DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid.

No abstract is available for this paper.

• Publication year

  2017

• Venue

  Biophysical Journal

• Publication date

  2017-06-06

• Fields of study

  Biology, Medicine, Physics

• Identifiers
  DOI 10.1016/j.bpj.2017.04.049PMID 28591599PMCID PMC5474843
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2011influential reference
• Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

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  2010influential reference
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  2007influential reference
• How proteins search for their specific sites on DNA: the role of DNA conformation.

  2006cited by this paper
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  2004cited by this paper
• Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.

  2004cited by this paper
• Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition.

  1998cited by this paper
• Osmotic compaction of supercoiled DNA into a bacterial nucleoid.

  1998cited by this paper
• A Combined Wormlike-Chain and Bead Model for Dynamic Simulations of Long Linear DNA

  1997cited by this paper
• Computer simulations of Brownian motion of complex systems

  1995cited by this paper
• Crumpled globule model of the three-dimensional structure of DNA

  1993cited by this paper
• The Biology of Nonspecific DNA Protein Interactions

  1990cited by this paper
• The role of topological constraints in the kinetics of collapse of macromolecules

  1988cited by this paper
• Dynamic simulation of hydrodynamically interacting particles

  1987influential reference
• Ewald sum of the Rotne-Prager tensor

  1986cited by this paper
• Diffusion‐controlled protein–DNA association: Influence of segemental diffusion of the DNA

  1984cited by this paper
• Calculation of the resistance and mobility functions for two unequal rigid spheres in low-Reynolds-number flow

  1984cited by this paper
• Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.

  1981cited by this paper
• Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor--operator interaction: equilibrium measurements.

  1981cited by this paper
• Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains

  1981cited by this paper
• The one-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations.

  1979cited by this paper
• Simulation of polymer dynamics. I. General theory

  1978cited by this paper
• Brownian dynamics with hydrodynamic interactions

  1978cited by this paper
• The one-dimensional diffusion coefficient of proteins absorbed on DNA hydrodynamic considerations.

  1975cited by this paper
• Reptation of a Polymer Chain in the Presence of Fixed Obstacles

  1971cited by this paper
• Transport Properties of Polymer Chains in Dilute Solution: Hydrodynamic Interaction

  1970cited by this paper
• The lac repressor-operator interaction. 3. Kinetic studies.

  1970cited by this paper
• The lac represser-operator interaction

  1970cited by this paper
• Variational Treatment of Hydrodynamic Interaction in Polymers

  1969cited by this paper

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  2021cites this paper
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  2020cites this paper
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  2020cites this paper
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  2020cites this paper
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  2020cites this paper
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  2020cites this paper
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  2020cites this paper
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  2018cites this paper
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