• Title/Summary/Keyword: Open complex

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Mechanism of E. coli RNA polymerase-promoter interactions

  • Roe, Jung-Hye;Record.Jr, M.Thomas
    • The Microorganisms and Industry
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    • v.13 no.1
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    • pp.4-9
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    • 1987
  • The regulation of gene expression in procaryotes is accomplished primarily at the level of transcription. Initiation of transcription is subject to numerous promoter-specific controls which act to ensure coordinate expression of disparate genes. The kinetics of formation of a functional("open") complex at a promoter, prior to the catalytic steps of RNA chain initiation and elongation, is thought to play a major role in controlling the efficiency of transcription of that promotor, since the subsequent processes of nucleotide binding and phosphodiester bond formation are rapid and are not promoter-specific (Mangel and Chamberlin, 1974 Shimamoto et al., 1981)

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Effect of sequence variations within DNA melting region on the rate of formation of open complexes at $\lambdaP_{R}$ promoter ($\lambdaP_{R}$ 프로모터 열린복합체 형성에 미치는 DNA melting 부위 염기서열의 영향)

  • 정현채;노정혜
    • Korean Journal of Microbiology
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    • v.28 no.1
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    • pp.19-26
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    • 1990
  • To examine the effects of sequence variations near the transcriptional start site on the rate of formation of the open complexes at bacteriophage $\lambda P_{R}$ promoter, two mutant promoters were created by site-specific mutagenesis using synthetic oligonucleotides. Mutant I coatains changes at positions -3 and -4 from TT to CC, thus having a 6-bp long G/C stretch between -10 region and transciptional start site (+1). Mutant II has changes at positions -5 and -6 from GG to AA, thereby having a 9-bp long A/T stretch between positions -11 and -3. Selective filter binding assays were performed to measure the rate of formation of the open complexes between the wild-type or two mutant $P_{R}$ promoters on 664 bp fragments and E. coli RNA polymerase at two temperatures. At 37.deg.C, the wild-type and two mutants showed similar rates for the formation of open complex. The second order rate constant $k_{a}$ and $\tau _{int}$, as determined from the .tau.-plot analysis, were $(6.0\pm0.4)\times10^{6}M^{-1}sec^{-1}$ and $11\pm5$sec, respectively. At 18.deg.C, however, the wild-type and two mutant promoters showed differences in the kinetic parameters. k for the wild-type promoter was (2.2$\pm$0.1)\times 10^{6}M^{-1}sec^{-1}$ and $\tau _{int}$ was 76$\pm$sec. Mutant I and II exhibited differences mainly in the rate of isomerization ($\tau_{int,I}=91\pm$10 sec, int,II=34$\pm$ sec), whereas the second order rate constant $k_{a}$ was similar to the wild type value. This result implies that at $18^{\circ}C$, the isomerization rate is determined by both protein conformational change and DNA melting, which are separable kinetically according to the 3-step mechanism of Roe et al.(1984,1985), and that the base changes affected mainly the rate of DNA melting as predicted.lting as predicted.

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A numerical study on the combined natural convection and radiation in a partially open complex enclosure with a heater and partitions (발열체와 격막이 있고 일부가 열린 복합공간내의 자연대류-복사열전달에 관한 수치적 연구)

  • Kim, Tae-Guk;Min, Dong-Ho;Han, Gyu-Ik;Son, Bong-Se;Seo, Seok-Ho
    • Transactions of the Korean Society of Mechanical Engineers B
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    • v.21 no.2
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    • pp.235-251
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    • 1997
  • A numerical simulation on the combined natural convection and radiation is carried out in a partially open rectangular enclosure with a heater by using the finite volume and the S-8 discrete ordinate methods. The fluid inside the enclosure is considered as an absorbing, emitting and anisotropic scattering media. The heater causes a natural circulation of the fluid (10$^{5}$ $^{9}$ ) which results in significant in-flow of the ambient cold fluid through the partially open wall. Comparing the results of pure convection with those of the combined convection- radiation, the combined heat transfer results with small Planck numbers (P$_{l}$ <1.0) show much stronger circulation than those of the pure convection, and the fluid circulation is more evident for larger Rayleigh numbers. When one of three radiative properties - the medium absorption coefficient, the wall reflectivity, and the scattering albedo - increases, the fluid circulation and the heat transfer in the enclosure are reduced. The location of the heater and the open ratio of the right wall are also shown to affect the fluid circulation and heat transfer significantly. However, the anisotropy of the scattering phase function is shown to be unimportant for the fluid circulation and heat transfer within the enclosure considered in this study.