Free Energy Calculations of the Interactions of c-Jun-based Synthetic Peptides with the c-Fos Protein Zhili Zuo, 1 Neha S. Gandhi, 1 Katja M. Arndt, 2 Ricardo L. Mancera 1,3 1 Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia 2 Institute of Biochemistry and Biology, University of Potsdam, Karl Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany 3 School of Pharmacy, Curtin University, GPO Box U1987, Perth, WA 6845, Australia Received 19 March 2012; accepted 25 May 2012 Published online 7 June 2012 in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/bip.22099 This article was originally published online as an accepted preprint. The ‘‘Published Online’’ date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley. com INTRODUCTION P rotein–protein interactions are crucial in signaling networks and virtually all cellular processes, such as signal transduction, gene regulation, and cell divi- sion. 1–3 Their imbalance is often associated with numerous diseases, such as cancer and diabetes. 4,5 The design of ligands, including small molecules, peptides, and proteins that bind to native protein targets is a promis- ing route to developing new diagnostic reagents and thera- pies against many diseases. Optimization of the specificity of interaction requires both positive design (the stabilization of a desired interaction) and negative design (the destabilization of undesired interactions). However, it has proved difficult to design high affinity, selective ligands for their intended tar- gets. The activator protein-1 (AP-1) complex is a dimeric tran- scription factor activator comprising the c-Jun, c-Fos, acti- vating transcription factor (ATF), and Maf proteins. It plays a crucial role in numerous cell pathways (proliferation, apo- Free Energy Calculations of the Interactions of c-Jun-based Synthetic Peptides with the c-Fos Protein Additional Supporting Information may be found in the online version of this article. Correspondence to: Ricardo L. Mancera; e-mail: r.mancera@curtin.edu.au ABSTRACT: The c-Fos–c-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c- Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions. # 2012 Wiley Periodicals, Inc. Biopolymers 97: 899–909, 2012. Keywords: free energy of binding; coiled-coil; molecular dynamics; MM/GBSA; leucine zipper V V C 2012 Wiley Periodicals, Inc. Biopolymers Volume 97 / Number 11 899