ISSN:
0006-3525
Keywords:
molecular dynamics
;
DNA curvature
;
DNA flexibility
;
TATA box functionality
;
TATA box binding protein (TBP)
;
TBP recognition
;
TBP binding
;
TBP transcriptional activation
;
Chemistry
;
Polymer and Materials Science
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
Notes:
Four 1.5 ns molecular dynamics (MD) simulations were performed on the d(GCTATAAAAGGG) · d(CCCTTTTATAGC) double helix dodecamer bearing the Adenovirus major late promoter TATA element and three iso-composition mutants for which physical and biochemical data are available from the same laboratory. Three of these DNA sequences experimentally induce tight binding with the TATA box binding protein (TBP) and induce high transcription rates; the other DNA sequence induces much lower TBP binding and transcription. The x-ray crystal structures have previously shown that the duplex DNA in DNA-TBP complexes are highly bent. We performed and analyzed MD simulations for these four DNAs, whose experimental structures are not available, in order to address the issue of whether inherent DNA structure and flexibility play a role in establishing these observed preferences. A comparison of the experimental and simulated results demonstrated that DNA duplex sequence-dependent curvature and flexibility play a significant role in TBP recognition, binding, and transcriptional activation. © 1998 John Wiley & Sons, Inc. Biopoly 46: 403-415, 1998
Additional Material:
6 Ill.
Type of Medium:
Electronic Resource
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