Chapter Three - Atomistic Modelling of Phosphopeptide Recognition for Modular Domains

Abstract

This review aims at discussing the molecular details of binding specificity, promiscuity and mechanisms of phosphopeptide recognition to modular domains using computational tools. Protein–phosphoprotein interactions are the driving forces that underline multiple signalling events which are important in cellular function. Understanding protein–phosphopeptide recognition assists designing phosphopeptide sequences as inhibitors to manipulate protein–protein interactions for cell biology studies and therapeutics. Notably, the modular domain–phosphopeptide binding is mostly promiscuous and weak binding, which significantly differs from most protein–ligand binding systems used for drug design. In this chapter, we review recent advances in computational work for modular domain–phosphopeptide binding and knowledge gained for their binding mechanisms. We discuss the phosphopeptide binding of modular domains in DNA damage responses, FHA and BRCT, the smallest modular domain WW and the tyrosine kinase binding domain, such as Cbl–TKB that recognizes phosphotyrosine. We also discuss challenges and possible future directions for improving peptide design as inhibitors for phosphoprotein–protein binding.