Volume 112, Issue 9, Pages 1761-1766 (May 2017) AESOP: A Python Library for Investigating Electrostatics in Protein Interactions  Reed E.S. Harrison, Rohith R. Mohan, Ronald D. Gorham, Chris A. Kieslich, Dimitrios Morikis  Biophysical Journal  Volume 112, Issue 9, Pages 1761-1766 (May 2017) DOI: 10.1016/j.bpj.2017.04.005 Copyright © 2017 Biophysical Society Terms and Conditions

Figure 1 Thermodynamic cycle for binding of protein subunits in a reference (top) and solvated (bottom) state. In the reference state, the dielectric constant, ε, is assumed to be uniform in the protein, εp, and solvent, εs; however, in the solvated state, the uniform dielectric constants may differ between the protein and solvent. For the solvent, we set the dielectric coefficient to 78.5, the value for water at room temperature. A parameter for ion accessibility, κ, is held constant within each state. This variable is related to the ionic strength of the solvent. Biophysical Journal 2017 112, 1761-1766DOI: (10.1016/j.bpj.2017.04.005) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 2 (A) Example output from the plotESD function. ESD values closer to zero are more similar in terms of electrostatics. (B) Example output from the plotDend function where differences in ESD between family members are shown in a hierarchical dendrogram. To see this figure in color, go online. Biophysical Journal 2017 112, 1761-1766DOI: (10.1016/j.bpj.2017.04.005) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 3 (A) Example output from plotScan for an alanine scan showing perturbations of free energy of association relative to the wild-type. Perturbations below zero indicate gain-of-binding mutations, and perturbations above zero indicate loss-of-binding mutations. Effects that are significant are typically greater than or less than 2.5 kJ/mol compared to the parent. (B) Example output from plotNetwork for an alanine scan showing electrostatic interactions between residues with changes in free energy of association relative to parent outside thermal effects (±2.5 kJ/mol). Edges indicate the presence of an interaction; nodes represent individual amino acids; and node colors are scaled according to the free energy of association. Each amino acid label consists of a one-letter amino acid code, the residue number, and the chain identification, in that order. To see this figure in color, go online. Biophysical Journal 2017 112, 1761-1766DOI: (10.1016/j.bpj.2017.04.005) Copyright © 2017 Biophysical Society Terms and Conditions