A Model of Sequence-Dependent Protein Diffusion Along DNA
نویسندگان
چکیده
منابع مشابه
A model of sequence-dependent protein diffusion along DNA.
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. Hydrogen bonds formed at the target site are used as the main sequence-dependent interaction between protein and DNA. The resulting dynamical properties and the p...
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We introduce a probabilistic model for the RNA-polymerase sliding motion along DNA during the promoter search. The model accounts for possible effects due to sequence-dependent interactions between the nonspecific DNA and the enzyme. We focus on T7 RNA-polymerase and exploit the available information about its interaction at the promoter site in order to investigate the influence of bacteriopha...
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Replication protein A (RPA) is a eukaryotic single-stranded DNA (ssDNA) binding protein that plays critical roles in most aspects of genome maintenance, including replication, recombination and repair. RPA binds ssDNA with high affinity, destabilizes DNA secondary structure and facilitates binding of other proteins to ssDNA. However, RPA must be removed from or redistributed along ssDNA during ...
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A boundary element model for the computation of sequence-dependent hydrodynamic properties of short DNA molecules is introduced. The hydrated surface is modeled as a curved tube of uniform radius with ends capped by hemispheres, and the axis of the tube is a general space curve whose length and curvature are determined locally by the sequence using a rigid basepair model of double-helical DNA w...
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A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all o...
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ژورنال
عنوان ژورنال: Journal of Biological Physics
سال: 2004
ISSN: 0092-0606
DOI: 10.1023/b:jobp.0000046728.51620.14