A Highly Charged Topic: Intrinsically Disordered Proteins and Protein pKa Values
Abstract
Intrinsically disordered proteins (IDPs) are known not only for their roles in disease but also for their conformational flexibility, which makes them elusive for experimentation. We consider the role played by theory and simulation in resolving important questions pertaining to IDP structure and dynamics, as well as the nature of the charged residues (e.g., glutamate, lysine, etc.) that enrich them. Specifically, we investigated how the deep learning trained AlphaFold2 (AF2) predictor estimates disorder content, revealing both strong performance in relation to conventional approaches and an important relationship between the AF2 confidence metric and IDP dynamics. We also assessed how modern molecular dynamics (MD) simulations could reproduce the ensembles of two highly charged peptides at various protonation states and two model IDPs for which new experimental data are available. Our results revealed notable performance discrepancies and the impact of a new Amber force field variant on the resultant structures. The charged residues enriched in IDPs are protonatable; depending on their pKa values, they will be (de)protonated at a specific solution pH. We considered how MD simulations alongside non-equilibrium free energy methods and theory could be used to compute coupled and uncoupled pKa values for more than 140 amino acid residues spanning 13 proteins. We achieved performance that matched or exceeded several state-of-the-art alternative approaches.