Hydrophobic core evolution of major histocompatibility complex class I chain-related protein A for dramatic enhancing binding affinity

Interface residues at sites of protein–protein interaction (PPI) are the focus for affinity optimisation. However, protein hydrophobic cores (HCs) play critical roles and shape the protein surface. We hypothesise that manipulating protein HCs can enhance PPI interaction affinities. A cell stress molecule, major histocompatibility complex class I chain-related protein A (MICA), binds to the natural killer group 2D (NKG2D) homodimer to form three molecule interactions. MICA was used as a study subject to support our hypothesis. We redesigned MICA HCs by directed mutagenesis and isolated high-affinity variants through a newly designed partial-denature panning (PDP) method. A few mutations in MICA HCs increased the NKG2D–MICA interaction affinity by 325–5613-fold. Crystal structures of the NKG2D–MICA variant complexes indicated that mutagenesis of MICA HCs stabilised helical elements for decreasing intermolecular interactive free energy (ΔG) of the NKG2D–MICA heterotrimer. The repacking of MICA HC mutants maintained overall surface residues and the authentic binding specificity of MICA. In conclusion, this study provides a new method for MICA redesign and affinity optimisation through HC manipulation without mutating PPI interface residues. Our study introduces a novel approach to protein manipulation, potentially expanding the toolkit for protein affinity optimisation. •Hydrophobic core mutation can dramatically enhance proteins interaction affinity.•A partial-denature-panning method is designed to efficiently isolate high affinity mutants.•There is no protein-protein interaction interface residue mutated.•Hydrophobic core mutations cause protein-protein interaction interface alterations.