A feasibility study on computational prediction on the death domain superfamily protein oligomers

• Main Author: Zhang, Jiawen
• Other Authors: Wu Bin
• Format: Thesis-Doctor of Philosophy
• Language: English
• Published: Nanyang Technological University 2020
• Subjects: Science::Biological sciences
• Online Access: https://hdl.handle.net/10356/144233
• Institution: Nanyang Technological University

Death Domain (DD) is one of the largest domain super-families, which comprises of the death domain(DD) subfamily, the death effector domain (DED) subfamily, the pyrin domain (PYD) subfamily, and the caspase recruitment domain (CARD) subfamily, that can lead to inflammatory response and cell death in innate immunity system. CARD-containing proteins are involved in processes relating to inflammation and apoptosis. The identity-defining step in this process is that the CARDs oligomerize into functional macromolecular protein complexes in a helical symmetry through direct interactions between individual CARDs motifs by mediating homotypic interaction. Computational predictions allow us to further characterise the mechanism of CARD:CARD interactions between different CARD-proteins. This computational work provides a framework to improve our understanding of death domain assembling oligomeric signalling complexes to direct innate immune and inflammatory responses.In order to investigate the signaling transduction process and validate our prediction and hypothesis, we conducted the structural study of the CARD8-CARD oligomeric complex by cryoEM. The CARD domain of CARD8 (CARD8-CARD) oligomerizes to form the filamentous structure in responses to upstream CARDs and activate Caspase1 to conduct the inflammatory response. We successfully resolved the structure of the filamentous CARD8-CARD complex with a resolution of 3.7Å(central segment). With the structure at near-atomic resolution, we managed to demonstrate the mechanism of CARD8-CARD crosstalk to upstream or downstream CARDs.