The NFKB signaling system mediates both transient inflammatory responses that involve highly dynamic control of transcription, and longer-term immunological responses and development that involve precise dose response control mechanisms (14, 29). All are critical to human health, as demonstrated by NFKB involvement in inflammatory disease and in lymphocytic malignancies (37). These fundamentally different functions are achieved by the interplay of distinct family members of transcriptional activators and inhibitor proteins, whose biophysical properties determine their half-life control, interaction specificity, and dynamic and dose response behavior. A predictive understanding of the functioning of the NFKB signaling system in physiology and pathology remains unrealized, primarily due to a lack of information about the fundamental regulatory mechanisms and associated molecular specificities of key NFKB and IKB family members, and our inability to integrate diverse information and link it to specific physiological functions of cells and animal model systems. The present proposal aims to address these deficiencies. It complements the other projects of the Programand involves highly integrated studies, leveraging the molecular biophysical insights about protein folding, degradation and molecular interaction, to develop a predictive understanding of cellular signaling processes in inflammation and immune responses. This is achieved through the integrated approaches of biochemistry, mathematical modeling, cell biology, and animal physiology.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Program Projects (P01)
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Special Emphasis Panel (ZRG1-BCMB-D)
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University of California San Diego
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Ramsey, Kristen M; Dembinski, Holly E; Chen, Wei et al. (2017) DNA and I?B? Both Induce Long-Range Conformational Changes in NF?B. J Mol Biol 429:999-1008
Dembinski, Holly E; Wismer, Kevin; Vargas, Jesse D et al. (2017) Functional importance of stripping in NF?B signaling revealed by a stripping-impaired I?B? mutant. Proc Natl Acad Sci U S A 114:1916-1921
Ferreiro, Diego U; Komives, Elizabeth A; Wolynes, Peter G (2017) Frustration, function and folding. Curr Opin Struct Biol 48:68-73
Polley, Smarajit; Passos, Dario Oliveira; Huang, De-Bin et al. (2016) Structural Basis for the Activation of IKK1/?. Cell Rep 17:1907-1914
Hsu, Che-Hsiung; Park, Sangho; Mortenson, David E et al. (2016) The Dependence of Carbohydrate-Aromatic Interaction Strengths on the Structure of the Carbohydrate. J Am Chem Soc 138:7636-48
Potoyan, Davit A; Zheng, Weihua; Ferreiro, Diego U et al. (2016) PEST Control of Molecular Stripping of NF?B from DNA Transcription Sites. J Phys Chem B 120:8532-8
Mukherjee, Sulakshana P; Quintas, Pedro O; McNulty, Reginald et al. (2016) Structural characterization of the ternary complex that mediates termination of NF-?B signaling by I?B?. Proc Natl Acad Sci U S A 113:6212-7
Dyson, H Jane (2016) Making Sense of Intrinsically Disordered Proteins. Biophys J 110:1013-6
Tsai, Min-Yeh; Zheng, Weihua; Balamurugan, D et al. (2016) Electrostatics, structure prediction, and the energy landscapes for protein folding and binding. Protein Sci 25:255-69
Tsai, Min-Yeh; Zhang, Bin; Zheng, Weihua et al. (2016) Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA. J Am Chem Soc :

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