Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA
✍ Scribed by Wolfgang Flader; Bernd Wellenzohn; Rudolf H. Winger; Andreas Hallbrucker; Erwin Mayer; Klaus R. Liedl
- Book ID
- 101718356
- Publisher
- Wiley (John Wiley & Sons)
- Year
- 2003
- Tongue
- English
- Weight
- 373 KB
- Volume
- 68
- Category
- Article
- ISSN
- 0006-3525
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✦ Synopsis
Abstract
Induced fit effects in the complex of a DNA decamer with two even‐skipped transcriptional repressor homeodomain molecules were investigated by means of molecular dynamics simulations. Dynamics of these effects are found to be in the time scale from pico‐ to nanoseconds. First steps are made by the fast‐moving DNA backbone phosphates, which upon binding change their B~I~/B~II~ substate distribution. Further rearrangements in the DNA double helix induced upon complexation, like bending of the helix axis, changes of the minor groove width, and of different helical parameters, are slower and occur within a few nanoseconds. The flexibility of the DNA, especially of its backbone, seems thereby to play an important role for specific DNA ligand recognition. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 139–149, 2003