title: Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis.
abstract: Histone modification plays a key role in gene regulation and gene expression. TRIM24 as a histone reader can recognize histone modification. However the specific recognition mechanism between TRIM24 and histone modification is unsolved. Here, systems biology method of dynamics correlation network based on molecular dynamics simulation was used to answer the question. Our network analysis shows that the dynamics correlation network of H3K23ac is distinctly different from that of wild type and other modifications. A hypothesis of "synergistic modification induced recognition" is then proposed to link histone modification and TRIM24 binding. These observations were further confirmed from community analysis of networks with mutation and network perturbation. Finally, a possible recognition pathway is also identified based on the shortest path search for H3K23ac. Significant difference of recognition pathway was found among different systems due to methylation and acetylation modifications. The analysis presented here and other studies show that the dynamic network-based analysis might be a useful general strategy to study the biology of protein post-translational modification and associated recognition.
authors.affiliation: State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
authors.forename: Jinmai
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Otolaryngology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, 160 Pujian Road, Pudong New Area, Shanghai 200127, China.
authors.forename: Huajie
authors.initials: H
authors.lastname: Luo
authors.affiliation: State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Ye
authors.affiliation: Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, Biomedical Engineering, University of California, Irvine, California 92697-3900, USA.
authors.forename: Ray
authors.initials: R
authors.lastname: Luo
authors.affiliation: State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.|Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China.
authors.forename: Hai-Feng
authors.initials: HF
authors.lastname: Chen
mesh_terms: D002352:Carrier Proteins / Q000737:chemistry / Q000378:metabolism*; D018360:Crystallography, X-Ray; D006657:Histones / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D025341:Principal Component Analysis; D011485:Protein Binding; D049490:Systems Biology
chemical_list: D002352:Carrier Proteins; D006657:Histones; C555317:TRIM24 protein, human