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Mechanism of DNA flexibility enhancement by HMGB proteins.

Zhang J, McCauley MJ, Maher LJ, Williams MC, Israeloff NE - Nucleic Acids Res. (2009)

Bottom Line: These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments.The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding.Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Northeastern University, Boston, MA 02115, USA.

ABSTRACT
The mechanism by which sequence non-specific DNA-binding proteins enhance DNA flexibility is studied by examining complexes of double-stranded DNA with the high mobility group type B proteins HMGB2 (Box A) and HMGB1 (Box A+B) using atomic force microscopy. DNA end-to-end distances and local DNA bend angle distributions are analyzed for protein complexes deposited on a mica surface. For HMGB2 (Box A) binding we find a mean induced DNA bend angle of 78 degrees, with a standard error of 1.3 degrees and a SD of 23 degrees, while HMGB1 (Box A+B) binding gives a mean bend angle of 67 degrees, with a standard error of 1.3 degrees and a SD of 21 degrees. These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments. The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding. Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model.

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Distribution of protein-site bend angles for (a) HMGB (Box A) and (b) HMGB (Box A+B). The distribution shows an average induced DNA bend angle of 78° with a SD of 23° for HMGB (Box A) protein. HMGB (Box A+B) induces an average DNA bend angle of 67° with a SD of 21°.
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Figure 5: Distribution of protein-site bend angles for (a) HMGB (Box A) and (b) HMGB (Box A+B). The distribution shows an average induced DNA bend angle of 78° with a SD of 23° for HMGB (Box A) protein. HMGB (Box A+B) induces an average DNA bend angle of 67° with a SD of 21°.

Mentions: Figure 4 shows images of DNA with bound HMGB proteins. As can be seen in the height profile (Figure 4b), the protein–DNA complexes project higher from the mica surface than bare DNA, typically by ∼0.5 nm. These bound proteins thus appear as light colored spots in the images. Figure 4c provides a 3D image rendering, clearly showing the bound proteins as relatively higher spikes. Thus, bound HMGB proteins were identified visually by this significant height difference. Protein-induced DNA bend angles could then be measured at the protein-binding sites, with a measurement error of ∼5°, and the distribution of these angles was determined (Figure 5). The distribution shows an average induced DNA bend angle of 78° with a SD of 23° for HMGB (Box A) protein and for HMGB (Box A+B) an average DNA bend angle of 67° with a SD of 21° was found. The error in the average bend angle measurement was ±1.3°.Figure 4.


Mechanism of DNA flexibility enhancement by HMGB proteins.

Zhang J, McCauley MJ, Maher LJ, Williams MC, Israeloff NE - Nucleic Acids Res. (2009)

Distribution of protein-site bend angles for (a) HMGB (Box A) and (b) HMGB (Box A+B). The distribution shows an average induced DNA bend angle of 78° with a SD of 23° for HMGB (Box A) protein. HMGB (Box A+B) induces an average DNA bend angle of 67° with a SD of 21°.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651801&req=5

Figure 5: Distribution of protein-site bend angles for (a) HMGB (Box A) and (b) HMGB (Box A+B). The distribution shows an average induced DNA bend angle of 78° with a SD of 23° for HMGB (Box A) protein. HMGB (Box A+B) induces an average DNA bend angle of 67° with a SD of 21°.
Mentions: Figure 4 shows images of DNA with bound HMGB proteins. As can be seen in the height profile (Figure 4b), the protein–DNA complexes project higher from the mica surface than bare DNA, typically by ∼0.5 nm. These bound proteins thus appear as light colored spots in the images. Figure 4c provides a 3D image rendering, clearly showing the bound proteins as relatively higher spikes. Thus, bound HMGB proteins were identified visually by this significant height difference. Protein-induced DNA bend angles could then be measured at the protein-binding sites, with a measurement error of ∼5°, and the distribution of these angles was determined (Figure 5). The distribution shows an average induced DNA bend angle of 78° with a SD of 23° for HMGB (Box A) protein and for HMGB (Box A+B) an average DNA bend angle of 67° with a SD of 21° was found. The error in the average bend angle measurement was ±1.3°.Figure 4.

Bottom Line: These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments.The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding.Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Northeastern University, Boston, MA 02115, USA.

ABSTRACT
The mechanism by which sequence non-specific DNA-binding proteins enhance DNA flexibility is studied by examining complexes of double-stranded DNA with the high mobility group type B proteins HMGB2 (Box A) and HMGB1 (Box A+B) using atomic force microscopy. DNA end-to-end distances and local DNA bend angle distributions are analyzed for protein complexes deposited on a mica surface. For HMGB2 (Box A) binding we find a mean induced DNA bend angle of 78 degrees, with a standard error of 1.3 degrees and a SD of 23 degrees, while HMGB1 (Box A+B) binding gives a mean bend angle of 67 degrees, with a standard error of 1.3 degrees and a SD of 21 degrees. These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments. The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding. Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model.

Show MeSH
Related in: MedlinePlus