Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 (United States)
- Hypnagogic Software, Vancouver, British Columbia V6K 1V6 (Canada)
- Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, Texas 78520 (United States)
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.
- OSTI ID:
- 22415328
- Journal Information:
- Journal of Chemical Physics, Vol. 141, Issue 17; Other Information: (c) 2014 Author(s); Country of input: International Atomic Energy Agency (IAEA); ISSN 0021-9606
- Country of Publication:
- United States
- Language:
- English
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