Abstract
Existing methods for predicting translational friction properties of complex molecules start by explicitly building up their three-dimensional shape with spherical subunits. This treatment has been used especially for two types of systems: rigid assemblies and flexible chain molecules. However, many protein/DNA complexes such as chromatin consist of a small number of globular, relatively rigid, bound protein interspersed by long stretches of flexible DNA chain. I present a higher level of treatment of such macromolecules that avoids explicit subunit modeling as much as possible. An existing analytical formulation of the hydrodynamics equations is shown to be accurate when used with the present treatment. Thus the approach is fast and can be applied to hydrodynamic studies of highly degenerate multiple equilibria, such as those encountered in problems of the regulation of chromatin structure. I demonstrate the approach by predicting the effect of a hypothetical unwinding process in dinucleosomes and by simulating the distribution of sedimentation coefficients for cooperative and random models for a chromatin saturation process.
Full text
PDF
Images in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Ausio J., Dong F., van Holde K. E. Use of selectively trypsinized nucleosome core particles to analyze the role of the histone "tails" in the stabilization of the nucleosome. J Mol Biol. 1989 Apr 5;206(3):451–463. doi: 10.1016/0022-2836(89)90493-2. [DOI] [PubMed] [Google Scholar]
- Bloomfield V., Dalton W. O., Van Holde K. E. Frictional coefficients of multisubunit structures. I. Theory. Biopolymers. 1967 Feb;5(2):135–148. doi: 10.1002/bip.1967.360050202. [DOI] [PubMed] [Google Scholar]
- Díaz F. G., Iniesta A., García de la Torre J. Hydrodynamic study of flexibility in immunoglobulin IgG1 using Brownian dynamics and the Monte Carlo simulations of a simple model. Biopolymers. 1990;30(5-6):547–554. doi: 10.1002/bip.360300507. [DOI] [PubMed] [Google Scholar]
- Garcia de la Torre J., Navarro S., Lopez Martinez M. C. Hydrodynamic properties of a double-helical model for DNA. Biophys J. 1994 May;66(5):1573–1579. doi: 10.1016/S0006-3495(94)80949-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hagerman P. J. Flexibility of DNA. Annu Rev Biophys Biophys Chem. 1988;17:265–286. doi: 10.1146/annurev.bb.17.060188.001405. [DOI] [PubMed] [Google Scholar]
- Hansen J. C., Ausio J. Chromatin dynamics and the modulation of genetic activity. Trends Biochem Sci. 1992 May;17(5):187–191. doi: 10.1016/0968-0004(92)90264-a. [DOI] [PubMed] [Google Scholar]
- Hayes J. J., Clark D. J., Wolffe A. P. Histone contributions to the structure of DNA in the nucleosome. Proc Natl Acad Sci U S A. 1991 Aug 1;88(15):6829–6833. doi: 10.1073/pnas.88.15.6829. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kovacic R. T., van Holde K. E. Sedimentation of homogeneous double-strand DNA molecules. Biochemistry. 1977 Apr 5;16(7):1490–1498. doi: 10.1021/bi00626a038. [DOI] [PubMed] [Google Scholar]
- Leuba S. H., Yang G., Robert C., Samori B., van Holde K., Zlatanova J., Bustamante C. Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11621–11625. doi: 10.1073/pnas.91.24.11621. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schmitz K. S., Ramsay-Shaw B. Chromatin conformation: a systematic analysis of helical parameters from hydrodynamic data. Biopolymers. 1977 Dec;16(12):2619–2633. doi: 10.1002/bip.1977.360161204. [DOI] [PubMed] [Google Scholar]
- Yao J., Lowary P. T., Widom J. Linker DNA bending induced by the core histones of chromatin. Biochemistry. 1991 Aug 27;30(34):8408–8414. doi: 10.1021/bi00098a019. [DOI] [PubMed] [Google Scholar]