Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-kB Essential Modulator/IKKβ Protein-Protein Interface

来自 ACS

阅读量：

作者：

MS Golden，SM Cote，M Sayeg，BS Zerbe，EA Villar，D Beglov，SL Sazinsky，RM Georgiadis，S Vajda，D Kozakov

展开

摘要：

We report a comprehensive analysis of binding energy hot spots at the protein-protein interaction (PPI) interface between nuclear factor kappa B (NF-kB) essential modulator (NEMO) and IkB kinase subunit β (IKKβ), an interaction that is critical for NF-kB pathway signaling, using experimental alanine scanning mutagenesis and also the FTMap method for computational fragment screening. The experimental results confirm that the previously identified NEMO binding domain (NBD) region of IKKβ contains the highest concentration of hot-spot residues, the strongest of which are W739, W741, and L742 (AAG = 4.3, 3.5, and 3.2 kcal/ mol, respectively). The region occupied by these residues defines a potentially draggable binding site on NEMO that extends for ～16 A to additionally include the regions that bind IKKβ L737 and F734. NBD residues D738 and S740 are also important for binding but do not make direct contact with NEMO, instead likely acting to stabilize the active conformation of surrounding residues. We additionally found two previously unknown hot-spot regions centered on IKKβ residues L708/V709 and L719/ I723. The computational approach successfully identified all three hot-spot regions on IKKβ. Moreover, the method was able to accurately quantify the energetic importance of all hot-spot residues involving direct contact with NEMO. Our results provide new information to guide the discovery of small-molecule inhibitors that target the NEMO/IKKβ interaction. They additionally clarify the structural and energetic complementarity between "pocket-forming" and "pocket-occupying" hot-spot residues, and further validate computational fragment mapping as a method for identifying hot spots at PPI interfaces.

展开

关键词：

Amino Acids NF-kappa B Recombinant Fusion Proteins X-Ray Diffraction Signal Transduction Protein Binding Genetic Vectors Mutagenesis I-kappa B Kinase Alanine