Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Nucleotide Sequence-Dependent Shape Effects and their Role in Protein-DNA Recognition

Recent work on Hox proteins has revealed that subtle sequence-dependent local variations in minor groove geometry provide a mechanism through which different proteins in the same family can recognize small differences in nucleotide sequence. Crystal structures were determined for ternary complexes involving the homeodomains of one of the eight Drosophila Hox proteins, Scr, and its Exd co-factor, and DNA. One complex contained a DNA binding site, fkh250, that was specific for Scr, while the other contained a consensus DNA site, fkh250con* , that binds other Hox proteins as well. Both complexes have the homeodomain recognition helices of the Scr protein and its Exd co-factor bound in the major groove. However, additional basic amino acids are seen in the crystal structure of the complex with the fkh250 site whereas they are disordered when presented with the fkh250 con* site. In vitro binding studies and probes of embryonic development suggest that these basic residues play a key role in determining in vivospecificity. The specific recognition of the fkh250sequence appears to be related to the narrow minor groove whereas the groove is much wider in the equivalent region of the fkh250 con* sequence. MC simulations indicate that this difference in shape is a property of the free DNA.

Calculations using the DelPhi program indicate that the effect of minor groove width on binding can be traced to the electrostatic potential of the DNA. Narrow grooves produce enhanced electrostatic potentials due to electrostatic focusing effects originally discovered for enzyme active sites. The effect of minor groove shape on electrostatic potential offers a new mode of protein-DNA recognition. Specifically, sequence-dependent variations in DNA shape can exploit corresponding variations in electrostatic potential to tune binding affinities, even among closely related members of the same protein family. It will also be shown that minor groove narrowing can often be traced to the presence of A-tracts in the DNA sequence thus defining a distinct biological role for this motif. On the protein side, shape is recognized by the specific placement of basic amino acids in conformations that enable them to interact optimally with subtle changes in electrostatic potential. Results will be presented for different protein families which suggest that this mechanism is widely used, and may also play a role in nucleosome positioning.

References and Footnotes
  1. R. Joshi, J.M. Passner, R. Rohs, R. Jain, A. Sosinsky, M.A. Crickmore, V. Jacob, A.K. Aggarwal, B. Honig, and R.S. Mann. Functional specificity of a hox protein mediated by the recognition of minor groove structure. Cell 131, 530-543 (2007).
  2. R. Rohs, S.M. West, P. Liu, and B. Honig. Nuance in the Double-Helix and its Role in Protein-DNA Recognition. Curr. Opin. Struct. Biol. 19-2 (2009), in press.

Remo Rohs
Barry Honig

Howard Hughes Medical Institute
Department of Biochemistry & Molecular Biophysics
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue, New York, NY 10032

ph: 212-851-4652
fx: 212-851-4650
email Remo Rohs
email Barry Honig