Transition state for protein–DNA recognition
- 5 August 2008
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 105 (31) , 10797-10802
- https://doi.org/10.1073/pnas.0802383105
Abstract
We describe the formation of protein-DNA contacts in the two-state route for DNA sequence recognition by a transcriptional regulator. Surprisingly, direct sequence readout establishes in the transition state and constitutes the bottleneck of complex formation. Although a few nonspecific ionic interactions are formed at this early stage, they mainly play a stabilizing role in the final consolidated complex. The interface is fairly plastic in the transition state, likely because of a high level of hydration. The overall picture of this two-state route largely agrees with a smooth energy landscape for binding that speeds up DNA recognition. This "direct" two-state route differs from the parallel multistep pathway described for this system, which involves nonspecific contacts and at least two intermediate species that must involve substantial conformational rearrangement in either or both macromolecules.Keywords
This publication has 43 references indexed in Scilit:
- Binding-Induced Folding of a Natively Unstructured Transcription FactorPLoS Computational Biology, 2008
- Comprehensive comparison of the interaction of the E2 master regulator with its cognate target DNA sites in 73 human papillomavirus types by sequence statisticsNucleic Acids Research, 2007
- Dynamic Basis for One-Dimensional DNA Scanning by the Mismatch Repair Complex Msh2-Msh6Molecular Cell, 2007
- Fly-Casting in Protein−DNA Binding: Frustration between Protein Folding and Electrostatics Facilitates Target RecognitionJournal of the American Chemical Society, 2007
- Stepwise binding and bending of DNA by Escherichia coli integration host factorProceedings of the National Academy of Sciences, 2006
- The recognition of local DNA conformation by the human papillomavirus type 6 E2 proteinNucleic Acids Research, 2006
- Specific Antibody−DNA Interaction: A Novel Strategy for Tight DNA RecognitionBiochemistry, 2003
- Experimental assignment of the structure of the transition state for the association of barnase and barstarJournal of Molecular Biology, 2001
- Intermediate species possessing bent DNA are present along the pathway to formation of a final TBP-TATA complex 1 1Edited by R. EbrightJournal of Molecular Biology, 1999
- Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DMA-binding domain bound to its DNA targetNature, 1992