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Versatile plant genome engineering using anti-CRISPR-Cas12a systems

Science china Life Sciences 2024年

作者： Yao He Shishi Liu Long Chen Dongkai Pu Zhaohui Zhong Tang Xu Qiurong Ren Chuan Dong Yawei Wang Danning Wang Xuelian Zheng Fengbiao Guo Tao Zhang Yiping Qi Yong Zhang Integrative Science Center of Germplasm Creation in western china (Chongqing) Science City Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization School of Life Sciences Southwest University Department of biotechnology School of Life Sciences and Technology Center for Informational Biology University of Electronic Science and Technology of China Sichuan Institute of Edible Fungi Sichuan Academy of Agricultural Sciences Jiangsu key laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding laboratory/key laboratory of Plant Functional Genomics of the ministry of Education College of AgricultureYangzhou University Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu key laboratory of Crop Genetics and Physiology Yangzhou University Department of Respiratory and Critical Care Medicine Zhongnan Hospital of Wuhan University key laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and School of Pharmaceutical Sciences Wuhan University Department of Plant Science and Landscape Architecture University of Maryland College Park 20742 Institute for Bioscience and biotechnology Research University of Maryland

CRISPR-Cas12a genome engineering systems have been widely used in plant research and crop breeding. To date, the performance and use of anti-CRISPR-Cas12a systems have not been fully established in plants. Here, we conduct in silico analysis to identify putative anti-CRISPR systems for Cas12a. These putative anti-CRISPR proteins, along with known anti-CRISPR proteins, are assessed for their ability to inhibit Cas12a cleavage activity in vivo and in planta. Among all anti-CRISPR proteins tested, AcrVA1 shows robust inhibition of Mb2Cas12a and LbCas12a in E. coli. Further tests show that AcrVA1 inhibits LbCas12a mediated genome editing in rice protoplasts and stable transgenic lines. Impressively, co-expression of AcrVA1 mitigates off-target effects by CRISPR-LbCas12a, as revealed by whole genome sequencing. In addition, transgenic plants expressing AcrVA1 exhibit different levels of inhibition to LbCas12a mediated genome editing, representing a novel way of fine-tuning genome editing efficiency. By controlling temporal and spatial expression of AcrVA1, we show that inducible and tissue specific genome editing can be achieved in plants. Furthermore, we demonstrate that AcrVA1 also inhibits LbCas12a-based CRISPR activation(CRISPRa) and based on this principle we build logic gates to turn on and off target genes in plant cells. Together, we have established an efficient anti-CRISPR-Cas12a system in plants and demonstrate its versatile applications in mitigating off-target effects, finetuning genome editing efficiency, achieving spatial-temporal control of genome editing, and generating synthetic logic gates for controlling target gene expression in plant cells.

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Biomimetic natural biomaterials for tissue engineering and regenerative medicine:new biosynthesis methods,recent advances,and emerging applications

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Military Medical Research 2024年第1期11卷 50-79页

作者： Shuai Liu Jiang-Ming Yu Yan-Chang Gan Xiao-Zhong Qiu Zhe-Chen Gao Huan Wang Shi-Xuan Chen Yuan Xiong Guo-Hui Liu Si-En Lin Alec McCarthy Johnson V.John Dai-Xu Wei Hong-Hao Hou Guangdong Provincial key laboratory of Construction and Detection in Tissue Engineering the Fifth Affiliated HospitalSchool of Basic Medical ScienceSouthern Medical UniversityGuangzhou 510900China Department of Orthopedics Tongren HospitalShanghai Jiao Tong UniversityShanghai 200336China The Eighth Affiliated Hospital Sun Yat-Sen UniversityShenzhen 518033GuangdongChina Engineering Research Center of Clinical Functional Materials and Diagnosis&Treatment Devices of Zhejiang Province Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou 325011ZhejiangChina Department of Orthopedics Union HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430022China Department of Orthopaedics and Traumatology Faculty of Medicinethe Chinese University of Hong KongHong Kong SAR 999077China Department of Functional Materials Terasaki Institute for Biomedical InnovationLos AngelesCA 90064USA Mary&Dick Holland Regenerative Medicine Program College of MedicineUniversity of Nebraska Medical CenterOmahaNE 68130USA Zigong Affiliated Hospital of Southwest Medical University Zigong Psychiatric Research CenterZigong Institute of Brain ScienceZigong 643002SichuanChina key laboratory of resource biology and biotechnology in western china Ministry of EducationSchool of MedicineDepartment of Life Sciences and MedicineNorthwest UniversityXi’an 710127China

Biomimetic materials have emerged as attractive and competitive alternatives for tissue engineering(TE)and regenerative *** contrast to conventional biomaterials or synthetic materials,biomimetic scaffolds based on natural biomaterial can offer cells a broad spectrum of biochemical and biophysical cues that mimic the in vivo extracellular matrix(ECM).Additionally,such materials have mechanical adaptability,micro-structure interconnectivity,and inherent bioactivity,making them ideal for the design of living implants for specific applications in TE and regenerative *** paper provides an overview for recent progress of biomimetic natural biomaterials(BNBMs),including advances in their preparation,functionality,potential applications and future *** highlight recent advances in the fabrication of BNBMs and outline general strategies for functionalizing and tailoring the BNBMs with various biological and physicochemical characteristics of native ***,we offer an overview of recent key advances in the functionalization and applications of versatile BNBMs for TE ***,we conclude by offering our perspective on open challenges and future developments in this rapidly-evolving field.

关键词： Biomimic Scaffold Biosynthesis Natural biomaterial Tissue engineering

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Phytoremediation capacity of the hyperaccumulator Solanum nigrum *** Solanum lycopersicum *** at the flowering stage in cadmium-polluted soil

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Pedosphere 2024年第3期34卷 676-680页

作者： Jibao JIA Huiping DAI Shuhe WEI Lidia SKUZA Jianming XUE Rong LI Quan SUN School of Agriculture Ningxia UniversityYinchuan 750021(China) School of Biological Science and Engineering Shaanxi University of TechnologyHanzhong 723001(China) key laboratory of Pollution Ecology and Environment Engineering Institute of Applied EcologyChinese Academy of SciencesShenyang 110016(China) Institute of biology Centre for Molecular Biology and BiotechnologyUniversity of SzczecinSzczecin 71-415(Poland) New Zealand Forest Research Institute(Scion) POB 29237Christchurch 8440(New Zealand)

Dear Editor,Remediation of cadmium(Cd)-contaminated soil is a popular topic in global environmental *** using hyperaccumulators or certain plants to accumulate and remove Cd from polluted soils is a promising *** et al.(2005)first described Solanum nigrum *** a Cd ***,various aspects of ***,including the protective effects on proline,physiological and biochemical responses,earthworms,arbuscular mycorrhizal fungi,and fertilizers and the intercropping with Solanum photeinocarpum,have been extensively studied(Xu et al.,2009;Khan et al.,2014;Wang et al.,2015;Tang et al.,2017;Yang et al.,2019).

关键词： soil cultivar cadmium

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Green light mediates atypical photomorphogenesis by dual modulation of Arabidopsis phytochromes B and A

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Journal of Integrative Plant biology 2024年第09期 1915-1933页

作者： Miqi Xu Yi-Yuan Wang Yujie Wu Xiuhong Zhou Ziyan Shan Kunying Tao Kaiqiang Qian Xuncheng Wang Jian Li Qingqing Wu Xing Wang Deng Jun-Jie Ling National Engineering laboratory of Crop Stress Resistance Breeding School of Life Sciences Anhui Agricultural University Province key laboratory of resource Insect biology and Innovative Utilization School of Life Sciences Anhui Agricultural University biotechnology Center State Key Laboratory of Tea Plant Biology and Utilization School of Tea and Food Sciences and TechnologyAnhui Agricultural University Beijing key laboratory of Environment Friendly Management on Fruit Diseases and Pests in North china Institute of Plant and Environment Protection Beijing Academy of Agriculture and Forestry Sciences College of Life Sciences Nanjing Normal University State key laboratory of Protein and Plant Gene Research Peking–Tsinghua Center for Life Sciences School of Advanced Agriculture Sciences and School of Life Sciences Peking University State key laboratory of Wheat Improvement Shandong Laboratory of Advanced Agricultural Sciences at Weifang Peking University Institute of Advanced Agricultural Sciences

Although green light(GL) is located in the middle of the visible light spectrum and regulates a series of plant developmental processes, the mechanism by which it regulates seedling development is largely unknown. In this study, we demonstrated that GL promotes atypical photomorphogenesis in Arabidopsis thaliana via the dual regulations of phytochrome B(phy B) and phy A. Although the Pr-to-Pfr conversion rates of phy B and phy A under GL were lower than those under red light(RL) in a fluence rate-dependent and time-dependent manner, long-term treatment with GL induced high Pfr/Pr ratios of phy B and phy A. Moreover, GL induced the formation of numerous small phy B photobodies in the nucleus, resulting in atypical photomorphogenesis, with smaller cotyledon opening angles and longer hypocotyls in seedlings compared to RL. The abundance of phy A significantly decreased after short-and long-term GL treatments. We determined that four major PHYTOCHROME-INTERACTING FACTORs(PIFs:PIF1, PIF3, PIF4, and PIF5) act downstream of phy B in GL-mediated cotyledon opening. In addition, GL plays opposite roles in regulating different PIFs. For example, under continuous GL, the protein levels of all PIFs decreased, whereas the transcript levels of PIF4 and PIF5 strongly increased compared with dark treatment. Taken together, our work provides a detailed molecular framework for understanding the role of the antagonistic regulations of phy B and phy A in GL-mediated atypical photomorphogenesis.

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约4900年前东亚和东南亚枢纽地区狩猎采集向农业的转变

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Science Bulletin 2024年第1期69卷 103-113页

作者：马敏敏卢敏霞孙瑞朱忠华 Dorian Q.Fuller 郭健新何光林杨晓敏谭玲玲芦永秀董佳佳刘睿良杨继帅李波郭天南李小瑞赵东月张颖王传超董广辉 key laboratory of western china’s Environmental Systems(ministry of Education) College of Earth and Environmental SciencesLanzhou UniversityLanzhou 730000China Zhaotong University Zhaotong 657000China Westlake laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China Yunnan Provincial Institute of Cultural Relics and Archaeology Kunming 650118China Institute of Archaeology University College LondonLondon WC1H 0PYUK School of Cultural Heritage Northwest UniversityXi’an 710069China State key laboratory of Cellular Stress biology School of Life SciencesXiamen UniversityXiamen 361102China Department of Anthropology and Ethnology Institute of AnthropologySchool of Sociology and AnthropologyXiamen UniversityXiamen 361005China State key laboratory of Marine Environmental Science Xiamen UniversityXiamen 361102China Westlake Omics(Hangzhou)biotechnology Co. Ltd.Hangzhou 310024China The Department of Asia British MuseumLondon WC1E 7JWUK Tonghai Cultural Relics Management Yuxi 652700China Group of Alpine Paleoecology and Human Adaptation Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China State key laboratory of Tibetan Plateau Earth System Resources and EnvironmentBeijing 100101China ministry of Education key laboratory of Contemporary Anthropology Department of Anthropology and Human GeneticsSchool of Life SciencesFudan UniversityShanghai 200433China

The southward expansion of East Asian farmers profoundly influenced the social evolution of Southeast Asia by introducing cereal ***,the timing and routes of cereal expansion in key regions are unclear due to limited empirical *** we report macrofossil,microfossil,multiple isotopic(C/N/Sr/O)and paleoproteomic data directly from radiocarbon-dated human samples,which were unearthed from a site in Xingyi in central Yunnan and which date between 7000 and 3300 a *** isotopes reveal the earliest arrival of millet ca.4900 a BP,and greater reliance on plant and animal agriculture was indicated between 3800 and 3300 a *** dietary differences between hunter-gatherer and agricultural groups are also evident in the metabolic and immune system proteins analysed from their skeletal *** results of paleoproteomic analysis indicate that humans had divergent biological adaptations,with and without *** combined application of isotopes,archaeobotanical data and proteomics provides a new approach to documenting dietary and health changes across major subsistence transitions.

关键词： Isotopes Proteomics Yunnan Millet Agricultural origins Human health

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Woody plant cell walls:Fundamentals and utilization

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Molecular Plant 2024年第1期17卷 112-140页

作者： Wei Li Ying-Chung Jimmy Lin Ying-Lan Chen Chenguang Zhou Shuang Li Nette De Ridder Dyoni M.Oliveira Lanjun Zhange Baocai Zhang Jack P.Wang Changzheng Xu Xiaokang Fu Keming Luo Ai-Min Wu Taku Demura Meng-Zhu Lu Yihua Zhou Laigeng Li Toshiaki Umezawa Wout Boerjan Vincent L.Chiang State key laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040China Department of Life Science National Taiwan UniversityTaipeiTaiwanChina Department of biotechnology and Bioindustry Sciences College of Bioscience and BiotechnologyNational Cheng Kung UniversityTainanTaiwanChina Department of Plant biotechnology and Bioinformatics Ghent UniversityTechnologiepark 719052 GhentBelgium VIB Center for Plant Systems biology Technologiepark 719052 GhentBelgium State key laboratory of Plant Genomics Insttute of Genetics and Developmental biology Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Forest biotechnology Group Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNC 27695USA Chongqing key laboratory of Plant resource Conservation and Germplasm Innovation Integrative Science Center of Germplasm CreationSchool of Life SciencesSouthwest UniversityChongqing 400715China Guangdong key laboratory for Innovative Developmentand Utilization of Forest Plant Germplasm College of Forestry and Landscape ArchitecturesSouth China Agricultural UniversityGuangzhou510642China Center for Digital Green-innovation Nara Institute of Science and TechnologykomaNara 630-0192Japan State key laboratory of Subtropical Siviculture College of Forestry and BiotechnologyZhejang A&F UniversityHangzhou 311300China CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences300 Fenglin RoadShanghai 200032China laboratoryof MetabolicScienceofForest Plants and Microorganisms Rsearch Institute for Sustainable HumanosphereKyoto UniversityUjiKyoto 611-0011 Japan

Cell walls in plants,particularly forest trees,are the major carbon sink of the terrestrial *** and biosynthetic features of plant cell walls were revealed early on,focusing mostly on herbaceous model *** developments in genomics,transcriptomics,epigenomics,transgenesis,and associated analytical techniques are enabling novel insights into formation of woody cell ***,we review multilevel regulation of cell wall biosynthesis in forest tree *** highlight current approaches to engineering cell walls as potential feedstock for materials and energy and survey reported field tests of such engineered transgenic *** outline opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell wall modification and utilization for biomaterials or for enhanced carbon capture and storage.

关键词： regulation of cell wall formation biosynthesis of cell wall components lignin cellulose hemicellulose cell wall utilization

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Strategies on biosynthesis and production of bioactive compounds in medicinal plants

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Chinese Herbal Medicines 2024年第1期16卷 13-26页

作者： Miaoxian Guo Haizhou Lv Hongyu Chen Shuting Dong Jianhong Zhang Wanjing Liu Liu He Yimian Ma Hua Yu Shilin Chen Hongmei Luo key Lab of Chinese Medicine resources Conservation State Administration of Traditional Chinese Medicine of ChinaInstitute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100193China Engineering Research Center of Chinese Medicine resource Ministry of EducationBeijing 100193China key laboratory of Hangzhou City for Ecosystem Protection and Restoration College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou 311121China Chengdu University of Traditional Chinese Medicine Chengdu 611137China

Medicinal plants are a valuable source of essential medicines and herbal products for healthcare and disease *** with chemical synthesis and extraction,the biosynthesis of natural products is a very promising alternative for the successful conservation of medicinal plants,and its rapid development will greatly facilitate the conservation and sustainable utilization of medicinal ***,we summarize the advances in strategies and methods concerning the biosynthesis and production of natural products of medicinal *** strategies and methods mainly include genetic engineering,plant cell culture engineering,metabolic engineering,and synthetic biology based on multiple“OMICS”technologies,with paradigms for the biosynthesis of terpenoids and *** also highlight the biosynthetic approaches and discuss progress in the production of some valuable natural products,exemplifying compounds such as vindoline(alkaloid),artemisinin and paclitaxel(terpenoids),to illustrate the power of biotechnology in medicinal plants.

关键词： biosynthetic strategies biotechnology natural products medicinal plants synthetic biology

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Population genetic insights into the conservation of common walnut(Juglans regia)in Central Asia

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Plant Diversity 2024年第5期46卷 600-610页

作者： Linjiang Ye Robabeh Shahi Shavvon Hailing Qi Hongyu Wu Pengzhen Fan Mohammad Nasir Shalizi Safiullah Khurram Mamadzhanov Davletbek Yerlan Turuspekov Jie Liu CAS key laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina key laboratory of Plant resources and Biodiversity of Jiangxi Province Jingdezhen UniversityJingdezhen 333400JiangxiChina Germplasm Bank of Wild Species&Yunnan key laboratory of Crop Wild Relatives Omics Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina Department of biology Faculty of ScienceYasouj UniversityYasouj 75918-74934Iran University of Chinese Academy of Sciences Beijing 100049China Department of Forestry and Environmental resources North Carolina State UniversityRaleighNC 27695United States Department of Forestry and Natural resources Faculty of AgricultureKabul UniversityKabul D-1006Afghanistan National Academy of Science of the Kyrgyz Republic Jalal-Abad Scientific CenterJalal-Abad 715600Kyrgyzstan laboratory of Molecular Genetics Institute of Plant Biology and BiotechnologyAlmaty 050040Kazakhstan

The common walnut(Juglans regia)is one of the most economically important nut trees cultivated *** its importance,no comprehensive evaluation of walnut tree population genetics has been undertaken across the range where it originated,Central *** this study,we investigated the genetic diversity and population structure of 1082 individuals from 46 populations across Central *** found moderate genetic diversity of *** across Central Asia,with 46 populations clustered into three groups with a weak relationship between genetic and geographic *** findings reveal that the western Himalaya might be the core region of common walnut genetic diversity in Central Asia and that,except for two populations in Gongliu Wild Walnut Valley,humans might have introduced walnut populations to Xinjiang,*** observed distribution of the genetic landscape has probably been affected by historical climate fluctuation,breeding system,and prolonged anthropogenic *** propose the conservation of the core genetic diversity resources in the western Himalaya and pay special attention to populations from Gongliu in *** findings enhance our understanding of the genetic variation throughout the distribution range of *** in Central Asia,which will provide a key prerequisite for evidence-based conservation and management.

关键词： Central Asia Genetic diversity Germplasm management Gongliu wild walnut valley Juglans regia western Himalaya

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Honey vesicle-like nanoparticles protect aged liver from non-alcoholic steatohepatitis

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Acta Pharmaceutica Sinica B 2024年第8期14卷 3661-3679页

作者： Baolong Liu Phuong Linh Nguyen Han Yu Xingzhi Li Huiren Wang Tram Gia Bao Nguyen Prakash Kumar Sahoo Meghna Sur Jay Reddy Sarah Sillman Stephen D.Kachman Bara Altartouri Guoqing Lu Sathish Kumar Natarajan Mahesh Pattabiraman Jiujiu Yu Department of Nutrition and Health Sciences University of Nebraska-LincolnLincolnNE 68583USA Shaanxi key laboratory of Molecular biology for Agriculture College of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China Department of Nutrition Case Western Reserve UniversityClevelandOH 44106USA School of Veterinary Medicine and Biomedical Sciences University of Nebraska-LincolnLincolnNE 68583USA Department of Statistics University of Nebraska-LincolnLincolnNE 68583USA Center for biotechnology University of Nebraska-LincolnLincolnNE 68588USA Department of biology University of Nebraska OmahaOmahaNE 68182USA Department of Chemistry University of Nebraska-KearneyKearneyNE 68849USA

Non-alcoholic steatohepatitis(NASH),an advanced form of non-alcoholic fatty liver disease(NAFLD),has emerged as the leading cause of liver failure and related ***,no medication is specifically approved to treat NAFLD or *** we report that oral administration of honey vesiclelike nanoparticles(H-VLNs)to naturally aged mice protects the liver from NASH development.H-VLNs are dominantly taken up by Kupffer cells in the liver and suppress hepatic chronic inflammation and further development of fibrosis and nodule formation in aged *** their reported antiinflammasome function,H-VLNs are found to inhibit the transcriptional activities of C-JUN and nuclear factor-kappa B(NF-κB).MicroRNAs miR5119 and miR5108 and phenolic compound luteolin in H-VLNs are identified in suppressing both the C-JUN and NF-kB ***,oral intake of H-VLNs represents a promising new user-friendly modality to prevent the development of NASH.

关键词： Honey Extracellular vesicles Exosomes Nanoparticles microRNAs Aging Inflammation Non-alcoholic steatohepatitis

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Effect of Denaturant Concentration on Hen-egg White Lysozyme Renaturation

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Chinese Journal of Chemistry 2006年第5期24卷 653-659页

作者：边六交杨晓燕 key laboratory of ministry of Education for resource biology and biotechnology in western china Northwest University Xi' an Shaanxi 710069 China

Based on three-state renaturation process of denatured proteins, an equation describing the effect of denaturant concentration on renaturation yield of denatured proteins was presented. By this equation, two parameters n（m1 -m2） and Ka can be obtained. The former indicates the difference in the number of denaturant molecules between the renaturation process of n number of refolding intermediates from refolding intermediate state to native state and their aggregate process from refolding intermediate state to aggregate state, the latter denotes the apparent aggregate equilibrium constant for protein molecules aggregated from native state to aggregate state, and from them, the characteristics of the renaturation process of denatured proteins in denaturant solution can be identified. This equation was tested by the renaturation processes of denatured egg white lysozyme in guanidine hydrochloride and urea solutions, with the results to show that when guanidine hydrochloride and urea concentrations were separately higher than 1.25 and 3.00 mol/L or separately lower than 1.00 and 3.00 mol/L, the refolding intermediates of egg white lysozymes were more easily aggregated to aggregate state or more easily renatured to native state, respectively. Under different initial total egg white lysozyme concentrations in urea solution, the refolding egg white lysozyme intermediates could be deduced to have a tendency to form a bimolecular intermediate aggregate, and this inference was further confirmed by their nonreducing SDS-PAGE and size exclusion chromatography.

关键词： egg white lysozyme urea guanidine hydrochloride renaturation yield denaturant concentration

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