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Volumn 308, Issue 4, 2001, Pages 681-703

Dynamic simulations of 13 TATA variants refine kinetic hypotheses of sequence/activity relationships

Author keywords

Flexibility; Sequence dependent bending; TATA variants; TBP; Transcriptional activity

Indexed keywords

DNA; TATA BINDING PROTEIN;

EID: 0034972522     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4617     Document Type: Article
Times cited : (27)

References (92)
  • 1
    • 0025278259 scopus 로고
    • Weight matrix descriptions of four eukaryotic RNA polymerise II promoter: Elements derived from 502 unrelated promoter sequences
    • (1990) J. Mol. Biol , vol.212 , pp. 563-578
    • Bucher, P.1
  • 13
    • 0025309524 scopus 로고
    • Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro
    • (1990) Mol. Cell. Biol , vol.10 , pp. 3859-3867
    • Wobbe, C.R.1    Struhl, K.2
  • 20
    • 0031782289 scopus 로고    scopus 로고
    • Selective binding of the TATA box-binding protein to the TATA box-containing promoter: Analysis of structural and energetic factors
    • (1998) Biophys. J , vol.75 , pp. 2411-2421
    • Pardo, L.1    Pastor, N.2    Weinstein, H.3
  • 28
    • 0026566106 scopus 로고
    • Yeast and human TFIID with altered DNA-binding specificity for TATA elements
    • (1992) Cell , vol.68 , pp. 721-730
    • Strubin, M.1    Struhl, K.2
  • 66
    • 0034714010 scopus 로고    scopus 로고
    • 1 Å crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium
    • (2000) J. Mol. Biol , vol.301 , pp. 915-945
    • Chiu, T.K.1    Dickerson, R.E.2
  • 80
    • 0000219318 scopus 로고    scopus 로고
    • Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN
    • (1998) J. Chem. Phys , vol.109 , pp. 1617-1632
    • Barth, E.1    Schlick, T.2
  • 81
    • 0002403441 scopus 로고    scopus 로고
    • Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics
    • (1999) J. Comput. Phys , vol.151 , pp. 74-113
    • Sandu, A.1    Schlick, T.2
  • 83
    • 0348244547 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
    • (2000) J , vol.21 , pp. 86-104
    • Foloppe, N.1    MacKerell, A.D.2
  • 88
    • 0031572854 scopus 로고    scopus 로고
    • Insight into the stabilization of A-DNA by specific ion association: Spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III)
    • (1997) Structure , vol.5 , pp. 1297-1311
    • Cheatham, T.E.1    Kollman, P.A.2
  • 89
    • 0008985494 scopus 로고    scopus 로고
    • Extrapolation versus impulse in multiple-timestepping schemes. II. Linear analysis and applications to Newtonian and Langevin dynamics
    • (1998) J. Chem. Phys , vol.109 , pp. 1633-1642
    • Barth, E.1    Schlick, T.2
  • 90
    • 0034892788 scopus 로고    scopus 로고
    • Time-trimming tricks for dynamic simulations: Splitting force updates to reduce computational work
    • (2001) Structure , vol.9 , pp. R45-R53
    • Schlick, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.