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de novo design of transmembrane nanopores

Science China Chemistry 2022年第11期65卷 2122-2143页

作者： Dan Qiao Yuang Chen Haojing Tan Ruhong Zhou Jiandong Feng Laboratory of Experimental Physical Biology Department of ChemistryZhejiang UniversityHangzhou 310027China Institute of Quantitative Biology College of Life SciencesZhejiang UniversityHangzhou 310058China Zhejiang Lab Hangzhou 31000China

Transmembrane nanopores are structurally stable and biocompatible, and have various applications in molecular sensing and selective transport. The relationship between the function and structure is crucial for transmembrane nanopores, but it is still challenging to design and precisely tune the structure of conventional protein nanopores from scratch, albeit of abundant previous work on natural and bioengineered transmembrane protein nanopores. Therefore, numerous types of artificial transmembrane nanopores that can be de novo designed are rapidly under development, such as molecular nanopores, peptide nanopores, and DNA origami nanopores. In this review, we compare different building blocks of “bottom-up” built nanopores in terms of construction methods, structures and applications, and also describe important advances in de novo designed proteins from the perspective of theoretical simulations as well as an outlook for artificial intelligence-assisted nanopore design.

关键词： nanopores de novo design macrocycle DNA origami protein design

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Quick photofabrication of functional nanospheres from de novo designed peptides for NIR fluorescence and MR imaging

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Nano Research 2023年第3期16卷 4029-4038页

作者： Jingyi Zhao Chen Li Xue-Wang Gao Ke Feng Hao Liu Sijie He Wenhua Zhao Shumin Yang Jianqun Shao Ling Ye Bin Chen Nan Xie Chen-Ho Tung Li-Zhu Wu School of Pharmaceutical Sciences Capital Medical UniversityBeijing 100069China Key Laboratory of Photochemical Conversion and Optoelectronic Materials Technical Institute of Physics and ChemistryChinese Academy of SciencesBeijing 100190China

Combining the noncovalent and covalent interactions,a series of peptide amphiphiles were designed de novo and synthesized to architect functional assemblies by means of *** strand of peptide sequence was structurally capped with photoactive tyrosine-tyrosine(YY)motifs at both termini,and the spacing was filled by alternating of hydrophilic D(L-aspartate)and hydrophobic X(ε-aminocaproic acid)*** visible-light irradiation,these de novo designed peptides underwent rapid photocrosslinking within merely 10 ***,the modulation of alternating D-X pairs in occupying spacer would adjust molecular amphiphilicity,regulate charge distribution,and control particle size and loading capacity of peptide nanospheres(PNS)in aqueous *** entirely peptide-based matrix,this PNS system could host cationic indicators of fluorescent rhodamine and magnetic GdIII for exemplar near infrared(NIR)fluorescence and magnetic resonance(MR)imaging,which paves a pathway to biomaterial and biomedical applications using de novo designed peptides.

关键词： synthetic peptide photocrosslinking de novo design encapsulable nanosphere imaging nanoprobe dityrosine

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Enabling technology and core theory of synthetic biology

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Science China(Life Sciences) 2023年第8期66卷 1742-1785页

作者： Xian-En Zhang Chenli Liu Junbiao Dai Yingjin Yuan Caixia Gao Yan Feng Bian Wu Ping Wei Chun You Xiaowo Wang Tong Si Faculty of Synthetic Biology Shenzhen Institute of Advanced TechnologyShenzhen 518055China Institute of Synthetic Biology Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Microbial Metabolism Shanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Tianjin Institute of Industrial Biotechnology Chinese Academy of SciencesTianjin 300308China Ministry of Education Key Laboratory of Bioinformatics Center for Synthetic and Systems BiologyBioinformatics DivisionBeijing National Research Center for Information Science and TechnologyDepartment of AutomationTsinghua UniversityBeijing 100084China

Synthetic biology provides a new paradigm for life science research(“build to learn”)and opens the future journey of biotechnology(“build to use”).Here,we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology,including synthesis and assembly of a genome,DNA storage,gene editing,molecular evolution and de novo design of function proteins,cell and gene circuit engineering,cell-free synthetic biology,artificial intelligence(AI)-aided synthetic biology,as well as *** also introduce the concept of quantitative synthetic biology,which is guiding synthetic biology towards increased accuracy and predictability or the real rational *** conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.

关键词： synthetic biology quantitative synthetic biology genome synthesis and assembly DNA storage molecular evolution de novo design computer-aided design cell engineering gene circuit chassis cell artificial intelligent(AI) biofoundry

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Folding Mechanism of a de novo designed βαβ Protein

Folding Mechanism of a De Novo Designed βαβ Protein

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第一届全国生物物理化学会议暨生物物理化学发展战略研讨会

作者：祝诚 Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable SpeciesCollege of Chemistry and Molecular EngineeringPeking University

＜正＞The folding process of a de novo designed βαβ small protein DS119,which contains two parallel β strands,was studied by stopped-flow fluorescence,T-jump infrared spectroscopy （IR） and a newly developed non-... 详细信息

关键词： protein folding de novo design βαβ protein stopped-flow fluorescence

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Gene knockdown by structure defined single-stem loop small non-coding RNAs with programmable regulatory activities

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Synthetic and Systems Biotechnology 2023年第1期8卷 86-96页

作者： Yang Wang Guobin Yin Huanjiao Weng Luyao Zhang Guocheng Du Jian Chen Zhen Kang The Science Center for Future Foods Jiangnan UniversityWuxi214122China The Key Laboratory of Industrial Biotechnology Ministry of EducationSchool of BiotechnologyJiangnan UniversityWuxi214122China The Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of EducationJiangnan UniversityWuxiChina

Gene regulation by trans-acting small RNAs(sRNAs)has considerable advantages over other gene regulation ***,synthetic sRNAs mainly take natural sRNAs(MicC or SgrS)as backbones and comprise three functional elements folding into two or more stem-loop structures:an mRNA base pairing region,an Hfq-binding structure,and a rho-independent *** to limited numbers of natural sRNAs and complicated backbone structures,synthetic sRNAs suffer from low activity programmability and poor structural ***,natural sRNA backbone sequences may increase the possibility of unwanted ***,we present a bottom-up approach for creating structure defined single-stem loop small non-coding RNAs(ssl-sRNAs),which contain a standardized scaffold of a 7 bp-stem-4 nt-loop-polyU-tail and a 24 nt basing pairing region covering the first eight ***,ssl-sRNA requires no independent Hfq-binding structure,as the polyU tail fulfills the roles of binding Hfq.A thermodynamic-based scoring model and a web server sslRNAD(http://***/)were developed for automated design of ssl-sRNAs with well-defined structures and programmable ***-sRNAs displayed weak polar effects when regulating polycistronic *** ssl-sRNA designed by sslRNAD showed regulatory activities in both Escherichia coli and Bacillus subtilis.A streamlined workflow was developed for the construction of customized ssl-sRNA and ssl-sRNA *** examples,the *** cell morphology was easily modified and new target genes of ergothioneine biosynthesis were quickly identified with ***-sRNA and its designer sslRNAD enable researchers to rapidly design sRNAs for knocking down target genes.

关键词： Regulatory RNA Metabolic engineering Synthetic biology de novo design Ergothioneine

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Current advances in design and engineering strategies of industrial enzymes

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Systems Microbiology and Biomanufacturing 2021年第1期1卷 15-23页

作者： Tanatarov Dinmukhamed Ziyang Huang Yanfeng Liu Xueqin Lv Jianghua Li Guocheng Du Long Liu Science Center for Future Foods Jiangnan UniversityWuxi 214122China Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of EducationJiangnan UniversityWuxi 214122China

Enzymes are considered as functional proteins,also known as biocatalysts,which are required for normal cellular *** commercial production of enzymes with distinct features always remains the top priority of researchers for industrial ***,the insufficient yield,low stability,low activity,formation of by-products,complex purification pro-cess,and many other factors are challenging for the enzyme production *** advancements in protein engineering,especially the combination of multidisciplinary techniques including post-translational enzyme modification,structured assisted protein tailoring and computational modeling approaches,open a new horizon to more efficient production of *** this review,we focus on the development process of enzyme modification design strategies,such as rational design,semi-rational design and de novo *** examples for each strategy,which are particularly useful for novel enzyme design,are *** hope this review is helpful for the development of biocatalysts for industrial application.

关键词： Enzymes Protein engineering design strategies de novo design

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Computer-designed orthogonal RNA aptamers programmed to recognize Ebola virus glycoproteins

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Biosafety and Health 2019年第2期1卷 105-111页

作者： Teng Yue Liu Shuxia Yang Shan Guo Xiaocan Zhang Yanwen Song Yajun Cui Yujun State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and EpidemiologyBeijing 100071China department of Computational Biology Beijing Computing CenterBeijing 100094China Massachusetts Institute of Technology 77 Massachusetts AvenueCambridgeMA 02139USA

Ebola virus (EBOV), a member of the filovirus family, is an enveloped negative-sense RNA virus that causes lethal infections in humans and primates. Thousands of people have died from the Ebola virus disease (EVD) in West Africa, and no specific antiviral medication and treatment have been approved for EVD. Although the development of an EBOV vaccine is promising, immunity to any vaccine is not immediate. Here, we computationally analysed the structure of EBOV glycoprotein GP2 (GP2EBOV) and designed RNA aptamers that recognize and inhibit it. The aptamers specifically bind to conserved arginine residues (Arg587 and Arg596) located in the C-terminal coiled-coil region of GP2EBOV. Molecular docking of the synthetic RNA aptamers with the ectodomain of GP2EBOV revealed that the optimized orthogonal RNA aptamers have strong binding affinities with the coiled-coil region of GP2EBOV. The characterized RNA aptamers may facilitate strategies to block replication of EBOV and related Filoviruses, and thus may serve as important antivirals to reduce mortality associated with these infections.

关键词： Ebola virus Glycoproteins RNA aptamers Molecular dynamic de novo design

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Computational TNFαpeptide antagonist design

Computational TNFαpeptide antagonist design

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：张长胜沈琦来鲁华 College of Chemistry and Molecular engineering Peking University Center for Quantitative Biology Peking University

Background:Computational designing of novel proteins that can bind to a specific target protein to modulate its functions is a promising and challenging approach in synthetical biology and therapeutical protein *** of designing a complicated new structure, short peptides with only one single helix can be used for some systems. Methods:We have developed a general method for designing helical peptides that can bind with a target ***,appropriate helix binding sites on the target protein surface are identified based on simple geometry matching and the buried surface hydrophobicity. Second,for a binding site,initial poly-alanine helices are ***,protein sequences and binding conformations are evolved in silico by a de novo protein design strategy,for example,the protein design program,Rosetta can be *** computer-generated sequences were screened by scoring functions which include estimation of binding affinity,folding stability,and aggregation,etc. Results:This method has been applied to design antagonist for tumor necrosis factor (TNF).Several single-helix binding sites on TNF at the TNF and receptor binding interface were identified,and the best one,for which the corresponding binding helices are along with theβ-strands in the TNF receptor,was selected for the subsequent *** designed peptides were expressed as GST fusion protein or chemically synthesized and tested by surface plasmon binding assay and cell based *** peptides were identified and their binding pose was verified by mutation study. Conclusions:We have developed a computational strategy for design P-helical peptides that can specifically bind to a protein target,and successfully applied it in designing a novel peptide that can bind with TNF and inhibit its *** method could easily be used to other cases to identify helix binding sites in proteins and de novo design binding peptides for the target.

关键词： protein-protein interaction design de novo design helix binding site

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AutoT &T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization

AutoT &T v.2: An Efficient and Versatile Tool for Lead Struc...

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中国化学会-生物物理化学专业委员会第四届全国生物物理化学会议

作者：王任小中科院上海有机化学研究所

In structure-based drug design, automated de novo design methods are helpful tools for lead discovery as well as lead optimization. In a previous study(J. Chem. Inf. Model., 2011, 51, 1474–1491), we reported a new de novo design method, namely Automatic Tailoring and Transplanting(Auto T&T). It overcomes some intrinsic problems in conventional fragment-based build-up methods. In this study, we describe an upgraded version, i.e. Auto T&T2. Structural operations conducted by Auto T&T2 have been largely optimized by introducing several new algorithms. As result, its overall efficiency in multi-round optimization jobs has been speeded up by a few thousand folds. With this improvement, it is now practical to conduct structural crossover among multiple lead molecules by using Auto T&T2. Three different test cases are described in this study, which demonstrate the new features and versatile applications of Auto T&T2. The Auto T&T2 software suite is available to the public. Besides, a web portal for running Auto T&T2 on-line is provided at http://***/software/att2 for testing.

关键词： structure-based drug design de novo design

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