Solvent Exposed Non-contacting Amino Acids Play a Critical Role in NF-κB/IκBα Complex Formation

IκBα inhibits transcription factor NF-κB activity by specific binding to NF-κB heterodimers composed of p65 and p50 subunits. It binds with slightly lower affinity to p65 homodimers and with significantly lower affinity to homodimers of p50. We have employed a structure-based mutagenesis approach coupled with protein–protein interaction assays to determine the source of this dimer selectivity exhibited by IκBα. Mutation of amino acid residues in IκBα that contact NF-κB only marginally affects complex binding affinity, indicating a lack of hot spots in NF-κB/IκBα complex formation. Conversion of the weak binding NF-κB p50 homodimer into a high affinity binding partner of IκBα requires transfer of both the NLS polypeptide and amino acid residues Asn202 and Ser203 from the NF-κB p65 subunit. Involvement of Asn202 and Ser203 in complex formation is surprising as these amino acid residues occupy solvent exposed positions at a distance of 20 Å from IκBα in the crystal structures. However, the same amino acid residue positions have been genetically isolated as determinants of binding specificity in a homologous system in Drosophila. X-ray crystallographic and solvent accessibility experiments suggest that these solvent-exposed amino acid residues contribute to NF-κB/IκBα complex formation by modulating the NF-κB p65 subunit NLS polypeptide.