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1.
Sequence dependence of DNA conformational flexibility 总被引:9,自引:0,他引:9
By using conformational free energy calculations, we have studied the sequence dependence of flexibility and its anisotropy along various conformational variables of DNA base pairs. The results show the AT base step to be very flexible along the twist coordinate. On the other hand, homonucleotide steps, GG(CC) and AA(TT), are among the most rigid sequences. For the roll motion that would correspond to a bend, the TA step is most flexible, while the GG(CC) step is least flexible. The flexibility of roll is quite anisotropic; the ratio of fluctuations toward the major and minor grooves is the largest for the GC step and the smallest for the AA(TT) and CG steps. Propeller twisting of base pairs is quite flexible, especially of A.T base pairs; propeller twist can reach 19 degrees by thermal fluctuation. We discuss the effect of electrostatic parameters, comparison with available experimental results, and biological relevance of these results. 相似文献
2.
The distributions of the junction sequences of homooligomer tracts of various lengths have been examined in prokaryotic DNA sequences and compared with those of eukaryotes. The general trends in the nearest and next to nearest neighbors to the tracts are similar for both groups. In both prokaryotes and eukaryotes A/T runs are preferentially flanked on either the 5' or the 3' ends by A and/or T. G/C runs are preferentially flanked by G and/or C. There is discrimination against A/T runs flanked by G or C and G/C runs flanked by A or T. However, whereas the distribution of prokaryotic homooligomer tract junction sequences was quite homogeneous, large variations were observed in the 5-fold larger eukaryotic database, increasing in magnitude from tracts of length 2 to 3 to 4 base pairs long. Possible DNA conformational implications and in particular DNA curvature and packaging aspects of prokaryotes and eukaryotes are discussed. 相似文献
3.
Souichi Morikawa Kazuhiro Ogata Ai Sekikawa Akinori Sarai Shunsuke Ishii Yoshifumi Nishimura Haruki Nakamura 《Journal of biomolecular NMR》1995,6(3):294-305
Summary The solution structure of a specific DNA complex of the minimum DNA-binding domain of the mouse c-Myb protein was determined by distance geometry calculations using a set of 1732 nuclear Overhauser enhancement (NOE) distance restraints. In order to determine the complex structure independent of the initial guess, we have developed two different procedures for the docking calculation using simulated annealing in four-dimensional space (4D-SA). One is a multiple-step procedure, where the protein and the DNA were first constructed independently by 4D-SA using only the individual intramolecular NOE distance restraints. Here, the initial structure of the protein was a random coil and that of the DNA was a typical B-form duplex. Then, as the starting structure for the next docking procedure, the converged protein and DNA structures were placed in random molecular orientations, separated by 50 Å. The two molecules were docked by 4D-SA utilizing all the restraints, including the additional 66 intermolecular distance restraints. The second procedure comprised a single step, in which a random-coil protein and a typical B-form DNA duplex were first placed 70 Å from each other. Then, using all the intramolecular and intermolecular NOE distance restraints, the complex structure was constructed by 4D-SA. Both procedures yielded the converged complex structures with similar quality and structural divergence, but the multiple-step procedure has much better convergence power than the single-step procedure. A model study of the two procedures was performed to confirm the structural quality, depending upon the number of intermolecular distance restraints, using the X-ray structure of the engrailed homeodomain-DNA complex.Abbreviations rmsd
root-mean-square deviation
- NOE
nuclear Overhauser enhancement
- 4D-SA
simulated annealing in four-dimensional space
- Myb-R2R3
repeats 2 and 3 of the DNA-binding domain of the c-Myb protein
- DNA 16
Myb-specific binding DNA duplex with 16 base pairs
- IHDD-C
residues 3 to 59 of the C-chain of the engrailed homeodomain-DNA complex
- DNA11
DNA duplex with base pairs 9 to 19 of the engrailed homeodomain-DNA complex 相似文献
4.
Linkage of Mercury, Cadmium, and Arsenate and Drug Resistance in Clinical Isolates of Pseudomonas aeruginosa 总被引:10,自引:4,他引:6 下载免费PDF全文
Hideomi Nakahara Tomoaki Ishikawa Yasunaga Sarai Isamu Kondo Hiroyuki Kozukue Simon Silver 《Applied microbiology》1977,33(4):975-976
Of the 787 isolates, 99.8% were metal resistant, with most (99.5%) showing multiple resistance. Fifty-three percent of the isolates were both metal and drug resistant, whereas only 19% were metal resistant and drug sensitive. 相似文献
5.
6.
Ruth Nussinov Akinori Sarai Gary W. Smythers David Wang Robert L. Jernigan 《Journal of biomolecular structure & dynamics》2013,31(3):707-722
Abstract Previous studies of the dinucleotides flanking both the 5′ and 3′ ends of homooligomer tracts have shown that some flanks are consistently preferred over others (1,2). In the first preferred group, the homooligomer tracts are flanked by the same nucleotide and/or the complementary nucleotides, e.g., ATAn, TTAn, CCGn, where n=2–5. Runs flanked by nucleotides with which they cannot base pair are distinctly disfavored. (In this group A/Tn are flanked by C and/or G; Gn/Cn are flanked by A/T, e.g., CGAn, TnGG, G., AT). The frequencies of runs flanked by AorT, and G or C (“mixed” group) are as expected. Here we seek the origin of this effect and its relevance to protein-DNA interactions. Surprisingly, within the first group, runs flanked by their complements with a pyrimidine-purine junction (e.g., TTAn, CnGG) are greatly preferred. The frequencies of their purine-pyrimidine junction mirror-images is just as expected. This effect, as well as additional ones enumerated below, is seen universally in eukaryotes and in prokaryotes, although it is stronger in the former. Detailed analysis of regulatory regions shows these strong trends, particularly in GC sequences. The potential relationship to DNA conformation and DNA-protein interaction is discussed. 相似文献
7.
Robert L. Jernigan Akinori Sarai Bruce Shapiro Ruth Nussinov 《Journal of biomolecular structure & dynamics》2013,31(4):561-567
Abstract We propose some specific DNA conformations that explain, in terms of molecular conformations, the anomalous gel electrophoretic behavior of the sequences (VA4T4X)1, and (V2A3X2)1 where V and X are either G or C. Previously (J. Biomole. Struct. Dyn. 4, 41, 1986) we considered hydrophobic interactions a mong aliphatic hydrocarbon groups in A/T sequences. In the sequences (T)n · (A)n, the T's are slightly bent to yield structures with tightly stacked methyl groups along one side of the major groove. By folding together the two pairs of stacked methyls on the opposite sides of the major groove, TTAA might yield a relatively sharp bend. On this basis, we show below that the sequences (VT4A4X)1 might form a very tightly coiled super-helix whereas the sequences (VA4T4X)1 form a broad super-helix of radius ~ 120 A for i = 25. The sequence (V2A3T3X2)1 forms a slightly smaller radius super-helix. The time of passage through the gel has been taken to be inversely proportional to the smallesuiimension of the molecule. Specifically we are taking the ratio of the apparent molecular weight to the actual molecular weight to be related to the moment of inertia I1 about the smallest principal axis of the molecular conformation. We find a good fit to the experimental gel mobility data of Hagerman (2) if we assume this ratio to be proportional to (I1)1/5. 相似文献
8.
Sarai Belchí-Navarro Lorena Almagro Ana Belén Sabater-Jara Francisco Fernández-Pérez Roque Bru Maria Angeles Pedreño 《Journal of plant physiology》2013
Suspension-cultured cells of Vitis vinifera cv Monastrell were used to investigate the effects of methyljasmonate, ethylene and salicylic acid separately or in combination with cyclodextrins on both trans-resveratrol production and the induction of defense responses. 相似文献
9.