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The Ninth National Symposium on Enzyme Engineering

作者： qi-shi du Ri-Bo Huang Guangxi Academy of Sciences State Key Laboratory of Non-food Biomass and Enzyme Technology

The 3D structures of biological macromolecules（proteins,RNA,and DNA）are determined by the molecular interactions forces between the structural ***,the biological functions of biological molecules are determined by the structures of *** addition to the three known interaction forces（hydrogen-bond interaction,electrostatic interaction,and van de Waals interaction）,there are several unconventional molecular interaction forces,such as cation-πinteractions,polar hydrogen-π（Hp-π）interactions,π-πstocking interactions,and coordinate interactions,which are less familiar to many *** the 20 natural amino acids 11 of them are involved in the polar hydrogen-π*** DAN and RNA the four nucleic acid components（adenine,guanine,cytosine,and thymine）possess aromatic rings and polar hydrogen atoms,which are the Hp-πinteraction acceptors and *** peptide bond units of protein backbones are also the Hp-πinteraction *** chemical method CCSD/6-311+G（d,p）+H-Bq is used in the study of Hp-π*** the polar hydrogen atom of a peptide unit perpendicularly points to theπ-plane of other peptide bond units,remarkable Hp-πinteraction *** Hp-πinteractions are distance and orientation dependent,and point-to-plane interaction,acting in a broad *** potential energy surface scanning calculations are performed on the quasiπ-plane of peptide bond unit,and around the torsion anglesΦandψbetween two connected peptide *** protein backbones the Hp-πinteraction energies are in the range from-13 to-22kj/mol,close to the hydrogen bond energies（-24 kj/mol）.The potential energy surface scanning for torsion anglesΦandψidentified four loop structural conformations,in which four different Hp-πinteraction types（H-π-l,H-π-2,H-π-3,H-π-4）maintain the shapes of *** physical nature and properties of Hp-πinteractions may provide useful concepts that are helpful for better understanding to the protein folding patterns,and to dev

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Interaction mechanism analysis between carbon dioxide(CO2)and three enzymes via molecular modeling and NMR experiment

Interaction mechanism analysis between carbon dioxide(CO2)an...

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2015中国酶工程与糖生物工程学术研讨会

作者： qi-shi du Nai-Kun Shen Ri-Bo Huang National Engineering Research Center for Non-food Biorefinery State key Laboratory of Bioenergy Enzyme TechnologyGuangxi Academy of Sciences

The interaction mechanism between amino acid residues and carbon dioxide(CO)in proteins is the theoretical basis of many the most important biological processes in life science,such as photosynthesis in plants and metabolic reaction of *** storage of CO in proteins is the first step in above important biological *** binding interactions between CO and amino acid side chains are calculated using MP2/6-311+G(d,p)*** interaction sites of CO in three proteins(phosphoenolpyruvate carboxykinase(PCK),rhodobacter capsulatus,and carbonic anhydraseⅡ)are analyzed using MD docking *** NMR spectrums of two pentapeptides(AARAA and AAKAA)are measured in solutions with and without CO,*** changes of chemical shifts of two pentapeptides are used for analyzing the interactions between CO and amino acids.(1)In proteins at least 13 of 20 natural amino acids possess remarkable interaction ability with CO molecules.(2)The best binding sites for CO molecules are the three alkaline amino acids(cations Arg,Lys,and His).(3)The acidic amino acids(anions Asp"and Glu")could maintain a suitable pH condition that is necessary for higher concentration of CO molecules in *** polar amino acids may provide transferring pathway for CO molecules.(4)Histidine plays the role of CO molecule deliver,because it frequently changes between protonated form Hisand neutral form His.(5)In most cases the binding interactions between CO molecules and amino acid side chains are electrostatic interactions,however,CO molecules could formπ—πstock interactions with aromatic amino acids(Phe,Tyr,and Trp),also can be packed by hydrophobic amino acids through hydrophobic interactions.

关键词： Protein-CO2 interaction Carbon dioxide storage Phosphoenolpyruvate carboxykinase(PCK) Rhodobacter capsulatus Carbonic anhydrase Ⅱ Amino acids interactions

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Flexible molecules dedicate to release strain of inverted inorganic perovskite solar cell

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Journal of Energy Chemistry 2025年第1期100卷 87-93页

作者： Hongrui Sun Sanlong Wang Pengyang Wang Yali Liu Shanshan qi Biao shi Ying Zhao Xiaodan Zhang Institute of Photoelectronic Thin Film Devices and Technology Renewable Energy Conversion and Storage Center State Key Laboratory of Photovoltaic Materials and CellsNankai University Key Laboratory of Photoelectronic Thin Film Devices and Technology of Tianjin Haihe Laboratory of Sustainable Chemical Transformations Engineering Research Center of Thin Film Photoelectronic Technology of Ministry of Education Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)

The tensile strain in inorganic perovskite films induced by thermal annealing is one of the primary factors contributing to the inefficiency and instability of inorganic perovskite solar cells （IPSCs）,which reduces the defect formation ***,a flexible molecule 5-maleimidovaleric acid （5-MVA） was introduced as a strain buffer to release the residual strain of *** anhydride and carboxyl groups in 5-MVA interact strongly with the uncoordinated Pb2+through Lewis acid-base reaction,thus tightly“pull”the perovskite *** in-between soft carbon chain increased the structural flexibility of CsPbI2.85Br0.15perovskite materials,which effectively relieved the intrinsic internal strain of CsPbI2.85Br0.15,resisted the corrosion of external strain,and also reduced the formation of defects such as VIand *** addition,the introduction of 5-MVA improved crystal quality,passivated residual defects,and narrowed energy level ***,power conversion efficiency （PCE） of NiOxbased inverted IPSCs increased from 19.25% to 20.82% with the open-circuit voltage enhanced from 1.164 V to 1.230 *** release of strain also improved the stability of CsPbI2.85Br0.15perovskite films and devices.

关键词： Perovskite solar cells

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A matrix metalloproteinase-responsive hydrogel system controls angiogenic peptide release for repair of cerebral ischemia/reperfusion injury

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Neural Regeneration Research 2025年第2期20卷 503-517页

作者： qi Liu Jianye Xie Runxue Zhou Jin Deng Weihong Nie Shuwei Sun Haiping Wang Chunying shi Department of Human Anatomy Histology and EmbryologySchool of Basic MedicineQingdao UniversityQingdaoShandong ProvinceChina Department of Neurology The Affiliated Hospital of Qingdao UniversityQingdaoShandong ProvinceChina Department of General Practice The Affiliated Hospital of Qingdao UniversityQingdaoShandong ProvinceChina

Vascular endothelial growth factor and its mimic peptide KLTWQELYQLKYKGI(QK)are widely used as the most potent angiogenic factors for the treatment of multiple ischemic ***,conventional topical drug delivery often results in a burst release of the drug,leading to transient retention(inefficacy)and undesirable diffusion(toxicity)in ***,a drug delivery system that responds to changes in the microenvironment of tissue regeneration and controls vascular endothelial growth factor release is crucial to improve the treatment of ischemic *** metalloproteinase-2(MMP-2)is gradually upregulated after cerebral ***,vascular endothelial growth factor mimic peptide QK was self-assembled with MMP-2-cleaved peptide PLGLAG(TIMP)and customizable peptide amphiphilic(PA)molecules to construct nanofiber hydrogel ***-TIMP-QK was found to control the delivery of QK by MMP-2 upregulation after cerebral ischemia/reperfusion and had a similar biological activity with vascular endothelial growth factor in *** results indicated that PA-TIMP-QK promoted neuronal survival,restored local blood circulation,reduced blood-brain barrier permeability,and restored motor *** findings suggest that the self-assembling nanofiber hydrogel PA-TIMP-QK may provide an intelligent drug delivery system that responds to the microenvironment and promotes regeneration and repair after cerebral ischemia/reperfusion injury.

关键词： angiogenesis biomaterial blood-brain barrier cerebral ischemia/reperfusion injury control release drug delivery inflammation QK peptides matrix metalloproteinase-2 neuroprotection self-assembling nanofiber hydrogel

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Single-cell technologies: current and near future

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Science China Life Sciences 2025年第01期 1-4页

作者： Chenfei Wang qi Liu Xiaohui Fan Tieliu shi Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration Ministry of EducationOrthopedics DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Key Laboratory of Advanced Theory and Application in Statistics and Data Science (MOE) School of StatisticsEast China Normal University

Single-cell technologies enable the indepth exploration of multiple biological hierarchies at the scale of individual cells,which have deepened our knowledge of cellular diversity, tissue organization, and overall organism function(Sun et al.,2024). In 2009, single-cell RNA sequencing(sc RNA-seq) was first developed as a powerful tool to dissect gene expression and uncover transcriptional *** the rapid advancement of technology, single-cell approaches have expanded to encompass other omics, such as genomics, epigenomics, proteomics,and metabolomics.

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High-selectivity electroreduction of low-concentration CO2 with large concentration fluctuation

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Science China Chemistry 2025年

作者： Mengyu qi Yanbin Ma Chao Zhang Bingwei Li Xueqing Yang Zhaolin shi Simeng Liu Changhua An Jiqing Jiao Tongbu Lu MOE International Joint Laboratory of Materials Microstructure Analysis and Testing CenterInstitute for New Energy Materials and Low Carbon TechnologiesSchool of Materials Science and EngineeringSchool of Chemistry and Chemical EngineeringTianjin University of Technology Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education) Nankai University

Electrochemical CO2reduction reaction（CO2RR） has been regarded as one of the most promising solutions to achieving “zero carbon emission”. In most of the CO2RR-related studies, high-purity CO2has been employed as the feed gas; however, in practice, CO2is generally emitted in low concentrations, so it is of great significance to realize high-selectivity electroreduction of low-concentration CO2with large concentration fluctuation. In this work, we constructed a dual-active-site catalyst and successfully achieved CO2local enrichment and conversion for low-concentration CO2. Operando experiments reveal that the catalyst has one type of site for activating CO2and one type of site for binding the reaction intermediates. The dual-active-site catalyst displays a selectivity for formic acid consistently above 97% over a broad potential window（from-0.9 to-1.6 V ***）. Even when fed with a low-concentration CO2stream（volume ratio from 50% down to 10%）, the dual-active-site catalyst could display high activity and selectivity（>91%）. In particular, the selectivity is still above 85% when the CO2volume ratio is as low as 5%. This work offers a feasible route for converting low-concentration CO2via a synergistic effect for dual-active-site catalysts.

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Multiple Field Three Dimensional Quantitative Structure-Activity Relationship（MF-3D-QSAR）

Multiple Field Three Dimensional Quantitative Structure-Acti...

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第九届全国计算（机）化学学术会议

作者： qi-shi du~(1,2*) Ri-Bo Huang~1 Yu-Tuo Wei~1 Li-qin du~1 Kuo-Chen Chou~(2,*) 1 Guangxi University,Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization,Nanning,Guangxi,530004,China 2 Gordon Life Science Institute,San Diego,California 92130,USA.

＜正＞A new drug design method,the multiple field three dimensional quantitative structure-activity relationship（MF-3D-OSAR）,is *** is a combination and development of classical 2D-OSAR and traditional *** addition to the electrostatic and van der Waals potentials,more potential fields（such as lipophilic potential,hydrogen bonding potential,and non thermodynamic factors）are integrated in the ***,a principal component analysis（PCA）and iterative double least square（IDLS）technique is developed for predicting the bioactivity of query drug *** an example,the MF-3D-QSAR is applied to the design of neuraminidase inhibitor and to prove its predictive power,and some useful findings are obtained for developing drugs against influenza ***-3D-QSAR model and PCA-IDLS technique is a main contribution to the QSAR *** has been applied to the CoMFA,CoMSIA,2D-OSAR, peptide and protein predictions successfully.

关键词： 3D-QSAR Potential fields Drug design Neuraminidase inhibitor H5N1 influenza

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关于土地开发整理项目水土保持有关问题的探讨

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水土保持学报 2003年第3期17卷 101-104页

作者：柳长顺齐实杜丽娟北京师范大学环境科学研究所水环境模拟国家重点实验室北京100875 北京林业大学水土保持学院北京100083

防治水土流失是土地开发整理项目的重要内容。土地开发整理项目本身是一项水土保持工程,其是否需要水土保持方案,如何编制是亟待解决的科学与生产问题。从分析其自身特点入手,从现状与法律的规定性两方面对此问题进行了探讨,认为把水土... 详细信息

防治水土流失是土地开发整理项目的重要内容。土地开发整理项目本身是一项水土保持工程,其是否需要水土保持方案,如何编制是亟待解决的科学与生产问题。从分析其自身特点入手,从现状与法律的规定性两方面对此问题进行了探讨,认为把水土保持方案设计的思路渗透到土地整理开发项目的相关设计中是目前解决该问题的最佳办法,并以山区、风沙区和丘陵区的3个项目为例进行了阐述。

关键词：土地开发整理项目水土保持方案编制设计特点

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Single-cell omics: experimental workflow, data analyses and applications

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Science China Life Sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao qinqin Wang Xin Dong Bin duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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Fragment-Based Quantitative Structure-Activity Relationship （FB-QSAR） for Fragment-Based Drug Design

Fragment-Based Quantitative Structure-Activity Relationship ...

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中国化学会第26届学术年会化学信息学与化学计量学分会场

作者： qi-shi du1,3, Ri-Bo Huang1,2, Yu-Tuo Wei1, Zong-Wen Pang1, Li-qin du1, Kuo-Chen Chou3 1Key Laboratory of Subtropical Bioresource Conservation and Utilization, Guangxi University, Nanning 530004 2Guangxi Academy of Sciences, Nanning 530004 3Gordon Life Science Institute, San Diego, California 92130, USA.

＜正＞In cooperation with the fragment-based design a new drug design method, the so-called "fragment-based quantitative structure-activity relationship" （FB-QSAR）, is proposed. The essence of the new method is that the molecular framework in a family of drug candidates is divided into several fragments according to their

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