Appendix E Salt dependence of the electrostatic energy of LacI / DNA with or without hinge region for 20 conformers Appendix F Characterization of the ion atmosphere of LacI / DNA based on the results of the MD simulations

The hinge region strengthens the nonspecific interaction between lac-repressor and DNA: a computer simulation study Lili Sun, Marcin Tabaka, Sen Hou, Lin Li, Krzysztof Burdzy, Aleksei Aksimentiev, Christopher Maffeo, Xuzhu Zhang and Robert Holyst Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland Computational Biophysics and Bioinformatics, Department of Physics,Clemson University, Clemson, SC 29634, USA Department of Mathematics, University of Washington, Seattle, WA 98195-4350, USA 4 Department of Physics, University of Illinois, Urbana, Illinois 61801, United States To whom correspondence should be addressed: Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland Corresponding author: E-mail: rholyst@ichf.edu.pl