Dataset Information

Mechanical transition from ?-helical coiled coils to ?-sheets in fibrin(ogen).

ABSTRACT: We characterized the ?-to-? transition in ?-helical coiled-coil connectors of the human fibrin(ogen) molecule using biomolecular simulations of their forced elongation and theoretical modeling. The force (F)-extension (X) profiles show three distinct regimes: (1) the elastic regime, in which the coiled coils act as entropic springs (F < 100-125 pN; X < 7-8 nm); (2) the constant-force plastic regime, characterized by a force-plateau (F ? 150 pN; X ? 10-35 nm); and (3) the nonlinear regime (F > 175-200 pN; X > 40-50 nm). In the plastic regime, the three-stranded ?-helices undergo a noncooperative phase transition to form parallel three-stranded ?-sheets. The critical extension of the ?-helices is 0.25 nm, and the energy difference between the ?-helices and ?-sheets is 4.9 kcal/mol per helical pitch. The soft ?-to-? phase transition in coiled coils might be a universal mechanism underlying mechanical properties of filamentous ?-helical proteins.

SUBMITTER: Zhmurov A

PROVIDER: S-EPMC3526676 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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Mechanical transition from α-helical coiled coils to β-sheets in fibrin(ogen).

Zhmurov Artem A Kononova Olga O Litvinov Rustem I RI Dima Ruxandra I RI Barsegov Valeri V Weisel John W JW

Journal of the American Chemical Society 20120925 50

We characterized the α-to-β transition in α-helical coiled-coil connectors of the human fibrin(ogen) molecule using biomolecular simulations of their forced elongation and theoretical modeling. The force (F)-extension (X) profiles show three distinct regimes: (1) the elastic regime, in which the coiled coils act as entropic springs (F < 100-125 pN; X < 7-8 nm); (2) the constant-force plastic regime, characterized by a force-plateau (F ≈ 150 pN; X ≈ 10-35 nm); and (3) the nonlinear regime (F > 17 ...[more]

PMID: 22953986

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Project description:ARCIMBOLDO solves the phase problem by combining the location of small model fragments using Phaser with density modification and autotracing using SHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers. ARCIMBOLDO_LITE has been run on single workstations on a test pool of 150 coiled-coil structures with 15-635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures using ARCIMBOLDO. Features from Phaser v.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification and SHELXE autotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode within ARCIMBOLDO for the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) or ARCIMBOLDO_LITE task interface in CCP4i.

Dataset Information

Mechanical transition from ?-helical coiled coils to ?-sheets in fibrin(ogen).

Publications

Mechanical transition from α-helical coiled coils to β-sheets in fibrin(ogen).

Similar Datasets

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