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. 2016 Sep 21;44(20):9990–10002. doi: 10.1093/nar/gkw841

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© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 5. — PWM logos for the SRY/DNA complex obtained from the analysis of MD trajectory. Tyrosine 74 dynamics generate three substates: binding to A6 (top left), binding to G5′ (top center), bidentate binding to A6/G5′ (top right). Components of recognition: indirect from DNA deformation energy (middle left), direct from DNA–protein interaction energy (middle center), overall (middle right). Experimental PWM logos from the JASPAR database: human SRY (bottom left), mouse SRY (bottom center and right). Each panel also shows the experimental consensus along the abscissa (W ≡ A/T, R ≡ A/G).