Computational Approaches to Identify the Structure-Function Relationships of IκB Proteins in Toll-like Receptor Signaling

Manavalan, Balachandran
일반대학원 분자과학기술학과
The Graduate School, Ajou University
Publication Year
Alternative Abstract
Abstract A variety of microbial components activate nuclear factor-κB (NF-κB), a transcription factor that plays an important role in both innate and adaptive immunity. Cytoplasmic IκB proteins are primary regulators that interact with NF-κB subunits in the cytoplasm of unstimulated cells. Upon stimulation, these IκB proteins are rapidly degraded, thus allowing NF-κB to translocate into the nucleus and activate the transcription of genes encoding various immune mediators. Subsequent to translocation, nuclear IκB proteins play an important role in the regulation of NF-κB transcriptional activity by acting either as activators or inhibitors. To date, molecular basis for the binding of IκBα and IκBβ along with their partners is known; however, the activation and inhibition mechanism of the remaining IκB (IκBNS, IκBε, IκBζ and Bcl-3) proteins remains elusive. Moreover, even though IκB proteins are structurally similar, it is difficult to determine the exact governing specificities of IκB proteins towards their respective binding partners. The three-dimensional structures of IκBNS, IκBζ and IκBε were modeled. Subsequently, we used an explicit solvent method to perform detailed molecular dynamic simulations of these proteins along with their known crystal structures (IκBα, IκBβ and Bcl-3). Detailed analyses of these trajectories have revealed that conformational changes takes place in loop regions (highly flexible). Furthermore, the refined models of IκBNS, IκBε, IκBζ and Bcl-3 were used for multiple protein-protein docking studies for the identification of IκBNS-p50/p50, IκBε-p50/p65, Bcl-3-p50/p50, IκBζ-p50/p65 and -p50/p50 complexes in order to study the structural basis of their activation and inhibition mechanism. The docking experiments revealed that IκBε masked the nuclear localization signal (NLS) of the p50/p65 subunits, thereby preventing its translocation into the nucleus. For the Bcl-3- and IκBNS-p50/p50 complexes, the results show that Bcl-3 mediated transcription takes place through its transactivation domain (TAD), while IκBNS inhibited transcription due to its lack of a TAD. Additionally, the opposite functions of IκBζ was revealed by our docking studies i.e., binding of IκBζ ankyrin repeats with the p50/p65 N-terminal DNA binding domain prevents NF-κB mediated transcriptional activation and IκBζ-p50/p50 dimer complex, which mediate transcriptional activation by its TAD, present at the N-terminal domain of IκBζ. These two different binding schemes of IκBζ may be responsible for its opposite function. The predicted complexes in our current study correlated well with the previous biochemical studies. Moreover, the numbers of identified flexible residues were equal in number among all IκB proteins except IκBζ. The presence of high number of flexible residues in IκBζ is responsible to mediate an interaction with different sets of nuclear protein, when compared with other IκB proteins. Finally, the identified flexible residues were not conserved among the IκB family members and this non-conservation could be the primary reason for their exhibited binding partner specificities. The current data obtained from our structural studies will be helpful for the future design of peptides that can target the NF-κB signaling for the development of novel anti-inflammatory or anti-cancer drugs.

Appears in Collections:
Graduate School of Ajou University > Department of Molecular Science and Technology > 3. Theses(Master)
Files in This Item:
There are no files associated with this item.
RIS (EndNote)
XLS (Excel)

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.