Local DNA stretching mimics the distortion caused by the TATA box-binding protein.

X-ray structures of the TATA box-binding protein complexed with its DNA target show that the nucleic acid is severely bent away from the protein and also strongly unwound. We have used molecular mechanics and energy mapping to understand how such an unusual conformation can be induced. The results show that simple deformation pathways involving local stretching or unwinding of DNA reproduce many features of the experimental structure. Notably, kinked junctions with the flanking B-DNA regions occur without the need for any specific local

[1]  Bhyravabhotla Jayaram,et al.  Monte Carlo Simulation Studies on the Structure of the Counterion Atmosphere of B-DNA. Variations on the Primitive Dielectric Model , 1990 .

[2]  H. Weinstein,et al.  Electrostatic analysis of DNA binding properties in lysine to leucine mutants of TATA-box binding proteins. , 1995, Protein Engineering.

[3]  R. Ornstein,et al.  DNA binding by TATA-box binding protein (TBP): a molecular dynamics computational study. , 1996, Journal of Biomolecular Structure and Dynamics.

[4]  W. Olson.  Spatial configuration of ordered polynucleotide chains: a novel double helix. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[5]  P. Sigler,et al.  Crystal Structure of the Yeast TFIIA/TBP/DNA Complex , 1996, Science.

[6]  A. Gronenborn,et al.  Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex , 1995, Cell.

[7]  R Lavery,et al.  Modelling DNA conformational mechanics. , 1994, Biophysical chemistry.

[8]  R. H. Ritchie,et al.  Dielectric effects in biopolymers: The theory of ionic saturation revisited , 1985 .

[9]  Z. Shakked,et al.  A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein , 1996, Nature Structural Biology.

[10]  S. A. Salisbury,et al.  Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C). , 1983, Journal of molecular biology.

[11]  R Lavery,et al.  Modelling extreme stretching of DNA. , 1996, Nucleic acids research.

[12]  L. J. Maher,et al.  DNA bending by asymmetric phosphate neutralization. , 1994, Science.

[13]  A Bensimon,et al.  Alignment and sensitive detection of DNA by a moving interface. , 1994, Science.

[14]  Steven Hahn,et al.  Crystal structure of a yeast TBP/TATA-box complex , 1993, Nature.

[15]  R. Lavery,et al.  Defining the structure of irregular nucleic acids: conventions and principles. , 1989, Journal of biomolecular structure & dynamics.

[16]  A M Gronenborn,et al.  Intercalation, DNA Kinking, and the Control of Transcription , 1996, Science.

[17]  Stephen K. Burley,et al.  1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG , 1994, Nature Structural Biology.

[18]  Stephen K. Burley,et al.  Co-crystal structure of TBP recognizing the minor groove of a TATA element , 1993, Nature.

[19]  T. Richmond,et al.  Crystal structure of a yeast TFIIA/TBP/DNA complex , 1996, Nature.

[20]  Heinz Sklenar,et al.  JUMNA (junction minimisation of nucleic acids) , 1995 .

[21]  R. Lavery,et al.  DNA: An Extensible Molecule , 1996, Science.

[22]  S. Burley,et al.  Crystal structure of a TFIIB–TBP–TATA-element ternary complex , 1995, Nature.

[23]  J. Andrew McCammon,et al.  The Low Dielectric Interior of Proteins is Sufficient To Cause Major Structural Changes in DNA on Association , 1996 .