Human NF-kappaB (NF-KB) transcription factors regulate the expression of large number of genes involvedin diverse biological activities. A sub-class of IKB proteins, known as prototypical IKB (IKBalpha, IKBbeta andiKBepsilon), inhibits NF-KB transcriptional activity by forming stable complexes with NF-KB dimers. Theseinhibited complexes define a paradigm of cell signaling where signal induced NF-KB activation is regulatedby the degradation of IKB. The prototypical IKB proteins undergo rapid turnover in resting cell when presentin the free state, compared to when present as complexes with NF-KB. Recent observations indicate that theprototypical IKBs are partly unfolded, which may stabilize upon binding NF-KB. Interestingly, criticalsegments of NF-KB that are involved in binding IKB are also unfolded in their free states. We hypothesizethat stability of IKB proteins regulates their turn over, NF-KB recognition and the lifetime of IKB/NF-KBcomplexes in quiescent cells. A separate class of IKB proteins, represented by Bcl3 and IKBzeta, carry outdifferent functions. It is likely that functional differences between these two classes of 1KB proteins maycorrelate with their differential stability. The focus of this proposal is to understand the mechanism ofproteasome-mediated degradation of IKB and how their stability relates to their degradation. We haveobserved structural differences between prototypical IKB proteins such as the presence of a disordered insertin IKBbeta. We will test if IKBalpha and IKBbeta display differential specificity towards specific NF-KB dimers, andhow structural differences between IKBalpha and IKBbeta play a role in such specificity-defining mechanisms.Finally, we will elucidate new structures of IKB/NF-KB complexes, which may provide insights into theirbiological functions. We will use X-ray crystallography, biochemistry and cell-based experiments to test ourhypotheses.
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