ArticlePLoS computational biology2014
Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 45 citations in OpenAlex.
- Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.PLoS computational biology · 2022Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- Effect of DNA Flexibility on Complex Formation of a Cationic Nanoparticle with Double-Stranded DNA.ACS omega · 2021Article
- What Are the Molecular Requirements for Protein Sliding along DNA?The journal of physical chemistry. B · 2021Article
- Modeling Effects of Surface Properties and Probe Density for Nanoscale Biosensor Design: A Case Study of DNA Hybridization near Surfaces.The journal of physical chemistry. B · 2021Article
- Value of Temporal Information When Analyzing Reaction Coordinates.Journal of chemical theory and computation · 2020Article
- ssDNA diffuses along replication protein A via a reptation mechanism.Nucleic acids research · 2020Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Diffusion of ring-shaped proteins along DNA: case study of sliding clamps.Nucleic acids research · 2018Article
- Theory of Site-Specific DNA-Protein Interactions in the Presence of Nucleosome Roadblocks.Biophysical journal · 2018Article
- DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid.Biophysical journal · 2017Article
- Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules.The Journal of chemical physics · 2016Article
- Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.The Journal of chemical physics · 2016Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction.Nucleic acids research · 2016Article
- Effects of confinement on models of intracellular macromolecular dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Searching target sites on DNA by proteins: Role of DNA dynamics under confinement.Nucleic acids research · 2015Article
- What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?Nucleic acids research · 2015Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
DNA binding proteins efficiently search for their cognitive sites on long genomic DNA by combining 3D diffusion and 1D diffusion (sliding) along the DNA. Recent experimental results and theoretical analyses revealed that the proteins show a rotation-coupled sliding along DNA helical pitch. Here, we performed Brownian dynamics simulations using newly developed coarse-grained protein and DNA models for evaluating how hydrodynamic interactions between the protein and DNA molecules, binding affinity of the protein to DNA, and DNA fluctuations affect the one dimensional diffusion of the protein on the DNA. Our results indicate that intermolecular hydrodynamic interactions reduce 1D diffusivity by 30%. On the other hand, structural fluctuations of DNA give rise to steric collisions between the CG-proteins and DNA, resulting in faster 1D sliding of the protein. Proteins with low binding affinities consistent with experimental estimates of non-specific DNA binding show hopping along the CG-DNA. This hopping significantly increases sliding speed. These simulation studies provide additional insights into the mechanism of how DNA binding proteins find their target sites on the genome.
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