Electrostatic interactions between arginines and the minor groove in the nucleosome.
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.
Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA.
Sean M
SM
West
Remo
R
Rohs
Richard S
RS
Mann
Barry
B
Honig
D000818:Animals; D001120:Arginine / Q000378:metabolism*; D001483:Base Sequence; D004331:Drosophila melanogaster / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009707:Nucleosomes / Q000737:chemistry* / Q000187:drug effects / Q000378:metabolism*; D012492:Salts / Q000494:pharmacology; D055672:Static Electricity; D014982:Xenopus laevis / Q000378:metabolism
D009707:Nucleosomes; D012492:Salts; D001120:Arginine