Journal
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
Volume 27, Issue 6, Pages 861-866Publisher
ADENINE PRESS
DOI: 10.1080/07391102.2010.10508587
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Funding
- National Institutes of Health (NIH) [GM54510, U54 CA121852]
- NATIONAL CANCER INSTITUTE [U54CA121852] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM054510] Funding Source: NIH RePORTER
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Proteins rely on a variety of readout mechanisms to preferentially bind specific DNA sequences. The nucleosome offers a prominent example of a shape readout mechanism where arginines insert into narrow minor groove regions that face the histone core. Here we compare DNA shape and arginine recognition of three nucleosome core particle structures, expanding on our previous study by characterizing two additional structures, one with a different protein sequence and one with a different DNA sequence. The electrostatic potential in the minor groove is shown to be largely independent of the underlying sequence but is, however, dominated by groove geometry. Our results extend and generalize our previous observation that the interaction of arginines with narrow minor grooves plays an important role in stabilizing the deformed DNA in the nucleosome.
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