ArticleBiophysical journal2006
Dissecting the contribution of diffusion and interactions to the mobility of nuclear proteins.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
- Single nucleosome imaging reveals principles of transient multiscale chromatin reorganization triggered by histone ADP-ribosylation at DNA lesions.Nature communications · 2025Article
- Receptor binding and tortuosity explain morphogen local-to-global diffusion coefficient transition.Biophysical journal · 2025Article
- ISWI catalyzes nucleosome sliding in condensed nucleosome arrays.Nature structural & molecular biology · 2024Article
- ISWI catalyzes nucleosome sliding in condensed nucleosome arrays.bioRxiv : the preprint server for biology · 2023Article
- Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture.PLoS computational biology · 2023Article
- Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells.Nucleic acids research · 2023Article
- RNAP Promoter Search and Transcription Kinetics in LiveThe journal of physical chemistry. B · 2023Article
- HPF1-dependent histone ADP-ribosylation triggers chromatin relaxation to promote the recruitment of repair factors at sites of DNA damage.Nature structural & molecular biology · 2023Article
- Phosphorylation of RCC1 on Serine 11 Facilitates G1/S Transition in HPV E7-Expressing Cells.Biomolecules · 2021Article
- Parameter estimation in fluorescence recovery after photobleaching: quantitative analysis of protein binding reactions and diffusion.Journal of mathematical biology · 2021Article
- DeepFRAP: Fast fluorescence recovery after photobleaching data analysis using deep neural networks.Journal of microscopy · 2021Article
- New Methodologies to Study DNA Repair Processes in Space and Time Within Living Cells.Frontiers in cell and developmental biology · 2021Review
- Lost in the Crowd: How Does Human 8-Oxoguanine DNA Glycosylase 1 (OGG1) Find 8-Oxoguanine in the Genome?International journal of molecular sciences · 2020Review
- The Multifaceted Roles of RCC1 in Tumorigenesis.Frontiers in molecular biosciences · 2020Review
- Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage.Nucleic acids research · 2019Article
- A Highly Accurate Pixel-Based FRAP Model Based on Spectral-Domain Numerical Methods.Biophysical journal · 2019Article
- The Development and Enhancement of FRAP as a Key Tool for Investigating Protein Dynamics.Biophysical journal · 2018Review
- MacroH2A histone variants limit chromatin plasticity through two distinct mechanisms.EMBO reports · 2018Article
- CHD3 and CHD4 recruitment and chromatin remodeling activity at DNA breaks is promoted by early poly(ADP-ribose)-dependent chromatin relaxation.Nucleic acids research · 2018Article
- EasyFRAP-web: a web-based tool for the analysis of fluorescence recovery after photobleaching data.Nucleic acids research · 2018Article
27 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Quantitative characterization of protein interactions under physiological conditions is vital for systems biology. Fluorescence photobleaching/activation experiments of GFP-tagged proteins are frequently used for this purpose, but robust analysis methods to extract physicochemical parameters from such data are lacking. Here, we implemented a reaction-diffusion model to determine the contributions of protein interaction and diffusion on fluorescence redistribution. The model was validated and applied to five chromatin-interacting proteins probed by photoactivation in living cells. We found that very transient interactions are common for chromatin proteins. Their observed mobility was limited by the amount of free protein available for diffusion but not by the short residence time of the bound proteins. Individual proteins thus locally scan chromatin for binding sites, rather than diffusing globally before rebinding at random nuclear positions. By taking the real cellular geometry and the inhomogeneous distribution of binding sites into account, our model provides a general framework to analyze the mobility of fluorescently tagged factors. Furthermore, it defines the experimental limitations of fluorescence perturbation experiments and highlights the need for complementary methods to measure transient biochemical interactions in living cells.
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