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Fast fixing and comprehensive identification to help improve real-time ligands discovery based on formaldehyde crosslinking, immunoprecipitation and SDS-PAGE separation

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机构: [1]Chinese Acad Med Sci, Peking Union Med Coll, Inst Basic Med Sci, Dept Physiol & Pathophysiol,Natl Key Lab Med Mol, Beijing 100005, Peoples R China; [2]China Japan Friendship Hosp, Clin Lab, Beijing 100029, Peoples R China; [3]Capital Med Univ, Beijing An Zhen Hosp, Dept Nephrol, Beijing 100029, Peoples R China
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关键词: Albumin Formaldehyde cross-linking Immunoprecipitation Mass spectrometry Protein-protein interactions

摘要:
Background: Fast Fixation is necessary to study real-time protein-protein interactions under physiological conditions. Fast formaldehyde cross-linking can fix transient and weak protein interactions, thereby reducing the number of false negatives but producing great complexity. To reduce this complexity, immunoaffinity purification can Fish out complexes that include particular target proteins, but affinity-based co-purification has a limited capacity to eliminate nonspecific binding to beads and/or antibodies. To Filter out these complexes, SDS-PAGE is used to disrupt non-covalent bonds, thereby eliminating uncross-linked complexes and simultaneously providing molecular weight information for identification. Results: We described a 4 F strategy to help improve real-time ligands discovery based on formaldehyde crosslinking, immunoprecipitation and SDS-PAGE separation: Fast Fix, Fish, and Filter, using albumin interactome as an example. The use of gel excision without staining makes this strategy comprehensive and sensitive. The target protein must be identified in the same slice as its ligands. The ligands must be identified in slices for the experimental group but not in the corresponding control slices. Only proteins that appear in the range of molecular weights equal to or greater than the sum of the proteins' theoretical molecular weights, together with the target, are considered ligands. In this study, 5 s of cross-linking with 10% formaldehyde was achieved in human blood. The use of this strategy identified 35 ligands for albumin. Comparison with four major previous studies of the albuminome revealed that 68.57% of the 35 ligands identified in our study were identified in these other studies. Conclusions: Fast cross-linking was achieved. The 4 F strategy can be used to identify real-time in situ interactions without prior intervention and to comprehensively identify ligands of particular target proteins with fewer false positives.

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出版当年[2013]版:
大类 | 3 区 生物
小类 | 3 区 生化研究方法
最新[2025]版:
大类 | 3 区 生物学
小类 | 3 区 生化研究方法
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出版当年[2012]版:
Q2 BIOCHEMICAL RESEARCH METHODS
最新[2023]版:
Q3 BIOCHEMICAL RESEARCH METHODS

影响因子: 最新[2023版] 最新五年平均 出版当年[2012版] 出版当年五年平均 出版前一年[2011版] 出版后一年[2013版]

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第一作者机构: [1]Chinese Acad Med Sci, Peking Union Med Coll, Inst Basic Med Sci, Dept Physiol & Pathophysiol,Natl Key Lab Med Mol, Beijing 100005, Peoples R China;
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通讯机构: [1]Chinese Acad Med Sci, Peking Union Med Coll, Inst Basic Med Sci, Dept Physiol & Pathophysiol,Natl Key Lab Med Mol, Beijing 100005, Peoples R China;
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