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Understanding intermolecular recognition in eukaryotic transcription: the TBP-TATA box complexes

Abstract

Recent molecular dynamics (MD simulations showed that the stability of the TBP-TATA box complex depends on sequence dependent flexibility, curvature, and bending of the TATA box upon binding by TBP. Some T-A to A-T mutations in the TATA box are not well tolerated. This result is difficult to rationalize, since it is widely accepted that recognition interactions in the minor groove of DNA are not able to distinguish A-T from T-A bp. The predicted structure of wild-type and mutant DNA sequences will be docked on to the saddle-like surface of TBP and the induced conformation of the DNA by TBP will be investigated by MD simulations. This work seeks to obtain an atomic level understanding of the recognition of different TATA box promoters by TBP and how this might affect transcription. (AU)

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