Title
Pulling chromatin fibers: Computer simulations of direct physical micromanipulations
Date Issued
07 January 2000
Access level
metadata only access
Resource Type
journal article
Author(s)
University of California Berkeley
Publisher(s)
Academic Press
Abstract
A low-resolution molecular model, which combines the known mechanical properties of protein-free DNA with the accumulating picture of chromatosome structure, has been developed to account for the stretching of single chromatin fibers by an imposed external force. Force-extension characteristics of sets of chains accumulated by Monte Carlo sampling are consistent with recently observed findings in the non-destructive regime (< 20 pN imposed force), where the structure of the chromatosome remains intact. The correspondence between simulation and the relaxation phase of the experiment limits the equilibrium entry-exit angle of linker DNA on the chromatosome to W = 50 (± 10)°and the effective DNA linker length to L(eff) = 40 (± 5) bp. The computed force-extension characteristics are relatively insensitive to other parameters of the model, precluding their accurate estimation. The introduction of an attractive potential between closely spaced nucleosomes reproduces the added initial resistance of single fibers to extension at high salt conditions. The consideration of elastic linkers also improves the fitting of assorted classical measurements of unstressed chromatin structure in solution. The overall picture of chromatin that emerges is an irregular, fluctuating, three-dimensional, zig-zag structure with intact, mechanically stable chromatosome units and deformable linkers. The modeled fiber undergoes large-scale configurational rearrangements without significant perturbation of the constituent chromatosome beads, collapsing into a highly condensed form in response to small (< 2kT) inter-nucleosomal attractions.
Start page
29
End page
40
Volume
295
Issue
1
Language
English
OCDE Knowledge area
Bioquímica, Biología molecular
Scopus EID
2-s2.0-0034614436
PubMed ID
Source
Journal of Molecular Biology
ISSN of the container
0022-2836
Sponsor(s)
The authors are grateful to Dr Alexander Vologodskii for helpful discussions. Support for this study has been provided by the US Public Health Service (NIH grants GM34809 to W.K.O. and GM32543 to C.B.), the National Science Foundation (grants MBC9118482 and DBI9732140 to C.B.), and the Program in Mathematics and Molecular Biology based at Florida State University (postdoctoral fellowship support to V.K.).
Sources of information: Directorio de Producción Científica Scopus