Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
Structural Polymorphism of the Nucleosomal DNA and Implications for Protein Binding
A nucleosome forms a basic unit of the chromosome structure. A biologically relevant question is how much of the nucleosomal conformational space is accessible to protein-free DNA, and what proportion of the nucleosomal conformations are induced by bound histones. To investigate this, we have analysed high resolution x-ray crystal structure datasets of DNA in protein-free as well as protein-bound forms, and compared the dinucleotide step parameters for the two datasets with those for high resolution nucleosome structures. Our analysis shows that most of the dinucleotide step parameter values for the nucleosome structures lie within the range accessible to protein-free DNA, indirectly indicating that the histone core plays more of a stabilising role. The nucleosome structures are observed to assume smooth and nearly planar curvature, implying that 'normal' B-DNA like parameters can give rise to a curved geometry at the gross structural level. Different nucleosome structures, as well as different fragments of the same nucleosome, are observed to assume different values of curvature, as well as out-of-plane components of curvature, reaffirming the wide ranging sequence dependent polymorphism of the double helical B-form DNA. We have compared the curvature of different fragments in the nucleosome structures to the curvature of highly distorted DNA fragments such as those bound to the catabolite activator protein and the integration host factor. This investigation throws light on the different modes of inherent and induced DNA curvature, and may lead to the prediction of DNA fragments vulnerable to the action of different proteins of the transcription machinery.
Molecular Biophysics Unit