March 1, Mon 2010
11:00 am, MRB 200 Conference Room
Dr. Remo Rohs
Howard Hughes Medical Institute, Columbia University
The Role of DNA Shape in Protein-DNA Recognition
The recognition of specific DNA sequences by proteins is often based on the interplay of two readout mechanisms: one that involves the formation of hydrogen bonds with specific bases (base readout), primarily in the major groove, and one involving sequence-dependent deformations of the DNA helix (shape readout). The comprehensive analysis of the three-dimensional structures of protein–DNA complexes shows that the binding of arginine residues to narrow minor grooves is a widely used mode for protein–DNA recognition. This readout mechanism exploits the phenomenon that narrow minor grooves strongly enhance the negative electrostatic potential of the DNA. The nucleosome core particle offers a prominent example of this effect. The reported findings indicate that the ability to detect local variations in DNA shape and electrostatic potential is a general mechanism that enables proteins to use information in the minor groove, which otherwise offers few opportunities for the formation of base-specific hydrogen bonds, to achieve DNA-binding specificity.