakia.
Tomáš
T
Bleha
D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013696:Temperature
D011506:Proteins