ArticleScientific reports2018
Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 47 citations in OpenAlex.
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
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- Modeling Facilitated Diffusion of Proteins in Crowded Environment.Sub-cellular biochemistry · 2025Review
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- Target search by an imported conjugative DNA element for a unique integration site along a bacterial chromosome during horizontal gene transfer.Nucleic acids research · 2023Article
- Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA.PloS one · 2023Article
- Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.Biophysical journal · 2022Article
- Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence.Molecules (Basel, Switzerland) · 2022Article
- In vivo macromolecular crowding is differentially modulated by aquaporin 0 in zebrafish lens: Insights from a nanoenvironment sensor and spectral imaging.Science advances · 2022Article
- Understanding protein diffusion on force-induced stretched DNA conformation.Frontiers in molecular biosciences · 2022Article
- Optical and theoretical study of strand recognition by nucleic acid probes.Communications chemistry · 2020Article
- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
- Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells.Biophysical reviews · 2019Review
- Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins.Biophysical journal · 2019Article
- Macromolecular Crowding Tunes Protein Stability by Manipulating Solvent Accessibility.Chembiochem : a European journal of chemical biology · 2019Article
- Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments.BMC biophysics · 2018Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent experiments suggest that cellular crowding facilitates the target search dynamics of proteins on DNA, the mechanism of which is not yet known. By using large scale computer simulations, we show that two competing factors, namely the width of the depletion layer that separates the crowder cloud from the DNA molecule and the degree of protein-crowder crosstalk, act in harmony to affect the target search dynamics of proteins. The impacts vary from nonspecific to specific target search regime. During a nonspecific search, dynamics of a protein is only minimally affected, whereas, a significantly different behaviour is observed when the protein starts forming a specific protein-DNA complex. We also find that the severity of impacts largely depends upon physiological crowder concentration and deviation from it leads to attenuation in the binding kinetics. Based on extensive kinetic study and binding energy landscape analysis, we further present a comprehensive molecular description of the search process that allows us to interpret the experimental findings.
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