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. 2016 Jan 19;110(2):455–469. doi: 10.1016/j.bpj.2015.12.010

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© 2016 The Authors

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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Deformation of the DNA helix induced by the connector channel. Average atomic densities of the connector (magenta, green, blue, red, and brown, and see Fig. 1) with the DNA (yellow) and from three independent simulations, (A) SimA, (B) SimB, and (C) SimC. (D) Deviations (solid line) and standard error (bars) from free, unperturbed DNA geometry along the channel axis of the base-step parameters X-displacement, inclination, helical-rise, and helical-twist. Top panel depicts the position distributions of charged residues that are located inside the channel. LOOP shows the combined distribution of K234, K235, E236, and R237. The position of D194 to K200 marks the bottom region; LOOP also marks the loop region of the connector. D202, D208, and K209 are located in the middle region.