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52. Structural view on the role of the TRD loop in regulating DNMT3A activity: a molecular dynamics study.

Author

Zhao, Hong, Yu, Jie, Weng, Gaoqi, Yu, Jiahui, Wang, Ercheng, Gao, Junbo, Liu, Huanxiang, Hou, Tingjun, Wang, Zhe, and Kang, Yu

Abstract

DNA methyltransferase 3A (DNMT3A) has been regarded as a potential epigenetic target for the development of cancer therapeutics. A number of DNMT3A inhibitors have been reported, but most of them do not have good potency, high selectivity and/or low cytotoxicity. It has been suggested that a non-conserved region around the target recognition domain (TRD) loop is implicated in the DNMT3A activity under the allosteric regulation of the ATRX-DNMT3-DNMT3L (ADD) domain, but the molecular mechanism of the regulation of the TRD loop on the DNMT3A activity needs to be elucidated. In this study, based on the reported crystal structures, the dynamics of the TRD loop in different multimerization with/without the bound guest molecule, namely the ADD domain or the DNA molecule, was investigated using conventional molecular dynamics (MD) and umbrella sampling simulations. The simulation results illustrate that the TRD loop exhibits relatively higher flexibility than the other components in the whole catalytic domain (CD), which could be well stabilized into different local minima through the binding with either the ADD domain or the DNA molecule by forming tight hydrogen-bond and salt-bridge networks involving distinct residues. Moreover, the movement of the TRD loop away from the catalytic loop upon activation could be triggered simply by the detachment of the ADD domain, but not necessarily induced by the ADD domain relocation on the CD. All these dynamic structural details could be a supplement to the previously reported crystal structure, which underlines the importance of the structural flexibility for the critical residues in the TRD loop, arousing more interest in the rational design of novel DNMT3A inhibitors targeting this region. [ABSTRACT FROM AUTHOR]

Published
2022
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62. PROTAC-DB: an online database of PROTACs

Author

Weng, Gaoqi, primary, Shen, Chao, additional, Cao, Dongsheng, additional, Gao, Junbo, additional, Dong, Xiaowu, additional, He, Qiaojun, additional, Yang, Bo, additional, Li, Dan, additional, Wu, Jian, additional, and Hou, Tingjun, additional

Published
2020
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75. New Evidence for Hydrothermal Sedimentary Genesis of the Ni-Mo Deposits in Black Rock Series of the Basal Cambrian, Guizhou Province: Discovery of Coarse-Grained Limestones and its Geochemical Characteristics

Author

Cheng Wei, Wei Huairui, Chen Ji-yan, Yang Ruidong, Gao Junbo, and Liu Kun

Subjects
Total inorganic carbon, chemistry, Rare-earth element, Isotopes of carbon, Geochemistry, Trace element, chemistry.chemical_element, Geology, Sedimentary rock, Carbon, Oil shale, Hydrothermal circulation
Abstract

The molybdenum-nickel deposits in Shuidong District of Nayong County (Guizhou Province, Southwest China) are found mainly in black shale series of Lower Cambrian Niutitang Formation, which is another Mo-Ni-rich region besides Zunyi District (Guizhou province). Our systematic study on the Mo-Ni deposits in Tangjiaba of Nayong reveals that layered coarse-grained limestones, spherical beaded limestones concretions are hosted at the lower seam of the Mo-Ni deposits. Its strong negative carbon isotope anomaly (the carbon isotope value of the coarse-grained limestones varies from –2.148‰ to 8.223‰) is similar to that in the modern submarine black smoker chimney. The carbon in the coarse-grained limestones from black rock series of Nayong County might be deep source inorganic carbon. The seams, coarse-grained limestones, ore-bearing coarse-grained limestones and the roof and floor of the deposits are characterized by co-variation on the trace element spider diagram, showing good homology. The extraordinary enrichment of Ag, As and Sb resembles hydrothermal sedimentation. Pro-Earth's core elements Se is strongly enriched in Ni-Mo ore-bearing coarse-grained limestones. The ore-bearing rock series has an extremely low Th/U value (0.012–0.19); in the logU-logTh Cartesian Coordinates, the samples of the roof and floor of the deposits and ore-bearing coarse-grained limestones are found in the East Pacific tise; and the samples of coarse-grained limestones are found between the paleo-hydrothermal dedimentary area and the East Pacific tise. The chondrite-normalized rare earth element patterns of the Ni-Mo deposits show LREE enrichment, Ce negative anomaly, and Eu negative anomaly (which is supposed to be influenced by the deep magmatic processes in an extensional environment) resembles the rare earth element distribution patterns of the fluid and its sediments in modern submarine hydrothermal system. It proves that coarse-grained limestones is characterized by typical hydrothermal limestones, being closely related with the genesis of Mo-Ni deposits in Nayong County, which provides new evidence for hydrothermal sedimentary genesis of Mo-Ni deposit and negative carbon anomaly in the basal Cambrian on a global scale.

Published
2012

76. Continuous spinning of a single-walled carbon nanotube-nylon composite fiber

Author

Gao, Junbo, Itkis, Mikhail E., Aiping Yu, Bekyarova, Elena, Bin Zhao, and Haddon, Robert C.

Subjects
Polymerization -- Research, Nanotubes -- Research, Carbon compounds -- Chemical properties, Chemistry
Abstract

A chemical processing technology that allows the continuous spinning of single-walled carbon nanotubes (SWNTs)-nylon 6 (PA6) fibers by the in-situ polymerization of caprolactam in the presence of SWNTs, which simultaneously optimizes the morphology of the composite, is reported. The results suggested that caprolactam is an excellent solvent for carboxylic-acid-fictionalized SWNTs (SWNT-COOH) and that this allows the efficient dispersal of the SWNTs.

Published
2005

80. Large-scale fabrication of aligned single-walled carbon nanotube array and hierarchical single-walled carbon nanotube assembly

Author

Gao, Junbo, Aiping Yu, Itkis, Mikhali E., Bekyarova, Elena, Haddon, Robert C., Bin Zhao, and Niyogi, Sandip

Subjects
Chemical vapor deposition -- Research, Nanotubes -- Research, Carbon compounds -- Chemical properties, Carbon compounds -- Electric properties, Chemistry
Abstract

Carbon nanotubes are aligned by post-treatment techniques utilizing electrical, magnetic, mechanical forces and self-assembly and in situ during their growth. The in situ method, which is mainly carried out by the chemical vapor deposition (CVD) process, requires high temperatures (>800 degree Celsius) and a reactive environment because of which it is not applicable to devices with limited stability.

Published
2004

81. Anti-NLRP3 inflammasome abietane diterpenoids from Callicarpa bodinieriand their structure elucidation

Author

Gao, Junbo, Zhang, Xingjie, Shang, Kun, Zhong, Weimao, Zhang, Ruihan, Dai, Xiaochang, Li, Xiaoli, Wang, Qi, Zou, Yan, and Xiao, Weilie

Abstract

Two new 9,10-seco and etherified abietane-type diterpenoids were isolated from Callicarpa bodinieri, and their structure were elucidated by detailed spectrometry data analysis and DP4+ NMR calculation methods.

Published
2020
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83. Facile synthesis of phenyl-capped oligoanilines using pseudo-high dilution technique

Author

Yao Zhou, Mitsuhiro Shibata, Wanjin Zhang, Zhongwen Wu, Ryutoku Yosomiya, Yiping Ji, Ce Wang, Li Ke, and Gao Junbo

Subjects
Reaction mechanism, Polymers and Plastics, Organic Chemistry, Diphenylamine, Hydrochloric acid, chemistry.chemical_compound, Deprotonation, chemistry, Polymer chemistry, Materials Chemistry, Oxidative coupling of methane, Ammonium, Ammonium persulfate, Phenylhydrazine
Abstract

Monodispersed phenyl-capped trianiline and tetraaniline were successfully synthesized by the reactions of diphenylamine with acetaldehyde-based Sckiff's bases of N-phenyl-1,4-phenylenediamine and 1,4-phenylenediamine, respectively, in the presence of ammonium persulfate and hydrochloric acid, subsequent deprotonation and reduction with phenylhydrazine. The reaction mechanism probably involves the slow hydrolysis of the Sckiff's bases and subsequent oxidative coupling reactions of the formed ammonium salts with diphenylamine at pseudo-high dilution condition of the salts.

Published
1999

84. A novel synthetic method to phenyl-capped penta- and hexaaniline

Author

Wanjin Zhang, Gao Junbo, Li Ke, Zhongwen Wu, Ce Wang, and Yiping Ji

Subjects
Reaction mechanism, Polymers and Plastics, Chemistry, Pentamer, Organic Chemistry, Diphenylamine, Random hexamer, chemistry.chemical_compound, Aniline, Tetramer, Oxidation state, Polymer chemistry, Materials Chemistry, Oxidative coupling of methane
Abstract

A new convenient method is reported for the synthesis of the phenyl-capped pentamer and hexamer of aniline. The method was accomplished by the reaction of the parent aniline tetramer in the pernigraniline oxidation state with diphenylamine and N-phenyl-1,4-phenylenediamine in the leucoemeraldine oxidation state, respectively. The mechanism probably involves the formation of cation radicals and their coupling.

Published
1999

87. Triterpenoids from Ganoderma gibbosum: A Class of Sensitizers of FLC-Resistant Candida albicansto Fluconazole

Author

Pu, Debing, Li, Xiaoning, Lin, Jing, Zhang, Ruihan, Luo, Ting, Wang, Yuan, Gao, Junbo, Zeb, Muhammad Aurang, Zhang, Xingjie, Li, Xiaoli, Wang, Ruirui, and Xiao, Weilie

Abstract

Fungal drug resistance is a major health threat, and reports of clinical resistance worldwide are becoming increasingly common. In a research program to discover new molecules to help overcome this problem, 14 new lanostane-type triterpenoids, gibbosicolids A–G (2–8) and gibbosic acids I–O (9–15), were isolated from the fruiting bodies of Ganoderma gibbosum, along with seven known triterpenoid derivatives. These compounds featured high levels of oxidation, epimerization, and γ-lactonization. Structures were elucidated by comprehensive spectroscopic analyses and HRMS data. Absolute configurations were assigned based on quantum chemical calculations, including calculated chemical shift with DP4+ analysis, coupling constants, and electronic circular dichroism (ECD) methods. Results show that the calculated NMR with DP4+ analysis could not reliably establish the overall spatial configuration of molecules possessing independent and free-rotational stereoclusters. All these compounds significantly increased the sensitivity of fluconazole (FLC)-resistant C. albicansto FLC. Compounds 2, 5, 9, 12, 16, 17, and 21exhibited strong antifungal activity against FLC-resistant C. albicanswhen combined with FLC, with MIC50values ranging from 3.8 to 8.8 μg/mL.

Published
2019
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92. Forming Mechanism Analysis of the Abnormally High δ S Baryte Deposits: A Case Study from the Zhenning–Ziyun Large Devonian Baryte Deposits, Guizhou Province, China.

Author

Gao, Junbo, Yang, Ruidong, Zheng, Lulin, Cheng, Wei, Chen, Jun, and Zhu, Mingjin

Subjects
*BARITE analysis, *BARITE rosettes, *BARITE content in soils, *SULFUR isotopes, *SCANNING electron microscopes
Abstract

Stratiform baryte deposits are widespread in Cambrian and Devonian strata in China and around the world. In this article, the authors studied the sulfur isotopic features and forming mechanism of the stratiform baryte deposits occurring within the Upper Devonian cherts of the Zhenning-Ziyun county, Guizhou province, located in the Southwestern margin of the Yangtze Platform. The sulfur isotopic data from 18 baryte ore samples of the Leji section of Zhenning county are presented herein with values that range from +41.9‰ to +68.4‰ (AVG = +59.9‰). The δ34S values of the baryte ore from the Mohao section of Ziyun county are stable and show a narrow range from +41.3‰ to +47.0‰ (AVG = +44.0‰). In the Luocheng section of Ziyun county, the δ34S values of the baryte ore vary from +27.6‰ to +36.4‰ (AVG = +32.7‰). The δ34S values of all samples are higher than those of the coeval seawater sulfates (+25‰). The scanning electron microscope analysis indicates that spherical, dumbbell-shaped, clavate bacterial and bacteria-like fossils were observed, as well as the irregular schistose and framboid forms of Fe oxides that occur around the surfaces of baryte grains and inter-grains. Fe oxides take irregular schistose and framboid forms. These findings imply the significant concentration of heavy sulfur related to the seawater sulfates with the action of bacterial sulfate reduction in a closed basin. In addition, the trend of the δ34S value of baryte ores is gradually decreasing from the Leji to Mohao and Luocheng sections, which suggests that Leji area is located in the deepwater area of the restricted rift basin, and in a more closed depositional environment. [ABSTRACT FROM PUBLISHER]

Published
2017
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93. Analysis of Opinion Leader in On-Line Communities

Author

Zhang Min, Wang Xu-fa, Jiang Fan, and Gao Junbo

Subjects
Small-world network, Operations research, Social network, business.industry, Computer science, Opinion leadership, Information technology, The Internet, Line (text file), Public relations, business, Construct (philosophy)
Abstract

In the 1940's, Paul proposed the concept of “opinion leader”, and with the development of information technology and network, the importance of on-line community in information spread has become more and more greater. So the information analysis on Internet is becoming quite important. We construct the social network with the replying relations between comments mapped to the comment authors' relations. Then we validate its characteristics of small world networks and find out the opinion leaders in on-line community.

Published
2005

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