Indirect readout of the trp-repressor-operator complex by B-DNA's backbone conformation transitions

Biochemistry
Bernd WellenzohnKlaus R Liedl

Abstract

Although the trp-repressor-operator complex is one of the best studied transcriptional controlling systems, some questions regarding the specific recognition of the operator by the repressor remain. We performed a 2.35 ns long molecular dynamics simulation to clarify the influence of the two B-DNA backbone conformational substates B(I) and B(II) on complexation. The trp-repressor-operator is an ideal biological system for this study because experimental results have already figured out that the interaction between the internucleotide phosphates and the protein is essential for the formation of the high affinity complex. Our simulation supports these results, but more important it shows a strong correlation between the B(I)/B(II) phosphate substate and the number of interactions with this phosphate. In particular the B(I) <==> B(II) transitions occur synchronous to hydrogen bond breaking or formation. To the best of our knowledge, this was observed for the first time. Thus, we conclude that the sequence specific B(I)/B(II) behavior contributes via indirect readout to sequence specific recognition. These results have implication for the design of transcription-controlling drugs in view of the recently published influence of minor...Continue Reading

References

May 20, 1994·Journal of Molecular Biology·J E LadburyP B Sigler
Dec 1, 1996·Quarterly Reviews of Biophysics·B Hartmann, R Lavery
Mar 27, 1999·Journal of Molecular Biology·A O GrilloC A Royer
Jul 18, 2001·Journal of the American Chemical Society·B WellenzohnK R Liedl

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Citations

Nov 26, 2002·Journal of Molecular Biology·Christine RauchKlaus R Liedl
Feb 11, 2004·Journal of Biomolecular Structure & Dynamics·Michael TriebKlaus R Liedl
May 28, 2005·Journal of Biomolecular Structure & Dynamics·A Madhumalar, Manju Bansal
Mar 31, 2007·Journal of Molecular Biology·Brahim HeddiBrigitte Hartmann
Jul 28, 2005·Biopolymers·Fajar R WibowoKlaus R Liedl
Mar 30, 2004·Biopolymers·Fajar R WibowoKlaus R Liedl
Jun 15, 2004·Current Opinion in Structural Biology·Thomas E Cheatham
Oct 24, 2009·Journal of Molecular Biology·Brahim HeddiBrigitte Hartmann
Jul 13, 2006·Journal of the American Chemical Society·Brahim HeddiBrigitte Hartmann
Jul 21, 2006·The Journal of Physical Chemistry. B·Fajar R WibowoKlaus R Liedl

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