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DNA nanomechanics: How proteins deform the double helix
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View: Figures


Image of FIG. 1.
FIG. 1.

Constraint force and externally applied force in a stereotyped double-well free energy landscape and thermal distribution (solid lines). Under an external force , the landscape is tilted (dashed lines).

Image of FIG. 2.
FIG. 2.

Rigid base-pair model. Atomic coordinates are reduced to the base-pair center position and orientation degrees of freedom, represented as bricks. Conformations of the Ippo-I complex before (left) and after (right) prerelaxation within a range of , see Sec. IV.

Image of FIG. 3.
FIG. 3.

Force and torque pairs acting on DNA to produce an excess of one base-pair step parameter in each row. Torque vectors shown in blue and force vectors in red. The same deformation of the central base-pair step can be produced by external force and torque pairs attacking directly (left column), at the nearest-neighbor base pairs (middle column), or seven base pairs away (right column). Sequence-averaged MP parameters. For plots of the base-pair step parameters associated with these equilibrium shapes, see Fig. supp-1.

Image of FIG. 4.
FIG. 4.

TFIIA(not shown)-TBP-DNA complex with force and torque vectors from three different TBP-DNA crystal structures (left). Corresponding energy, force magnitude, and torque magnitude profiles (right). Here and in the following figures, linear forces are shown as red arrows and torques as blue arrows; base pairs are represented as numbered small boxes with the following sequence coloring: “A,” red; “T,” blue; “G,” green; “C,” yellow; the two viewpoints are rotated by 90° around the vertical axis. Sequence (, base pair 1)-GGGGGGGCTATAAAAGG-(, base pair 17). Allowed relaxation range in all complexes. MP parameter set. The three-dimensional representations of base pairs, force, and torque vectors used for this figure are available, as detailed in Sec. IV (supplementary material data S1).

Image of FIG. 5.
FIG. 5.

Complex of lac repressor and DNA. NMR structure of 1 out of 20 conformers with ensemble mean force and torque vectors (left). Two magnified views of the encircled region, middle column, with force and torque vectors of all conformers. Ensemble energy, torque, and force magnitude profiles (right); the ensemble standard deviation profiles and of force and torque vectors are shown in black. MP parameter set. Sequence (, base pair 1)-GAATTGTGAGCGGATAACAATTT-(, base pair 23). The three-dimensional representations in data S2.

Image of FIG. 6.
FIG. 6.

Ippo-I DNA complex. The points of single-strand cuts in the functional complex are indicated. Relaxation range . The MP parameter set was used for vectors and MP (solid line) and P (dashed line) parameter sets for profiles (right). Sequence (, base-pair 1)-TGACTCTCTT AAGAGAGTCA-(, base pair 20). Three-dimensional representations in data S3.


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: DNA nanomechanics: How proteins deform the double helix