TABLE 2.

Comparison of the nucleosomal DNA bending energies predicted within the classical elastic rod theory with those observed in the simulations reported here

Arc length, φ, rad	2.0	π	3.7
End-to-end distance, Å	411	318	257
Classical Ebend, kcal/mol	2.3	5.8	8.0
〈E〉 of snapshots in Fig. 6, Kcal/mol	−19.1	−12.8	−12.5

The classical values are computed assuming bending through perfectly circular arcs of specified end-to-end distance; Eq. 2 is used with the persistence length of L_p = 500 Å. Conformational energies are computed as averages over the following representative points in Fig. 6, as one moves along the horizontal axis: five rightmost points, five in the middle (interval [300, 325] Å), and five leftmost points. Their average energies 〈E〉 and end-to-end distances are reported. Note that each interval contains 500 of the original molecular dynamics conformations, 100 per each point. Since only the snapshots from the last 4 ns of the MD are included in the energy analysis, the energy of the initially fully stretched DNA conformation (end-to-end distance ∼500 Å, φ = 0) is not computed, and can be considered as an unknown constant offset.