We acknowledge the following funding:
SFB 1027: “Physical modeling of non-equilibrium processes in biological systems”
DFG project: “How posttranslational modifications and alternative splicing affect protein-peptide interactions”
Large-scale proteomics and transcriptomics studies have unraveled that about half of all proteins in biological cells are targets of post-translational modfications and 95% of all multi-exon genes in higher eukaryotes are alternatively spliced. Since both processes may have crucial consequences on the protein interactions involving the respective proteins, this severely complicates our understanding of the cellular protein interactome. Only few model systems have sofar been characterized in structural and thermodynamic terms. For this project, we selected two such model systems, 14-3-3 domains and PDZ domains, that both bind to hundreds of other proteins in human cells. Based on X-ray crystallographic data for the bound complexes, we will study how well molecular dynamics computer simulations can capture the influence of peptide phosphorylation on their binding to 14-3-3 adaptor domains and the influence of alternative splicing on the binding of peptides to PDZ domains. We will characterize the dynamic conformations of bound complexes, association-, dissociation-pathways and binding free energies of the peptide ligands, and the competitive binding between target peptides and small-molecule protein-protein inhibitors. This project will explore the potential and limitations of molecular dynamics simulations to contribute to the systematic proteomic mapping of the consequences of post-translational modifications and alternative splicing on the cellular protein interactome.