Structure Determination of Challenging Protein–Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations

Abstract

Intrinsically disordered regions of proteins often mediate important protein–protein interactions. However, the folding-upon-binding nature of many polypeptide–protein interactions limits the ability of modeling tools to predict the three-dimensional structures of such complexes. To address this problem, we have taken a tandem approach combining NMR chemical shift data and molecular simulations to determine the structures of peptide–protein complexes. Here, we use the MELD (Modeling Employing Limited Data) technique applied to polypeptide complexes formed with the extraterminal domain (ET) of bromo and extraterminal domain (BET) proteins, which exhibit a high degree of binding plasticity. This system is particularly challenging as the binding process includes allosteric changes across the ET receptor upon binding, and the polypeptide binding partners can adopt different conformations (e.g., helices and hairpins) in the complex. In a blind study, the new approach successfully modeled bound-state conformations and binding poses, using only protein receptor backbone chemical shift data, in excellent agreement with experimentally determined structures for moderately tight ( K d ∼100 nM) binders. The hybrid MELD + NMR approach required additional peptide ligand chemical shift data for weaker ( K d ∼250 μM) peptide binding partners. AlphaFold also successfully predicts the structures of some of these peptide–protein complexes. However, whereas AlphaFold can provide qualitative peptide rankings, MELD can directly estimate relative binding affinities. The hybrid MELD + NMR approach offers a powerful new tool for structural analysis of protein–polypeptide complexes involving disorder-to-order transitions upon complex formation, which are not successfully modeled with most other complex prediction methods, providing both the 3D structures of peptide–protein complexes and their relative binding affinities.