DNA Bends in TATA-binding Protein·TATA Complexes in Solution Are DNA Sequence-dependent
2001; Elsevier BV; Volume: 276; Issue: 18 Linguagem: Inglês
10.1074/jbc.m004402200
ISSN1083-351X
AutoresJiong Wu, Kay M. Parkhurst, Robyn M. Powell, Michael Brenowitz, Lawrence J. Parkhurst,
Tópico(s)Bacterial Genetics and Biotechnology
ResumoThe TATA-binding protein (TBP) initiates assembly of transcription preinitiation complexes on eukaryotic class II promoters, binding to and restructuring consensus and variant "TATA box" sequences. The sequence dependence of the DNA structure in TBP·TATA complexes has been investigated in solution using fluorescence resonance energy transfer. The mean 5′dye-3′dye distance varies significantly among oligomers bearing the adenovirusmajor late promoter sequence (AdMLP) and five single-site variants bound to Saccharomyces cerevisiae TBP, consistent with solution bend angles for AdMLP of 76° and for the variants ranging from 30° to 62°. These solution bends contrast sharply with the corresponding co-crystal structures, which show ∼80° bends for all sequences. Transcription activities for these TATA sequences are strongly correlated with the solution bend angles but not with TBP·DNA binding affinities. Our results support a model in which transcription efficiency derives primarily from the sequence-dependent structure of the TBP·TATA binary complex. Specifically, the distance distribution for the average solution structure of the TBP·TATA complex may reflect the sequence-dependent probability for the complex to assume a conformation in which the TATA box DNA is severely bent. Upon assumption of this geometry, the binary complex becomes a target for binding and correctly orienting the other components of the preinitiation complex. The TATA-binding protein (TBP) initiates assembly of transcription preinitiation complexes on eukaryotic class II promoters, binding to and restructuring consensus and variant "TATA box" sequences. The sequence dependence of the DNA structure in TBP·TATA complexes has been investigated in solution using fluorescence resonance energy transfer. The mean 5′dye-3′dye distance varies significantly among oligomers bearing the adenovirusmajor late promoter sequence (AdMLP) and five single-site variants bound to Saccharomyces cerevisiae TBP, consistent with solution bend angles for AdMLP of 76° and for the variants ranging from 30° to 62°. These solution bends contrast sharply with the corresponding co-crystal structures, which show ∼80° bends for all sequences. Transcription activities for these TATA sequences are strongly correlated with the solution bend angles but not with TBP·DNA binding affinities. Our results support a model in which transcription efficiency derives primarily from the sequence-dependent structure of the TBP·TATA binary complex. Specifically, the distance distribution for the average solution structure of the TBP·TATA complex may reflect the sequence-dependent probability for the complex to assume a conformation in which the TATA box DNA is severely bent. Upon assumption of this geometry, the binary complex becomes a target for binding and correctly orienting the other components of the preinitiation complex. TATA-binding protein adenovirus major late promoter fluorescence resonance energy transfer carboxytetramethylrhodamine TATA-bearing 14-base double-labeled DNA oligomer with 5′-TAMRA and 3′-fluorescein duplex DNA corresponding to T*14-mer*F top strand corresponding single-labeled 14-mer with 3′-fluorescein -B, and -D, class II general transcription initiation factors A, -B, and -D base pair(s) The TATA-binding protein (TBP)1 binds to eukaryotic class II promoters at specific sequences of DNA of the consensus sequence TATA(a/t)A(a/t)N, nucleating assembly of the proteins required for transcription. Atomic resolution co-crystal structures of complexes of DNA bearing consensus strong promoter sequences bound toSaccharomyces cerevisiae (1Kim Y. Geiger J.H. Hahn S. Sigler P.B. Nature. 1993; 365: 512-519Crossref PubMed Scopus (1007) Google Scholar), Arabidopsis thaliana (2Kim J.L. Nikolov D.B. Burley S.K. Nature. 1993; 365: 520-527Crossref PubMed Scopus (963) Google Scholar), and human (3Nikolov D.B. Chen H. Halay E.D. Hoffmann A. Roeder R.G. Burley S.B. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 4862-4867Crossref PubMed Scopus (256) Google Scholar, 4Juo Z.S. Chiu T.K. Leiberman P.M. Baikalov I.B. Berk A.J. Dickerson R.E. J. Mol. Biol. 1996; 261: 239-254Crossref PubMed Scopus (283) Google Scholar) TBPs are extremely similar, characterized by a TBP-induced ∼80° bend in the DNA helix. TBP also binds to numerous variant TATA sequences, many of which occur naturally in promoters (5Hahn S. Buratowski S. Sharp P. Guarente L. Proc. Natl. Acad. Sci. U. S. A. 1989; 86: 5718-5722Crossref PubMed Scopus (215) Google Scholar, 6Wobbe C.R. Struhl K. Mol. Cell. Biol. 1990; 10: 3859-3867Crossref PubMed Scopus (238) Google Scholar). For 21 such single-point mutants of the adenovirus major late promoter (AdMLP) TATA box sequence, in vitrotranscription activity was found to range from <1% to 107% of that of the reference AdMLP TATA sequence (6Wobbe C.R. Struhl K. Mol. Cell. Biol. 1990; 10: 3859-3867Crossref PubMed Scopus (238) Google Scholar).The wide range of observed transcription activities suggested that TBP does not bind similarly to all TATA elements. Gel electrophoresis circular permutation analysis of TBP·DNA complexes shows that the electrophoretic mobility of the complexes is TATA sequence-dependent, with bend angles from <34° to 106° inferred from the gel mobility patterns (7Starr D.B. Hoopes B.C. Hawley D.K. J. Mol. Biol. 1995; 250: 434-446Crossref PubMed Scopus (158) Google Scholar). In contrast, the co-crystal structures of 11 TATA sequence variants of varying affinity bound to A. thaliana TBP are all very similar, with the DNA helix bent as in the strong promoters (3Nikolov D.B. Chen H. Halay E.D. Hoffmann A. Roeder R.G. Burley S.B. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 4862-4867Crossref PubMed Scopus (256) Google Scholar, 8Patikoglou G.A. Kim J.L. Sun L. Yang S.H. Kodadek T. Burley S.K. Genes Dev. 1999; 13: 3217-3230Crossref PubMed Scopus (235) Google Scholar).The present study was undertaken to further explore the TATA box sequence dependence of TBP binding and DNA structure using native, full-length S. cerevisiae TBP together with the AdMLP TATA sequence and five single-base-pair variant sequences. End-to-end distance distributions for these duplexes, free and TBP-bound, were extracted from measurements of time-resolved fluorescence emission in conjunction with fluorescence resonance energy transfer (FRET). Bend angles for the DNA within each of the TBP·DNA complexes were determined using three models. The reference AdMLP and five variant TATA sequences bound to TBP have significantly different mean end-to-end distances in solution. These distances are consistent with DNA bend angles ranging from 29.9° to 61.8° for the variant sequences and 76.2° for the native AdMLP. The latter bend angle is in excellent accord with the bends observed in the co-crystal structures. A strong correlation is observed between the solution bend angles and the transcription activities (6Wobbe C.R. Struhl K. Mol. Cell. Biol. 1990; 10: 3859-3867Crossref PubMed Scopus (238) Google Scholar). These findings are consistent with the structure of TBP·TATA complexes being a principal determinant of TATA-box-dependent transcription activity. A model is proposed that reconciles the sequence dependence of bend angles and transcription activities measured in solution with the DNA structures observed in the co-crystals.DISCUSSIONTime-resolved fluorescence resonance energy transfer provides a rigorous approach to the determination of the structure and dynamics of macromolecules in solution. The primary experimental findings from this work are 1) the existence in solution of DNA sequence-dependent differences in the trajectory of the DNA as it passes through TBP·TATA complexes and 2) the inverse correlation between the observed DNA bend angle and the breadth of the corresponding distance distribution.DNA Bend Angles in TBP·TATA Complexes and the Corresponding Probability Distributions Are DNA Sequence-dependentThe FRET data clearly demonstrate sequence-dependent differences in the trajectory of the DNA as it passes through TBP·DNA complexes. In sharp contrast to this result and similar conclusions drawn from circular permutation and DNA phasing studies (7Starr D.B. Hoopes B.C. Hawley D.K. J. Mol. Biol. 1995; 250: 434-446Crossref PubMed Scopus (158) Google Scholar, 25Bareket-Samish A. Cohen I. Haran T.E. J. Mol. Biol. 2000; 299: 965-977Crossref PubMed Scopus (50) Google Scholar), eleven variant TATA sequences bound to TBP, including all of the sequences in this study, have essentially identical ∼ 80° DNA bends in the atomic resolution structures determined for TBP·DNA co-crystals (3Nikolov D.B. Chen H. Halay E.D. Hoffmann A. Roeder R.G. Burley S.B. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 4862-4867Crossref PubMed Scopus (256) Google Scholar, 8Patikoglou G.A. Kim J.L. Sun L. Yang S.H. Kodadek T. Burley S.K. Genes Dev. 1999; 13: 3217-3230Crossref PubMed Scopus (235) Google Scholar). These contrasting results are accommodated within a two-state allosteric model, based on an equilibrium between transcriptionally active and inactive TBP·DNA conformations (discussed below). The apparent conundrum presented by the solution and co-crystal structures is then definitively explained in the accompanying paper (24Wu J. Parkhurst K.M. Powell R.M. Parkhurst L.J. J. Biol. Chem. 2001; 276: 14623-14627Abstract Full Text Full Text PDF PubMed Scopus (31) Google Scholar).Also important for consideration of the underlying mechanism of this observation are the differences in the breadths of the corresponding distance distributions provided by the time-resolved FRET data. Clearly both structure and dynamics contribute to TBP·TATA function. The AdMLP sequence alone shows only a slight increase in the value of ς, the S.D. of the end-to-end distance distribution, upon TBP binding. A plausible hypothesis is that the complementarity of the protein-duplex interface confines the helix and restricts additional motion. This slight increase in the breadth of the distribution for the tightly bound AdMLP may derive from the presence of multiple conformers at equilibrium, each with bent DNA but differing, for example, in the extent of phenylalanine intercalation (11Parkhurst K.M. Richards R.M. Brenowitz M. Parkhurst L.J. J. Mol. Biol. 1999; 289: 1327-1341Crossref PubMed Scopus (72) Google Scholar). An integrated hydroxyl radical footprinting and molecular dynamics study of the TBP-AdMLP interface supports this view of its dynamic nature (26Pastor N. Weinstein H. Jamison E. Brenowitz M. J. Mol. Biol. 2000; 304: 55-68Crossref PubMed Scopus (132) Google Scholar).The variant sequences show a general trend toward increasingly broader distributions as the extent of bending decreases, up to Δς = 6.2 Å for the T6 variant. The inverse correlation between bending extent and distribution broadening may derive from the increasing misfit along the protein-DNA interface as helical bending decreases, including retention of solvent molecules at the interface. Indeed, complexes of TBP with the variant duplexes may be present in multiple conformations with the DNA bent very differently among those conformers, as discussed further in the following section. The broadened distribution would then result from equilibrium exchange among such conformers occurring on a time scale that is slow relative to the nanosecond time scale of the measurements, i.e.microseconds. In this case, the broader distribution of distances wouldnot derive from any high frequency torsional and bending motions of the duplex that occur on time scales faster than nanoseconds, because such motion would be averaged out in these measurements (27Okonogi T.M. Reese A.W. Alley S.C. Hopkins P.B. Robinson B.H. Biophys. J. 1999; 77: 3256-3276Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar).A Bi-modal Distribution Model Reconciling the Solution and Co-crystal Bend AnglesA two-state model is hypothesized, unifying into a coherent perspective the sequence-dependent solution bend angles reported herein and the x-ray results in which only an AdMLP-like structure was crystallized. Each variant duplex bound to TBP is proposed to exist in two conformations, one (conformerML) with the DNA bound and bent as in the AdMLP·TBP complex and the other (conformerTI) with the DNA significantly less bent (Fig.4 A). Only conformerML has the correct geometry to allow binding of subsequent transcription proteins and effect measurable mRNA synthesis. ConformerTI is transcriptionally inactive and has the same overall conformation for all variant DNA·TBP complexes, although the local structural and energetic features of the protein-DNA interface are sequence-dependent. The presence of conformerML is assumed for all variants, because such a conformer is crystallized (except A3 (8Patikoglou G.A. Kim J.L. Sun L. Yang S.H. Kodadek T. Burley S.K. Genes Dev. 1999; 13: 3217-3230Crossref PubMed Scopus (235) Google Scholar)), although the solution conditions for the crystallizations differed from those employed in the present study. The two-state model provides a unifying and simple relationship among the variants to explain their observed differences in bend angle and distance distribution variance, rather than necessitating that each variant, with a unique set of conformers, be considered separately. 7This two-state model is conceptually analogous to the allosteric model, with an R-state active form, a T-state inactive form and L, the allosteric constant, defining the R-T equilibrium. Myriad hemoglobins are well described by these two states but have widely variable value of L, depending on how substitutions alter the α1β1/α2β2interface.If the equilibrium for conformerTI ↔ conformerML occurs on a time scale significantly slower than that of the nanosecond measurements, the measured fluorescence decay for a given sequence would derive from both conformers. In fact, the probability distributions for all of the bound variant duplexes, P(R)i,bound, are very well fit globally by two constrained Gaussian distributions 8Whereas at least two distinct distributions are required to fit various higher-order DNA structures (28Yang M. Millar D.P. Biochemistry. 1996; 35: 7959-7967Crossref PubMed Scopus (43) Google Scholar), each of the structures investigated herein were very well fit by a single distribution. It is only in the model-dependent global analysis of all bound sequences that two distributions can be distinguished, in varying proportions, accounting for all observed decays. corresponding to conformerML and conformerTI,P(R)i,bound=ΦMLP(R)ML,bound+ΦTIP(R)TI,boundEquation 8 where i specifies the variant, Φ = mole fraction, and ΦTI = 1 − ΦML. In this analysis, the values of RML,bound and ςML,bound for conformerML were fixed at 47.1 and 8.5 Å (Table II), respectively. The values obtained for the two fitted parameters were RTI,bound = 53.3 Å and ςTI,bound = 9.9 Å. The relative mole fractions of conformerML and conformerTI for each variant,i, were determined concurrently as a function of the fitted value of RTI,bound and the measured values of RML,bound andRi,bound.Bend angles corresponding to the two-state model were then calculated for each variant, i, using Eq. 6 with appropriate weighting for RML,bound andRTI,bound,αi,calc=2cos−1R̄ML,boundΦML+R̄TI,boundΦTI−L2R̄i,free−L2Equation 9 where 〈Ri,free〉 is the observed mean end-to-end distance for a given free duplex. The relationship of the calculated (Eq. 9) and observed bend angles (TableIII) with the mole fraction of conformerML is shown in Fig.4 B.If the exchange between conformerTI and conformerML is fast relative to subsequent binding processes, the transcription factors "see" and appear macroscopically to bind to an average TBP·DNA structure that is sequence-dependent. The model predicts that the more AdMLP-like the average binary structure, the more efficiently transcription will proceed. Implicit in this model is a correspondence between the structure of the TBP·TATA complex and transcription activity, which is explored further below.Minimal Correspondence of TBP·DNA Complex Lifetime to Bend Angle or Transcriptional ActivityHawley and coworkers (7Starr D.B. Hoopes B.C. Hawley D.K. J. Mol. Biol. 1995; 250: 434-446Crossref PubMed Scopus (158) Google Scholar), inferring bend angles from gel mobility shifts for TBP-bound AdMLP and eight variant sequences, also observed sequence-dependent differences in bend angles. However, for the sequences common to both studies, those angles differ from those reported herein in magnitude, by up to a factor of two, but more significantly, in the ordering of sequences by decreasing bend.Although a correlation was asserted between bend angles inferred from circular permutation analysis and TBP·TATA complex stability (7Starr D.B. Hoopes B.C. Hawley D.K. J. Mol. Biol. 1995; 250: 434-446Crossref PubMed Scopus (158) Google Scholar), careful inspection of those data reveal a minimal correspondence between these two properties. A plot of the lifetime of the TBP·DNA complex versus bend angle from Table I (7Starr D.B. Hoopes B.C. Hawley D.K. J. Mol. Biol. 1995; 250: 434-446Crossref PubMed Scopus (158) Google Scholar) shows no general linear correlation (correlation = 0.76, coefficient of determination = 0.59); rather, the data form two distinct sets. The first of these sets of five sequences is composed of unstable TBP·TATA complexes, with lifetimes ≤ 0.08 that of the wild type, but with bend angles ranging from 100-fold differences observed in transcription efficiency could not have arisen from differences in TBP·DNA affinity.Figure 5The correlation between the solution bend angles of the TBP-bound duplexes and the corresponding in vivo (A) and in vitro(B) transcription activities reported by Wobbe and Struhl (6Wobbe C.R. Struhl K. Mol. Cell. Biol. 1990; 10: 3859-3867Crossref PubMed Scopus (238) Google Scholar), with the activity of the AdMLP sequence set at ++ and 1.00, respectively. The bend angles were determined using the two-kink model (Fig. 2 B). For B, the correlation = 0.98 and the coefficient of determination = 0.97. These data show a minimal relationship between transcription activity and the association equilibrium constant (correlation = 0.88 and coefficient of determination = 0.77).View Large Image Figure ViewerDownload Hi-res image Download (PPT)Suppose, however, that only the tightly bound AdMLP sequence was saturated and the variant sequences were fractionally saturated in accord with their respective binding constants, so that transcription activity did reflect differences in affinity. Then, for example, were the AdMLP sequence 95% bound (as a lower limit), the transcription activity for the T6 sequence would be 86% that of AdMLP, based on theKa values shown in Table I. In contrast, the experimentally observed transcription activity for T6 was only 10% that of AdMLP (6Wobbe C.R. Struhl K. Mol. Cell. Biol. 1990; 10: 3859-3867Crossref PubMed Scopus (238) Google Scholar). Thus, several independent lines of evidence support the conclusion that differences in TBP·DNA binding affinity cannot account for the observed differences in transcription efficiency.In contrast, a significant correlation is observed between the solution bend angles and transcription activity. Wobbe and Struhl (6Wobbe C.R. Struhl K. Mol. Cell. Biol. 1990; 10: 3859-3867Crossref PubMed Scopus (238) Google Scholar) similarly concluded that the in vivo activity of a TATA element is directly affected by the binary TBP·TATA structure. This conclusion was based on the close similarity between the in vitroactivity of yeast TBP (and human TFIID) and transcription activity in yeast cells. The strong correspondence between the solution geometry of the TBP·DNA complex and transcription activity is further supported by a comparison of Figs. 4 B and 5B. The relationship between transcription efficiency and bend angle is strikingly similar to the relationship between the fractional population of the allosteric conformerML and bend angle. The extent to which conformerML is populated, for a given sequence, thus closely corresponds to the relative transcription activity.The relatively large values of ς determined herein for the bound duplexes with less favorable TATA box sequences are consistent with low frequency DNA flexibility within the binary complexes. Such duplex motions cannot be effectively distinguished from multiple conformations (29Naimushin A.N. Fujimoto B.S. Schurr J.M. Biophys. J. 2000; 78: 1498-1518Abstract Full Text Full Text PDF PubMed Scopus (31) Google Scholar). The observed correlation between the extent of DNA bending and transcription activity thus leads us to propose that the probability for a given TBP·TATA complex to assume the conformation required for binding of subsequent proteins determines the corresponding transcription efficiency. For the bound variants, as the deviation from ∼ 80° increases, severe distortions of the duplex DNA to approach 80° become increasingly less probable. In terms of such fluctuations, a dependence of transcription efficiency on the average conformation of the binary TBP·promoter complex seems reasonable. Both biochemical and crystallographic results show that flanking sequences up- and downstream of the TATA box are contacted by TFIIA (30Lagrange T. Kim T.-K. Orphanides G. Ebright Y.W. Ebright R.H. Reinberg D. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 10620-10625Crossref PubMed Scopus (92) Google Scholar, 31Coulombe B. Li J. Greenblatt J. J. Biol. Chem. 1994; 269: 19962-19967Abstract Full Text PDF PubMed Google Scholar) and TFIIB (32Lee S. Hahn S. Nature. 1995; 376: 609-612Crossref PubMed Scopus (77) Google Scholar, 33Lagrange T. Kapanidis A.N. Tang H. Reinberg D. Ebright R.H. Genes Dev. 1998; 12: 34-44Crossref PubMed Scopus (304) Google Scholar, 34Tsai F.T.F. Sigler P.B. EMBO J. 2000; 19: 25-36Crossref PubMed Scopus (139) Google Scholar), with TFIIB contacting both. Appropriately bent DNA in the TBP·DNA target may thus be critical for formation of stable ternary and quaternary complexes involving these proteins.The trajectories of the helical axes resulting from different bends diverge rapidly (Fig. 6). For example, for a 14-bp duplex centered on the TATA box, the difference in the 5′-3′ distance between a 40° and an 80° bend is ∼4 Å. Extension of the duplex by only 6 bp up- and downstream, for example, more than triples that difference, from ∼4 to ∼13 Å. TBP-bound T6 and AdMLP have angles of ∼40° and ∼80°, respectively, and 6-bp extensions correspond generally to the flanking contact regions for TFIIA and -B. Formation of a stable higher-order structure is thus predicted to be less probable for the TBP·T6 complex than for the TBP·AdMLP complex, due to the spatial requirements.Figure 6The helical trajectories corresponding to 40° (dotted lines) and 80° (solid lines) DNA bends. The lighter segments of each trajectory correspond to that part of the 14-mer duplex beyond the 5′ and 3′ phenylalanine insertion sites, beginning with positions −31 and −24, respectively. The −20 position downstream of the TATA box (●) and the −38 position upstream (○) delineate the TFIIB contact regions and the −42 position (⊗), the TFIIA contact region. The distance between the up- and downstream TFIIB contacts (double arrows) differs by ∼7 Å for 40° (T6) and 80° (AdMLP) bends.View Large Image Figure ViewerDownload Hi-res image Download (PPT)In drawing a correlation between the apparent bend angle and transcriptional activity, however, consideration must be given to the experimental conditions of the respective studies. The in vitro transcription assays were performed in the presence of osmolyte (6Wobbe C.R. Struhl K. Mol. Cell. Biol. 1990; 10: 3859-3867Crossref PubMed Scopus (238) Google Scholar, 35Sawadogo M. Roeder R.G. Proc. Natl. Acad. Sci. U. S. A. 1985; 82: 4394-4398Crossref PubMed Scopus (366) Google Scholar). As shown in the accompanying paper (24Wu J. Parkhurst K.M. Powell R.M. Parkhurst L.J. J. Biol. Chem. 2001; 276: 14623-14627Abstract Full Text Full Text PDF PubMed Scopus (31) Google Scholar), the conformations of some bound variant sequences are sensitive to the presence of osmolyte. Because a significant correlation is observed between bend angle and transcriptional activity both in vitro and in vivo (Fig. 5, A andB), it is plausible that the extremely small differences in energy between conformers for these sequences (24Wu J. Parkhurst K.M. Powell R.M. Parkhurst L.J. J. Biol. Chem. 2001; 276: 14623-14627Abstract Full Text Full Text PDF PubMed Scopus (31) Google Scholar) are compensated in osmolyte by protein·protein interactions among multiple transcription factors. How the binding of even one additional transcription protein, in osmolyte, might affect the equilibrium among sequence-dependent TBP·DNA conformers is not known. Thus, effects of osmolytes on the conformation of the binary complex within multiprotein complexes require further exploration.However, unequivocal new insight is provided by elucidation of the solution structures of TBP·AdMLP and TBP·A3. These binary complexes with the high and low extremes of the observed bend angles correspond to the high and low extremes of transcriptional activity. The solution geometries of these two complexes are insensitive to the presence of osmolyte (24Wu J. Parkhurst K.M. Powell R.M. Parkhurst L.J. J. Biol. Chem. 2001; 276: 14623-14627Abstract Full Text Full Text PDF PubMed Scopus (31) Google Scholar) and establish clearly the relationship between transcription activity and the structure of the binary complex.ConclusionsThe geometries of the TBP-bound variant TATA sequences in solution vary significantly and differ from their corresponding co-crystal structures. These solution conformations are consistent with DNA bend angles ranging from ∼30 to ∼76° based on a two-kink bending model. A strong correlation between the solution bend angles and relative transcription activity, but not with TBP·DNA affinity, is observed. This correlation is particularly notable, because efficient transcription requires complex geometric relationships among many proteins and to summarize such complexity with a single, simple bend angle must be, to some extent, an oversimplification.This model contrasts with models in which the TBP·DNA binary complex structure is conserved (8Patikoglou G.A. Kim J.L. Sun L. Yang S.H. Kodadek T. Burley S.K. Genes Dev. 1999; 13: 3217-3230Crossref PubMed Scopus (235) Google Scholar) and sequence-dependent differences in transcription efficiency derive primarily from sequence-dependent differences in the stability of that complex (7Starr D.B. Hoopes B.C. Hawley D.K. J. Mol. Biol. 1995; 250: 434-446Crossref PubMed Scopus (158) Google Scholar, 8Patikoglou G.A. Kim J.L. Sun L. Yang S.H. Kodadek T. Burley S.K. Genes Dev. 1999; 13: 3217-3230Crossref PubMed Scopus (235) Google Scholar). Our results support a model in which transcription efficiency derives in significant part from the sequence-dependent structure of the TBP·TATA binary complex. More specifically, the distance distribution for the average solution structure of the TBP·TATA complex may reflect the sequence-dependent probability for the complex to assume a conformation in which the TATA box DNA is severely bent. Upon assumption of this geometry, the binary complex becomes a target for binding and co
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