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1. chinaXiv:201710.00016 [pdf]

Organization and Exploration Fined-grained Historical Knowledge on Contemporary China Based on Semantic Mining

Zhang, Zhixiong; Wang, Ying; Sun, Hui; Lei, Feng
Subjects: Library Science,Information Science >> Library Science

China has a huge volume of historical resources on its contemporary history. Lots of valuable knowledge are hidden in those resources and cannot be utilized easily. It is an urgent problem to mine the implicit semantic knowledge scattered in a large number of historical resources and to reorganize the historical knowledge and facts in a fined-grained manner, so that can help user to explore the historical knowledge for research and education. This paper proposes a method, which is called “Mining down, Organizing up”, to semantically represent and organize historical knowledge on contemporary China hidden in historical encyclopedia text. Based on the proposed historical ontology of contemporary Chinese, this method extracts knowledge objects and facts from the unstructured historical text items by utilizing text mining technologies, represents the historical knowledge in semantically enriched way, and interlinks the related historical knowledge objects and facts to form a historical knowledge network of the contemporary China. By mining the historical facts and the historical knowledge network, the authors get more valuable patterns from the historical knowledge which could be used to form the new organization scheme to reorganize the historical knowledge in a more vivid way. Based on this method, the authors developed a system which can represent and organize historical knowledge of contemporary China in a fined-grained manner, support user to explore historical knowledge by providing functions such as semantic retrieval, historical objects and facts clustering, visualization navigation, association analysis, and chronicle facts reconstruction etc.

submitted time 2017-10-20 Hits22422Downloads858 Comment 0

2. chinaXiv:201605.01519 [pdf]

Biochemical and structural characterization of a novel ubiquitin-conjugating enzyme E2 from Agrocybe aegeria reveals Ube2w family-specific properties

Qi, Chao; Li, De-Feng; Feng, Lei; Hou, Yanjie; Wang, Da-Cheng; Qi, Chao; Sun, Hui; Liu, Wei
Subjects: Biology >> Biophysics

Ubiquitination is a post-translational modification that is involved in myriad cellar regulation and disease pathways. The ubiquitin-conjugating enzyme (E2) is an important player in the ubiquitin transfer pathway. Although many E2 structures are available, not all E2 families have known structures, and three-dimensional structures from fungal organisms other than yeast are lacking. We report here the crystal structure of UbcA1, which is a novel ubiquitin-conjugating enzyme identified from the edible and medicinal mushroom Agrocybe aegerita and displays potential antitumor properties. The protein belongs to the Ube2w family and shows similar biochemical characteristics to human Ube2w, including monomer-dimer equilibrium in solution, alpha-NH2 ubiquitin-transfer activity and a mechanism to recognize backbone atoms of intrinsically disordered N-termini in substrates. Its structure displays a unique C-terminal conformation with an orientation of helix alpha 3 that is completely different from the reported E2 structures but similar to a recently reported NMR ensemble of Ube2w. A mutagenesis study on this novel enzyme revealed that an intact C-terminus is significant for protein dimerization and enzymatic activity. As the first crystallized full-length protein of this family, UbcA1 may supersede the truncated X-ray structure of Ube2w (PDB entry 2A7L) as the representative structure of the Ube2w family.

submitted time 2016-05-12 Hits1963Downloads999 Comment 0

3. chinaXiv:201605.01391 [pdf]

Structural Basis of Specific Recognition of Non-Reducing Terminal N-Acetylglucosamine by an Agrocybe aegerita Lectin

Ren, Xiao-Ming; Li, De-Feng; Hu, Yonglin; Wang, Da-Cheng; Ren, Xiao-Ming; Jiang, Shuai; Lan, Xian-Qing; Sun, Hui
Subjects: Biology >> Biophysics

O-linked N-acetylglucosaminylation (O-GlcNAcylation) is a reversible post-translational modification that plays essential roles in many cellular pathways. Research in this field, however, is hampered by the lack of suitable probes to identify, accumulate, and purify the O-GlcNAcylated proteins. We have previously reported the identification of a lectin from the mushroom Agrocybe aegerita, i.e., Agrocybe aegerita lectin 2, or AAL2, that could bind terminal N-acetylglucosamine with higher affinities and specificity than other currently used probes. In this paper, we report the crystal structures of AAL2 and its complexes with GlcNAc and GlcNAc beta 1-3Gal beta 1-4GlcNAc and reveal the structural basis of GlcNAc recognition by AAL2 and residues essential for the binding of terminal N-acetylglucosamine. Study on AAL2 may enable us to design a protein probe that can be used to identify and purify O-GlcNAcylated proteins more efficiently.

submitted time 2016-05-12 Hits1103Downloads595 Comment 0

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