Dataset Information

TRIM72 cross-linked by the higher-order assembly on the negatively charged liposome surface

ABSTRACT: Plasma membrane repair is a rapid cellular response for resealing of membrane for cell survival. In the early step of repair process, TRIM72 is known to a key initiator for facilitating patch membrane to the damaged membrane site. When acute membrane injury happens, TRIM72 is also known to sensitively generate disulfide bonds formations by reactive oxygen species and further oligomerize with each other. We tried to clarify this repair system using in vitro reconstruction of TRIM72-liposome complex and find critical sites using cross-linker mass spectrometry. Using each four different length of sulfhydryl reactive cross-linkers, TRIM72 cross-linked with each other on the negatively charged liposome surface only. We also identified that the cross-linking bridges were highly conserved except bismaleimidoethane as a shortest arm length about 8 Å only. Our results indicated that the B2-box/B2-box locates closely with each other on the liposome surface. Furthermore, freely open RING domain is rearranged into the specific conformation, where located near the H2 helix of coiled coil domain. It suggests that the conformational changes of TRIM72 are induced by higher order assembly on the negative charged membrane surface.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Sehwan Jang

LAB HEAD: Hyun Kyu Song

PROVIDER: PXD024946 | Pride | 2024-01-26

REPOSITORIES: Pride

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Publications

Structure and activation of the RING E3 ubiquitin ligase TRIM72 on the membrane.

Park Si Hoon SH Han Juhyun J Jeong Byung-Cheon BC Song Ju Han JH Jang Se Hwan SH Jeong Hyeongseop H Kim Bong Heon BH Ko Young-Gyu YG Park Zee-Yong ZY Lee Kyung Eun KE Hyun Jaekyung J Song Hyun Kyu HK

Nature structural & molecular biology 20230928 11

Defects in plasma membrane repair can lead to muscle and heart diseases in humans. Tripartite motif-containing protein (TRIM)72 (mitsugumin 53; MG53) has been determined to rapidly nucleate vesicles at the site of membrane damage, but the underlying molecular mechanisms remain poorly understood. Here we present the structure of Mus musculus TRIM72, a complete model of a TRIM E3 ubiquitin ligase. We demonstrated that the interaction between TRIM72 and phosphatidylserine-enriched membranes is nece ...[more]

PMID: 37770719

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Project description:DM64 is a toxin-neutralizing serum glycoprotein isolated from the South American opossum Didelphis aurita. This ophiophagous marsupial is naturally resistant to snake envenomation and has evolved such biochemical defense as a trophic adaptation. The endogenous antitoxin is a human α1B-glycoprotein homolog of 64 kDa, specifically targeting myotoxic phospholipases A2, which account for most local tissue damage associated with viper snakebites. This study investigated the noncovalent complex formed between native DM64 and myotoxin II, a myotoxic calcium-independent phospholipase-like protein from Bothrops asper venom. Analytical ultracentrifugation, size exclusion chromatography, and small-angle X-ray scattering (SAXS) data indicated that DM64 is monomeric in solution and binds equimolar amounts of the toxin. Initial attempts to solve the structure of DM64 experimentally failed due to technical limitations caused by N-glycan heterogeneity and low recovery of heterologous protein. Classical molecular modeling techniques were impaired by the lack of templates with more than 25% sequence identity with DM64. An integrative structural biology approach was then applied to generate a refined three-dimensional model of the inhibitor bound to myotoxin II. The five immunoglobulin-like domains of DM64 were individually modeled using the I-TASSER suite. Distance constraints generated by cross-linking mass spectrometry of the complex guided the docking of DM64 domains to the crystal structure of myotoxin II (1CLP), using the Rosetta docking suite. The model of the DM64-myotoxin II complex was successfully fitted to a SAXS envelope. Inter-protein cross-links and limited hydrolysis analyses shed light on the inhibitor's regions involved with toxin interaction, revealing the critical participation of the first, third, and fifth domains of DM64. Our data showed that the fifth domain of DM64 binds to myotoxin II’s amino-terminal and -wing regions. The third domain of the inhibitor acts in a complementary way to the fifth domain. Their binding to these toxin regions presumably interferes with dimerization, a critical step in the allosteric activation of myotoxic PLA2-like proteins. Additionally, the first domain of DM64 likely interacts with the functional site of the toxin putatively associated with membrane anchorage. We propose that both mechanisms concur to effectively inhibit myotoxin II toxicity by DM64 binding. In summary, we argue such topological characterization of this toxin-antitoxin complex to constitute an essential first step toward the rational design of novel peptide-based antivenom therapies targeting snake venom myotoxins.

Dataset Information

TRIM72 cross-linked by the higher-order assembly on the negatively charged liposome surface

Publications

Structure and activation of the RING E3 ubiquitin ligase TRIM72 on the membrane.

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