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Green Carbon 2024年第3期2卷 337-338页

作者： yingang feng Carl J.Yeoman CAS Key Laboratory of Biofuels Shandong Provincial Key Laboratory of Synthetic BiologyShandong Engineering Laboratory of Single Cell OilQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao 266101China Shandong Energy Institute Qingdao 266101China Qingdao New Energy Shandong Laboratory Qingdao 266101China Department of Animal and Range Sciences Montana State UniversityBozemanMTUSA Department of Microbiology and Immunology Montana State UniversityBozemanMTUSA

Carbon neutrality goals have been established in more than 150 ***,as a renewable biomass resource,has the potential to replace a considerable portion of fossil-derived fuels and chemicals,so the conversion and utilization of lignocellulose is one of the main means during the steps toward achieving carbon neutrality ***,molecular machines that efficiently degrade and transform lignocellulose,are of special interest[1].They are closely related to the cycle of carbon elements in the environment,the feed efficiency and greenhouse gas emission of livestock,as well as the development of biomass bioconversion techniques and other biotechnology developments[1,2].A recent study based on the analysis of metagenomic-assembled genomes(MAGs),published by Moraïs and Mizrahi et *** Science[3],identified three new cellulosome-producing bacterial species in the human gastrointestinal tract(GIT).These species belong to the genus Ruminococcus,whose members are mainly found in gastrointestinal *** analysis of the prevalence of these new Ruminococcus species in 1989 GIT samples of human and other animal species worldwide,the authors found that the abundance of cellulosome-producing Ruminococcus was closely related to the extent of dietary fiber intake,which is considered a key factor in human *** suggests an interesting linkage may exist between cellulosome-producing Ruminococcus species and human health,in addition to livestock productivity,carbon neutralization,and the carbon cycle(Fig.1).

关键词： neutral linkage replace

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Cellulosomal hemicellulases:Indispensable players for ensuring effective lignocellulose bioconversion

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Green Carbon 2024年第1期2卷 57-69页

作者： Min Xiao Ya-Jun Liu Edward A.Bayer Akihiko Kosugi Qiu Cui yingang feng CAS Key Laboratory of Biofuels Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao 266101China Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao 266101China Shandong Engineering Laboratory of Single Cell Oil Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao 266101China Shandong Energy Institute Qingdao 266101China Qingdao New Energy Shandong Laboratory Qingdao 266101China University of Chinese Academy of Sciences Beijing 100049China Department of Biomolecular Sciences The Weizmann Institute of ScienceRehovot 7610001Israel Department of Life Sciences and the National Institute for Biotechnology in the Negev Ben-Gurion University of the NegevBeer-Sheva 8499000Israel Biological Resources and Post-harvest Division Japan International Research Center for Agricultural Sciences(JIRCAS)1-1 OhwashiTsukubaIbaraki 305-8686Japan

The bioconversion of lignocellulose has attracted global attention,due to the significant potential of agricultural and forestry wastes as renewable zero-carbon resources and the urgent need for substituting fossil *** cellulosome system is a multi-enzyme complex produced by anaerobic bacteria,which comprises cellulases,hemicellulases,and associated enzymatic and non-enzymatic components that promote biomass *** enhance their efficiency in degrading recalcitrant lignocellulosic matrices,cellulosomes have been employed to construct biocatalysts for lignocellulose bioconversion,such as consolidated bioprocessing and consolidated ***,the second most abundant polysaccharides in plant cell walls,hold valuable application potential but can also induce inhibitory effects on cellulose hydrolysis,thus highlighting the indispensable roles of hemicellulases within the cellulosome *** review evaluated current research on cellulosomal hemicellulases,comparing their types,abundance,and regulation,primarily focusing on eight known cellulosome-producing species of different *** also reviewed their growth conditions,their hemicellulose-degrading capabilities,and the inhibitory effects of hemicellulose on cellulosome-based lignocellulose ***,we proposed strategies for targeted enhancement of hemicellulase in cellulosomes to improve lignocellulose bioconversion in future studies.

关键词： Cellulosome Lignocellulose Hemicellulase Saccharification Biocatalyst

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Glutathione regulates the transfer of iron-sulfur cluster from monothiol and dithiol glutaredoxins to apo ferredoxin

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Protein & Cell 2012年第9期3卷 714-721页

作者： Lei Wang Bingjie Ouyang Yifei Li yingang feng Jean-Pierre Jacquot Nicolas Rouhier Bin Xia Beijing Nuclear Magnetic Resonance Center Peking UniversityBeijing 100871China College of Chemistry and Molecular Engineering Peking UniversityBeijing 100871China School of Life Sciences Peking UniversityBeijing 100871China UMR 1136 IaM IFR 110Faculty of SciencesNancy UniversityVandoeuvre 54506France

Holo glutaredoxin(Grx)is a homo-dimer that bridges a[2Fe-2S]cluster with two glutathione(GSH)*** this study,both monothiol and dithiol holo Grxs are found capable of transferring their iron-sulfur(FeS)cluster to an apo ferredoxin(Fdx)through direct interaction,regardless of FeS cluster stability in holo *** ligand GSH molecules in holo Grxs are unstable and can be exchanged with free GSH,which inhibits the FeS cluster transfer from holo Grxs to apo *** phenomenon suggests a novel role of GSH in FeS cluster trafficking.

关键词： iron-sulfur cluster glutaredoxin glutathione ferredoxin CD NMR

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Protein-protein complexation in bioluminescence

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Protein & Cell 2011年第12期2卷 957-972页

作者： Maxim S.Titushin yingang feng John Lee Eugene S.Vysotski Zhi-Jie Liu National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of SciencesQingdao 266101China Department of Biochemistry and Molecular Biology University of GeorgiaAthensGA 30602USA Laboratory of Photobiology Institute of Biophysics Russian Academy of SciencesSiberian BranchKrasnoyarsk 660036Russia

In this review we summarize the progress made towards understanding the role of protein-protein interactions in the function of various bioluminescence systems of marine organisms,including bacteria,jellyfish and soft corals,with particular focus on methodology used to detect and characterize these *** some bioluminescence systems,protein-protein interactions involve an“accessory protein”whereby a stored substrate is efficiently delivered to the bioluminescent enzyme *** types of complexation mediate energy transfer to an“antenna protein”altering the color and quantum yield of a bioluminescence *** structures of the complexes reveal an important role of electrostatic forces in governing the corresponding weak interactions and define the nature of the interaction *** most reliable structural model is available for the protein-protein complex of the Ca2+-regulated photoprotein clytin and green-fluorescent protein(GFP)from the jellyfish Clytia gregaria,solved by means of Xray crystallography,NMR mapping and molecular *** provides an example of the potential strategies in studying the transient complexes involved in *** is emphasized that structural studies such as these can provide valuable insight into the detailed mechanism of bioluminescence.

关键词： green-fluorescent protein(GFP) photoprotein luciferase lumazine protein Förster resonance energy transfer(FRET) docking

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New insights into the structural basis of DNA recognition by HINa and HINb domains of IFI16

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分子细胞生物学报:英文版 2016年第1期8卷 51-61页

作者： Xiangmin Ni Heng Ru feng Ma Lixia Zhao Neil Shaw yingang feng Wei Ding Weibin Gong Qiaofeng Wang Songying Ouyang Genhong Cheng Zhi-Jie Liu Institute of Molecular and Clinical Medicine Kunming Medical UniversityKunming 650500China National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China Department of Microbiology Immunology and Molecular GeneticsUniversity of California Los AngelesLos AngelesCA 90095USA The Qingdao Engineering Laboratory of Single Cell Oil and Shandong Provincial Key Laboratory of Energy Genetics Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao 266101China iHuman Institute ShanghaiTech UniversityShanghai 201210China

Interferon gamma-inducible protein 16(IFI16)senses DNA in the cytoplasm and the nucleus by using two tandem hematopoietic interferon-inducible nuclear(HIN)domains,HINa and HINb,through the cooperative assembly of IFI16 filaments on double-stranded DNA(dsDNA).The role of HINa in sensing DNA is not clearly ***,we describe the crystal structure of the HINa domain in complex with DNA at 2.55A°resolution and provide the first insight into the mode of DNA binding by the HINa *** structure reveals the presence of two oligosaccharide/nucleotide-binding(OB)folds with a unique DNA-binding *** uses loop L45 of the canonical OB2 fold to bind to the DNA *** dsDNA is recognized as two single strands of ***,deletion of HINb compromises the ability of IFI16 to induce IFN-b,while HINa mutants impaired in DNAbinding enhance the production of *** results shed light on the roles of IFI16 HIN domains in DNA recognition and innate immune responses.

关键词： interferon gamma-inducible protein 16(IFI16) hematopoietic interferon-inducible nuclear(HIN)domain DNA recognition innate immune responses

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Mechanism of the Rpn13-induced activation of Uch37

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Protein & Cell 2014年第8期5卷 616-630页

作者： Lianying Jiao Songying Ouyang Neil Shaw Gaojie Song yingang feng fengfeng Niu Weicheng Qiu Hongtao Zhu Li-Wei Hung Xiaobing Zuo V. Eleonora Shtykova Ping Zhu Yu-Hui Dong Ruxiang Xu Zhi-Jie Liu National Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China iHuman Institute ShanghaiTech University Shanghai 201210 China Shandong Provincial Key Laboratory ofEnergy-Genetics Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences Qingdao 266101 China Physics Division 'Los Alamos National Laboratory Los Alamos NM 87545 USA X-ray Science Division Argonne National Laboratory 9700 South Cass Avenue Argonne IL 60439 USA Institute of Crystallography~ Russian Academy of Sciences 59 Leninsky Pr. 117333 Moscow Russian Federation Center for Multi-disciplinary Research Institute of High Energy Physics Chinese Academy of Sciences Beijing 100049China Department of Nerosurgery The Military General Hospital of Beijing PLA Beijing 100700 China

Uch37 is a de-ubiquitinating enzyme that is activated by Rpn13 and involved in the proteasomal degradation of proteins. The full-length Uch37 was shown to exhibit low iso-peptidase activity and is thought to be auto-inhibited. Structural comparisons revealed that within a homo- dimer of Uch37, each of the catalytic domains was blocking the other＇s ubiquitin （Ub）-binding site. This blockage likely prevented Ub from entering the active site of Uch37 and might form the basis of auto-inhibition. To understand the mode of auto-inhibition clearly and shed light on the activation mechanism of Uch37 by Rpn13, we investigated the Uch37-Rpn13 complex using a combi- nation of mutagenesis, biochemical, NMR, and small- angle X-ray scattering （SAXS） techniques. Our results also proved that Uch37 oligomerized in solution and had very low activity against the fluorogenic substrate ubi- quitin-7-amino-4-methylcoumarin （Ub-AMC） of de-ubiq- uitinating enzymes. Uch37AHb＇Hc＇KEKE, a truncation removal of the C-terminal extension region （residues 256- 329） converted oligomeric Uch37 into a monomeric form that exhibited iso-peptidase activity comparable to that of a truncation-containing the Uch37 catalytic domain only. We also demonstrated that Rpn13C （Rpn13 residues 270- 407） could disrupt the oligomerization of Uch37 by sequestering Uch37 and forming a Uch37-Rpn13 com- plex. Uch37 was activated in such a complex, exhibiting 12-fold-higher activity than Uch37 alone. Time-resolved SAXS （TR-SAXS） and FRET experiments supported the proposed mode of auto-inhibition and the activation mechanism of Uch37 by Rpn13. Rpn13 activated Uch37 by forming a 1：1 stoichiometric complex in which the active site of Uch37 was accessible to Ub.

关键词： Uch37-Rpn13 complex de-ubiquitination,SAXS analysis oligomerization iso-peptidase

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Possessing one rigid “stabilizer-core” unit is the molecular origin of the extreme thermostability of P62A-mutant archaeal Ssh10b

Possessing one rigid “stabilizer-core” unit is the molecul...

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第十二届北京分析测试学术报告会暨展览会(BCEIA 2007)

作者： Xianyang Fang Qiu Cui Yufeng Tong yingang feng Lu Shan Li Huang Jinfeng Wang

The dimeric solution structure of the P62A-mutant hyperthermophilic archaeal Ssh10b([P62A]Ssh10b)has been solved by multi-dimensional NMR *** H/D backbone amide exchange in the absence and presence of Gdm SCN and back...

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Biochemical and Crystal Structural Insights into Substrate Specificity and Thermostability of a Novel Glycoside Hydrolase 5 Lichenase from Caldicellulosiruptor sp.F32

Biochemical and Crystal Structural Insights into Substrate S...

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2015中国酶工程与糖生物工程学术研讨会

作者： Dong-Dong Meng Xi Liu Ye-Fei Wang Kun-Di Zhang Xinquan Wang Li-Shan Yao yingang feng Fu-Li Li Key Laboratory of Biofuels Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences University of Chinese Academy of Sciences Ministry of Education Key Laboratory of Protein Science Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China Qingdao Engineering Laboratory of Single Cell Oil Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences

Understanding the structural basis for thermostable lichenin-degrading enzyme is important forβ-1,3-1,4-mixed linkage glucan degradation and industrial application.A novel lichenase F32EG5 belonging to the glycoside hydrolase(GH)family 5 was identified from an extremely thermophilic bacterium Caldicellulosiruptor *** analysis indicated that F32EG5 is a non-metalloprotein lichenase with the optimal temperature and pH at 80℃and 5.5,respectively,and a half-life at 80℃of 8 *** exhibited a specific and high activity onβ-1,3-1,***-layer chromatography and NMR analyses further indicated that F32EG5 hydrolysed theβ-1,3 linkage after aβ-1,4 linkage,as well as the P-1,4 linkage before a p-1,3 linkage,which is different from the extensively studied GH family 16 lichenase with a cleavage site on theβ-1,4linkage after aβ-1,3 *** crystal structure of F32EG5 was determined to 2.8 A resolution,which showed a typical(β/α)-barrel fold of the GH family 5 *** of the structure revealed that the exit subsites of substrate binding sites contribute to thermostability and substrate specificity of *** catalytic mechanism and substrate selectivity of F32EG5 was further verified by site-directed mutagenesis and molecular docking of different glucotetraoses.F32EG5 is a novel type of lichenase with a distinct cleavage pattern forβ-1,3-1,4-mixed linkage glucan and shows potential in industrial processes,such as the brewing and feed industries.

关键词： Crystal structure Lichenase Thermostability Catalytic mechanism molecular docking NMR

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裂殖壶菌SD116油脂的胞内核磁共振研究

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生物物理学报 2014年第3期30卷 193-206页

作者：兰君谭延振宋晓金崔球冯银刚山东省能源生物遗传资源重点实验室中国科学院生物燃料重点实验室中国科学院青岛生物能源与过程研究所山东青岛266101

胞内核磁共振方法通常用于在原位对细胞内的标记蛋白质进行分析。产油微生物胞内油脂含量极高,理论上也可以使用胞内核磁共振方法对其油脂进行研究。作者使用一株高产多不饱和脂肪酸DHA的裂殖壶菌SD116,对其进行了胞内核磁共振分析。归... 详细信息

胞内核磁共振方法通常用于在原位对细胞内的标记蛋白质进行分析。产油微生物胞内油脂含量极高,理论上也可以使用胞内核磁共振方法对其油脂进行研究。作者使用一株高产多不饱和脂肪酸DHA的裂殖壶菌SD116,对其进行了胞内核磁共振分析。归属了胞内核磁共振氢谱和碳谱的谱峰,鉴定了胞内核磁共振谱图中饱和脂肪酸和多不饱和脂肪酸的特征谱峰,并对比了大肠杆菌和产油酵母的胞内核磁共振谱图。结果表明,胞内核磁共振方法可以有效地分析产油微生物细胞中的油脂。

关键词：胞内核磁共振油脂裂殖壶菌多不饱和脂肪酸

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NMR study of E43S mutant of SNase bound to single-stranded DNA

NMR study of E43S mutant of SNase bound to single-stranded D...

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第九届全国酶学学术讨论会暨邹承鲁诞辰85周年纪念会

作者： Tao Xie Lu Shan yingang feng Yufeng Tong and Jinfeng Wang National Laboratory of Biomacromolecules,Center for Structural and Molecular Biology,Institute of Biophysics,Chinese Academy of Sciences,15 Datun Road,Beijing 100101

Objective:In order to learn more about DNA hydrolysis mechanism of SNase,it is essential to analyze the structure and dynamics of SNase-DNA complex;Method: Enzyme activity test,gel filtration,H-NMR,H-N HSQC,NMR diffus... 详细信息

关键词： SNase protein-DNA interaction NMR backbonedynamics.

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