The role of DNA shape in protein-DNA recognition
Rohs, R. and West, S.M. and Sosinsky, Alona and Liu, P. and Mann, R.S. and Honig, B. (2009) The role of DNA shape in protein-DNA recognition. Nature (461), pp. 1248-1253. ISSN 0028-0836.
Abstract
The recognition of specific DNA sequences by proteins is thought to depend on two types of mechanism: one that involves the formation of hydrogen bonds with specific bases, primarily in the major groove, and one involving sequence-dependent deformations of the DNA helix. By comprehensively analysing the three-dimensional structures of protein–DNA complexes, here we show 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. Minor-groove narrowing is often associated with the presence of A-tracts, AT-rich sequences that exclude the flexible TpA step. These 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.
Metadata
| Item Type: | Article |
|---|---|
| School: | School of Science > Biological Sciences |
| Depositing User: | Administrator |
| Date Deposited: | 04 Aug 2010 14:09 |
| Last Modified: | 11 Oct 2016 11:58 |
| URI: | https://eprints.bbk.ac.uk/id/eprint/1097 |
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