Methods for measuring rates of protein binding to insoluble scaffolds in living cells: histone H1-chromatin interactions

UMMS Affiliation

Department of Cell Biology

Publication Date


Document Type



Animals; Cell Nucleus; Chromatin; Fluorescence Recovery After Photobleaching; Histones; Humans; Mathematics; Mice; Models, Theoretical; NIH 3T3 Cells; Protein Binding; Recombinant Fusion Proteins


Cell Biology


Understanding of cell regulation is limited by our inability to measure molecular binding rates for proteins within the structural context of living cells, and many systems biology models are hindered because they use values obtained with molecules binding in solution. Here, we present a kinetic analysis of GFP-histone H1 binding to chromatin within nuclei of living cells that allows both the binding rate constant k(ON) and dissociation rate constant k(OFF) to be determined based on data obtained from fluorescence recovery after photobleaching (FRAP) analysis. This is accomplished by measuring the ratio of bound to free concentration of protein at steady state, and identifying the rate-determining step during FRAP recovery experimentally, combined with mathematical modeling. We report k(OFF) = 0.0131/s and k(ON) = 0.14/s for histone H1.1 binding to chromatin. This work brings clarity to the interpretation of FRAP experiments and provides a way to determine binding kinetics for nuclear proteins and other cellular molecules that interact with insoluble scaffolds within living cells.

DOI of Published Version



J Cell Biochem. 2006 Dec 1;99(5):1334-42. Link to article on publisher's site

Journal/Book/Conference Title

Journal of cellular biochemistry

Related Resources

Link to Article in PubMed

PubMed ID