| Autor: |
Richard H. Lathrop, G. Wesley Hatfield, Michael L. Opel, Vira Tretyachenko-Ladokhina, Kimberly A. Aeling, N.R. Steffen, Donald F. Senear |
| Rok vydání: |
2006 |
| Předmět: |
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| Zdroj: |
Journal of Biological Chemistry. 281:39236-39248 |
| ISSN: |
0021-9258 |
| DOI: |
10.1074/jbc.m606363200 |
| Popis: |
Integration host factor (IHF) is a bacterial histone-like protein whose primary biological role is to condense the bacterial nucleoid and to constrain DNA supercoils. It does so by binding in a sequence-independent manner throughout the genome. However, unlike other structurally related bacterial histone-like proteins, IHF has evolved a sequence-dependent, high affinity DNA-binding motif. The high affinity binding sites are important for the regulation of a wide range of cellular processes. A remarkable feature of IHF is that it employs an indirect readout mechanism to bind and wrap DNA at both the nonspecific and high affinity (sequence-dependent) DNA sites. In this study we assessed the contributions of pre-formed and protein-induced DNA conformations to the energetics of IHF binding. Binding energies determined experimentally were compared with energies predicted for the IHF-induced deformation of the DNA helix (DNA deformation energy) in the IHF-DNA complex. Combinatorial sets of de novo DNA sequences were designed to systematically evaluate the influence of sequence-dependent structural characteristics of the conserved IHF recognition elements of the consensus DNA sequence. We show that IHF recognizes pre-formed conformational characteristics of the consensus DNA sequence at high affinity sites, whereas at all other sites relative affinity is determined by the deformational energy required for nearest-neighbor base pairs to adopt the DNA structure of the bound DNA-IHF complex. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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