Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA.
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.
Flader
Wolfgang
W
Institute of General, Inorganic and Theoretical Chemistry University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
Wellenzohn
Bernd
B
Winger
Rudolf H
RH
Hallbrucker
Andreas
A
Mayer
Erwin
E
Liedl
Klaus R
KR
D000818:Animals; D001426:Bacterial Proteins; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics*; D018398:Homeodomain Proteins / Q000235:genetics*; D008958:Models, Molecular; D008968:Molecular Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012097:Repressor Proteins / Q000235:genetics*; D012680:Sensitivity and Specificity; D014157:Transcription Factors
D001426:Bacterial Proteins; D029721:Drosophila Proteins; D018398:Homeodomain Proteins; D009838:Oligodeoxyribonucleotides; D012097:Repressor Proteins; D014157:Transcription Factors; C052837:eve protein, Drosophila; D004247:DNA