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Atomistic characterization of binding modes and affinity of peptide inhibitors to amyloid-

Fufeng LIU,Wenjie DU,Yan SUN,Jie ZHENG,Xiaoyan DONG

《化学科学与工程前沿（英文）》 2014年 第8卷 第4期   页码 433-444 doi: 10.1007/s11705-014-1454-6

摘要： The aggregation of amyloid -protein (A ) is tightly linked to the pathogenesis of Alzheimer’s disease. Previous studies have found that three peptide inhibitors (i.e., KLVFF, VVIA, and LPFFD) can inhibit A aggregation and alleviate A -induced neurotoxicity. However, atomic details of binding modes and binding affinities between these peptide inhibitors and A have not been revealed. Here, using molecular dynamics simulations and molecular mechanics Poisson Boltzmann surface area (MM/PBSA) analysis, we examined the effect of three peptide inhibitors (KLVFF, VVIA, and LPFFD) on their sequence-specific interactions with A and the molecular basis of their inhibition. All inhibitors exhibit varied binding affinity to A , in which KLVFF has the highest binding affinity, whereas LPFFD has the least. MM/PBSA analysis further revealed that different peptide inhibitors have different modes of interaction with A , consequently hotspot binding residues, and underlying driving forces. Specific residue-based interactions between inhibitors and A were determined and compared for illustrating different binding and inhibition mechanisms. This work provides structure-based binding information for further modification and optimization of these three peptide inhibitors to enhance their binding and inhibitory abilities against A aggregation.

关键词： Alzheimer’s disease     amyloid β-protein     peptide inhibitors     protein-protein interaction     molecular dynamics simulation    

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of a heptapeptide eliminates its cytotoxicity and significantly increases its inhibition effect on amyloid

Shuai Ma, Huan Zhang, Xiaoyan Dong, Linling Yu, Jie Zheng, Yan Sun

《化学科学与工程前沿（英文）》 2018年 第12卷 第2期   页码 283-295 doi: 10.1007/s11705-017-1687-2

摘要： Amyloid- (A ) protein aggregation is the main hallmark of Alzheimer’s disease (AD). Inhibition of A fibrillation is thus a promising therapeutic approach to the prevention and treatment of AD. Recently, we designed a heptapeptide inhibitor, LVFFARK (LK7). LK7 shows a promising inhibitory capability on A fibrillation, but is prone to self-assembling and displays high cytotoxicity, which would hinder its practical application. Herein, we modified LK7 by a head-to-tail cyclization and obtained a cyclic LK7 (cLK7). cLK7 exhibits a different self-assembly behavior from LK7, and has higher stability against proteolysis than LK7 and little cytotoxicity to SH-SY5Y cells. Thermodynamic analysis revealed that both LK7 and cLK7 could bind to A by electrostatic interactions, hydrogen bonding and hydrophobic interactions, but the binding affinity of cLK7 for A ( = 4.96 µmol/L) is six times higher than that of LK7 ( = 32.2 µmol/L). The strong binding enables cLK7 to stabilize the secondary structure of A and potently inhibit its nucleation, fibrillation and cytotoxicity at extensive concentration range, whereas LK7 could only moderately inhibit A fibrillation and cytotoxicity at low concentrations. The findings indicate that the peptide cyclization is a promising approach to enhance the performance of peptide-based amyloid inhibitors.

关键词： Alzheimer’s disease     amyloid β-protein     cyclic peptide     inhibition     protein aggregation    

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Construction of a CaHPO4-PGUS1 hybrid nanoflower through protein-inorganic self-assembly, and its application

Tian Jiang, Yuhui Hou, Tengjiang Zhang, Xudong Feng, Chun Li

《化学科学与工程前沿（英文）》 2019年 第13卷 第3期   页码 554-562 doi: 10.1007/s11705-019-1834-z

摘要： Glycyrrhetinic acid 3- -mono- -D-glucuronide (GAMG), an important pharmaceutical intermediate and functional sweetener, has broad applications in the food and medical industries. A green and cost-effective method for its preparation is highly desired. Using site-directed mutagenesis, we previously obtained a variant of -glucuronidase from Li-3 (PGUS1), which can specifically transform glycyrrhizin (GL) into GAMG. In this study, a facile method was established to prepare a CaHPO -PGUS1 hybrid nanoflower for enzyme immobilization, based on protein-inorganic hybrid self-assembly. Under optimal conditions, 1.2 mg of a CaHPO -PGUS1 hybrid nanoflower precipitate with 71.2% immobilization efficiency, 35.60 mg∙g loading capacity, and 118% relative activity was obtained. Confocal laser scanning microscope and scanning electron microscope results showed that the enzyme was encapsulated in the CaHPO -PGUS1 hybrid nanoflower. Moreover, the thermostability of the CaHPO -PGUS1 hybrid nanoflower at 55°C was improved, and its half-life increased by 1.3 folds. Additionally, the CaHPO -PGUS1 hybrid nanoflower was used for the preparation of GAMG through GL hydrolysis, with the conversion rate of 92% in 8 h, and after eight consecutive runs, it had 60% of its original activity.

关键词： β-glucuronidase     enzyme-inorganic hybrid nanoflower     biotransformation     glycyrrhizin     glycyrrtinic acid 3-O-mono-β-D-glucuronide    

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Proteomics study of Mycoplasma pneumoniae pneumonia reveals the Fc fragment of the IgG-binding protein

《医学前沿（英文）》 2022年 第16卷 第3期   页码 378-388 doi: 10.1007/s11684-021-0840-y

摘要： Macrolide and corticosteroid resistance has been reported in patients with Mycoplasma pneumoniae (MP) pneumonia (MPP). MP clearance is difficult to achieve through antibiotic treatment in sensitive patients with severe MPP (SMPP). SMPP in children might progress to airway remodeling and even bronchiolitis/bronchitis obliterans. Therefore, identifying serum biomarkers that indicate MPP progression and exploring new targeted drugs for SMPP treatment require urgency. In this study, serum samples were collected from patients with general MPP (GMPP) and SMPP to conduct proteomics profiling. The Fc fragment of the IgG-binding protein (FCGBP) was identified as the most promising indicator of SMPP. Biological enrichment analysis indicated uncontrolled inflammation in SMPP. ELISA results proved that the FCGBP level in patients with SMPP was substantially higher than that in patients with GMPP. Furthermore, the FCGBP levels showed a decreasing trend in patients with GMPP but the opposite trend in patients with SMPP during disease progression. Connectivity map analyses identified 25 possible targeted drugs for SMPP treatment. Among them, a mechanistic target of rapamycin kinase (mTOR) inhibitor, which is a macrolide compound and a cell proliferation inhibitor, was the most promising candidate for targeting SMPP. To our knowledge, this study was the first proteomics-based characterization of patients with SMPP and GMPP.

关键词： severe Mycoplasma pneumoniae pneumonia     children     proteomics     Fc fragment of the IgG-binding protein     mechanistic target of rapamycin kinase inhibitor    

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Production of rhamnolipids-producing enzymes of

Kata Kiss,Wei Ting Ng,Qingxin Li

《化学科学与工程前沿（英文）》 2017年 第11卷 第1期   页码 133-138 doi: 10.1007/s11705-017-1637-z

摘要： Rhamnolipids are a class of biosurfactants that have a great potential to be used in industries. Five proteins/enzymes, namely RhlA, RhlB, RhlC, RhlG and RhlI, are critical for the production of rhamnolipids in . Four of the 5 proteins except RhlC were successfully over-expressed in and three of them (RhlA, RhlB and RhlI) were purified and obtained in milligram quantities. The purified proteins were shown to be folded in solution. Homology models were built for RhlA, RhlB and RhlI. These results lay a basis for further structural and functional characterization of these proteins to favor the construction of super strains for rhamnolipids production.

关键词： rhamnolipids     Pseudomonas     RhlA     RhlB     RhlI     protein folding    

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Mechanisms of connective tissue formation and blocks of mitogen activated protein kinase

Irina A SHURYGINA, Michael G SHURYGIN, Nataliya I AYUSHINOVA, Galina B GRANINA, Nikolay V ZELENIN

《化学科学与工程前沿（英文）》 2012年 第6卷 第2期   页码 232-237 doi: 10.1007/s11705-012-1286-1

摘要： Ninety male Wistar rats were selected under the “Guide for the Care and Use of Laboratory Animals” for skin-muscle wound models. Three groups of animals were examined respectively for inoculation of inhibitor of p38 MAPK (mitogen activated protein kinase) SB 203580 and JNK inhibitor SP 600125, and a control. Light microscopy, immunohistochemistry, and tensometry revealed that the inhibition of p38 or JNK cascades have modified the formation of the connective tissue scar. The degree of connective tissue growth in the area of surgical wound had been significantly reduced by the end of observation (30 d) as the SB 203580 was applied (% volume of collagen 43.60 (41.05 – 60.15) 73.54 (66.87 – 78.01) in control, = 0.002). Conversely, when we have applied the JNK blocker, the density of collagen in scar tissue increased (78.14 (72.77 – 81.14), = 0.022 control). SB203580 inhibits the expression of p38, c-Jun and c-Fos. When we have used the JNK blocker, the expression of c-Fos and c-Jun decreased, but the expression of p38 increased. This determines the high functional activity of fibroblasts after using SP 600125. Obtained results show the importance of studying regulators of cell differentiation as potential drugs, which significantly affect the outcome of the pathological processes.

关键词： connective tissue     mitogen activated protein kinase (MAPK)     p38     JNK    

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immune mapped protein 1 (NcIMP1) is a novel vaccine candidate against neosporosis

Xia CUI,Daoyu YANG,Tao LEI,Hui WANG,Pan HAO,Qun LIU

《农业科学与工程前沿（英文）》 2015年 第2卷 第1期   页码 66-72 doi: 10.15302/J-FASE-2015047

摘要： The immune mapped protein 1 (NcIMP1) was identified as a membrane protein, and a previous study indicated that NcIMP1 could be a promising vaccine candidate against neosporosis. In this study, the immune response and protection efficacy of NcIMP1 were evaluated. The coding sequence of NcIMP1 was inserted into the eukaryotic expression vector pcDNA 3.1(+), resulting in the recombination plasmid pcDNA-IMP1, which was used for the intramuscular immunization of BALB/c mice. After immunization, the immune response was evaluated using a lymphoproliferative assay and cytokine and antibody measurements. Quantification of the cerebral parasite burden of mice challenged with 2 × 10 was performed 14 days after the last immunization. The results showed that the mice immunized with pcDNA-IMP1 developed a high level of specific antibody responses against recombinant NcIMP1, with a mixed IgG1/IgG2a response and a predominance of IgG2a production. The cellular immune response was associated with the production of IFN-γ, IL-2, IL-4 and IL-10 cytokines. The experiment was terminated 30 days p.i., and the cerebral parasite burden in each mouse was assessed by quantitative PCR. The parasite burden was significantly reduced in the pcDNA-IMP1-vaccinated mice. These data suggest that IMP1 is a promising vaccine candidate against neosporosis.

关键词： Neospora caninum     immune mapped protein 1 (IMP1)     vaccine candidate     BALB/c mice    

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Fabrication of high-capacity cation-exchangers for protein adsorption: Comparison of grafting-from and

Ming Zhao, Run Liu, Jian Luo, Yan Sun, Qinghong Shi

《化学科学与工程前沿（英文）》 2019年 第13卷 第1期   页码 120-132 doi: 10.1007/s11705-018-1730-y

摘要： In this work, we have synthesized two polymer-grafted cation exchangers: one via the grafting-from approach, in which sulfopropyl methacrylate (SPM) is grafted through atom transfer radical polymerization onto Sepharose FF (the thus resulting exchanger is referred as Sep- -SPM), and another via the grafting-to approach, in which the polymer of SPM is directly coupled onto Sepharose FF (the thus resulting exchanger is called as Sep- SPM). Protein adsorption on these two cation exchangers have been also investigated. At the same ligand density, Sep- -SPM has a larger accessible pore radius and a smaller depth of polymer layer than Sep- SPM, due to the controllable introduction of polymer chains with the regular distribution of the ligand. Therefore, high-capacity adsorption of lysozyme and -globulin could be achieved simultaneously in Sep- -SPM with an ionic capacity (IC) of 308 mmol·L . However, Sep- SPM has an irregular chain distribution and different architecture of polymer layer, which lead to more serious repulsive interaction to proteins, and thus Sep- SPM has a lower adsorption capacity for -globulin than Sep- -SPM with the similar IC. Moreover, the results from protein uptake experiments indicate that the facilitated transport of adsorbed -globulin occurs only in Sep- SPM and depends on the architecture of polymer layers. Our research provides a clear clue for the development of high-performance protein chromatography.

关键词： polymer-grafted ionic exchanger     grafting technique     protein adsorption     atom transfer radical polymerization     γ-globulin    

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Characterization of polyclonal antibodies against nonstructural protein 9 from the porcine reproductive

Mengmeng ZHAO,Juanjuan QIAN,Jiexiong XIE,Tiantian CUI,Songling FENG,Guoqiang WANG,Ruining WANG,Guihong ZHANG

《农业科学与工程前沿（英文）》 2016年 第3卷 第2期   页码 153-160 doi: 10.15302/J-FASE-2016097

摘要： Porcine reproductive and respiratory syndrome (PRRS) is considered to be one of the most important infectious diseases impacting the swine industry and is characterized by reproductive failure in late term gestation in sows and respiratory disease in pigs of all ages. The nonstructural protein 9 gene, , encoding the RNA-dependent RNA polymerase, is generally regarded as fairly conserved when compared to other viral proteins. Antibodies against 9 will be of great importance for the diagnosis and treatment of the causal agent, PRRS virus. A study was undertaken to generate polyclonal antibodies against the immunodominant 9. For this purpose, the 9 was expressed in and subsequently used as an antigen to immunize New Zealand rabbits. Antiserum was identified via an indirect ELISA, and then verified based on the ability to react with both naturally and artificially expressed 9. Results of virus neutralization test showed that this antiserum could not neutralize the PRRSV. Nevertheless, this antiserum as a diagnostic core reagent should prove invaluable for further investigations into the mechanism of PRRS pathogenesis.

关键词： PRRSV     Nsp9     expression     antibody     neutralize    

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Transgenic technologies in cassava for nutritional improvement and viral disease resistance: a key strategy for food security in Africa

Maliwan NACONSIE,Peng ZHANG

《农业科学与工程前沿（英文）》 2016年 第3卷 第4期   页码 285-294 doi: 10.15302/J-FASE-2016119

摘要： As a major staple food source in Africa and other tropical developing countries, cassava ( ) provides basic sustenance for many subsistence farmers. However, cassava roots mainly accumulate starch with limited contribution of other nutrients such as proteins and vitamins. Also, two viral diseases, cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), cause great losses in cassava production in sub-Saharan Africa and the Indian sub-continent. Genetic engineering provides promising approaches to improve nutritional value and increase resistance to viral diseases in cassava. This report presents several successful case studies on engineering protein content by overexpression of nutritious storage proteins and improving cassava resistance to viral diseases by RNA interference. Perspectives on the sustainable acquisition of new knowledge and development of biotechnology to solve these bottlenecks are discussed.

关键词： Manihot esculenta     protein enhancement     RNA interference     transgenesis     virus resistance    

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新型冠状病毒HCoV-19 S蛋白与人ACE2蛋白表面糖链和独特翻译后修饰的质谱分析 Article

孙泽宇, 任科燚, 张兴, 陈景华, 姜正一, 江静, 季飞洋, 欧阳晓希, 李兰娟

《工程（英文）》 2021年 第7卷 第10期   页码 1441-1451 doi: 10.1016/j.eng.2020.07.014

摘要： 质谱分析（MS）发现，在HCoV-19 S蛋白的21个潜在糖基化修饰位点中，有20个位点完全被<i>Ni>-糖链占据，其糖型以低聚甘露糖为主。人血管紧张素转换酶2（hACE2）的7个糖基化位点完全被复合型<i>Ni>-糖链占据。然而，糖基化修饰并不能直接影响HCoV-19 S蛋白与hACE2之间的结合亲和力。通过在最近发表的冷冻电镜（cryo-EM）结构的基础上加入<i>Ni>-糖链和蛋白质翻译后修饰（PTM），我们构建了HCoV-19 S蛋白和hACE2的精细结构模型。

关键词： <i>Ni>-糖基化     COVID-19     棘突蛋白     hACE2     蛋白结构    

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Development of a new method for RMR and Q classification method to optimize support system in tunneling

Asghar RAHMATI,Lohrasb FARAMARZI,Manouchehr SANEI

《结构与土木工程前沿（英文）》 2014年 第8卷 第4期   页码 448-455 doi: 10.1007/s11709-014-0262-x

摘要： Rock mass classification system is very suitable for various engineering design and stability analysis. classification method is confirmed by Japan Highway Public Corporation that this method can figure out either strength or deformability of rock mass, further appropriating the amount of rock bolts, thickness of shotcrete, and size of pitch of steel ribs just after the blasting procedure. Based on these advantages of method, in this study, according to data of five deep and long tunnels in Iran, two equations for estimating the value of method from and classification systems were developed. These equations as a new method were able to optimize the support system for and classification systems. From classification and its application in these case studies, it is pointed out that the method for the design of support systems in underground working is more reliable than the and classification systems.

关键词： JH classification     Q and RMR classification     new method    

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抗白粉病基因 <i>Pm40i> 在我国“后 <i>Pm21i> 时代”小麦育种中的重要作用 Perspective

唐圣雯,胡玉亭,钟胜福,罗培高

《工程（英文）》 2018年 第4卷 第4期   页码 500-506 doi: 10.1016/j.eng.2018.06.004

摘要：

由小麦白粉菌[Blumeria graminis f. sp. tritici（Bgt）] 引起的小麦白粉病是一种重要的小麦叶部病害，对小麦的产量产生很大的影响。20 世纪80 年代，通过簇毛麦（Heuchera villosa）的6VS 染色体与小麦6AL 染色体易位将抗白粉病基因Pm21 转移到普通小麦中。最近，在一些地方发现了对Pm21 有毒的Bgt，虽然这些菌株的病理学特性还有待研究，但这一现象提醒小麦育种者应注意应用Pm21 的风险。来源于普通小麦与中间偃麦草（Thinopyrum intermedium）杂种后代的抗白粉病基因Pm40，被定位在小麦7BS 染色体上，对Bgt 具有广谱和持久的抗性。通过细胞学研究，并未在Pm40 的载体品种中发现大片段外缘染色体。过去几年的研究发现，Pm40 的载体品种具有优良的农艺性状。因此，我们相信在未来的育种工程中，Pm40 将会在Pm21 的抗性被克服之后起巨大的作用。另外，Pm21 和Pm40 都来源于外缘物种，这暗示着外源基因的抗性可能比小麦本身的基因更为持久和有效。

关键词： 小麦     白粉病     <i>Pm21i>     <i>Pm40i>     外源基因     内源抗性    

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NiFeRuO<i>xi> nanosheets on Ni foam as an electrocatalyst for efficient

《化学科学与工程前沿（英文）》 2023年 第17卷 第11期   页码 1698-1706 doi: 10.1007/s11705-023-2334-8

摘要： The electrocatalyst NiFeRuOx/NF, comprised of NiFeRuOx nanosheets grown on Ni foam, was synthesized using a hydrothermal process followed by thermal annealing. NiFeRuOx/NF displays high electrocatalytic activity and stability for overall alkaline seawater splitting: 98 mV@ 10 mA∙cm−2 in hydrogen evolution reaction, 318 mV@ 50 mA∙cm−2 in oxygen evolution reaction, and a cell voltage of 1.53 V@ 10 mA∙cm−2, as well as 20 h of durability. A solar-driven system containing such a bifunctional NiFeRuOx/NF has an almost 100% Faradaic efficiency. The NiFeRuOx coating around Ni foam is an anti-corrosion layer and also a critical factor for enhancement of bifunctional performances.

关键词： NiFeRuOx nanosheets     Ni foam     electrocatalysis     overall seawater splitting     solar-driven system    

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羊种布鲁氏菌双抗原纳米结合疫苗的生物合成与免疫效果评估 Article

黄竞, 王玉飞, 王康丰, 李淑磊, 孙鹏, 郭艳, 刘建凯, 杨瑞馥, 曾明, 潘超, 王恒樑, 朱力

《工程（英文）》 2023年 第29卷 第10期   页码 95-109 doi: 10.1016/j.eng.2023.04.007

摘要：

布鲁氏菌病是由布鲁氏菌引起的最常见的人畜共患疾病之一。然而，目前还没有供人类使用的疫苗上市。尽管一些减毒活疫苗已被批准用于动物，但保护效果并不理想。在本研究中，我们开发了一种含有多糖和蛋白质两种抗原的双抗原纳米结合疫苗来对抗布鲁氏菌感染。首先，我们使用蛋白-聚糖生物偶联技术将抗原多糖与外膜蛋白Omp19共价偶联，然后通过SpyTag/SpyCatcher系统将其装载到纳米载体上。在证实双抗原纳米结合疫苗的免疫激活能力和安全性后，我们在小鼠中通过不同的给药途径，进一步证明了疫苗免疫能够对两种抗原产生特异性血清抗体应答以及在非致死性和致死性布鲁氏菌感染模型中具有显著的保护作用。这些结果表明，双抗原纳米结合疫苗增强了辅助T细胞（Th）1和Th2免疫应答，并保护小鼠免受布鲁氏菌感染。此外，我们发现这种保护作用至少维持了18周。据我们所知，这是第一种在单个纳米颗粒上携带多种布鲁氏菌抗原（包括蛋白质和多糖）的布鲁氏菌病疫苗。因此，我们还提出了一种有吸引力的技术以共同递送不同类型的抗原，这也适用于其他传染病疫苗的制备策略。

关键词： 蛋白-聚糖偶联技术（PGCT）     双抗原     纳米结合疫苗     羊种布鲁氏菌    

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标题 作者 时间 类型 操作

Atomistic characterization of binding modes and affinity of peptide inhibitors to amyloid-

Fufeng LIU,Wenjie DU,Yan SUN,Jie ZHENG,Xiaoyan DONG

期刊论文

of a heptapeptide eliminates its cytotoxicity and significantly increases its inhibition effect on amyloid

Shuai Ma, Huan Zhang, Xiaoyan Dong, Linling Yu, Jie Zheng, Yan Sun

期刊论文

Construction of a CaHPO4-PGUS1 hybrid nanoflower through protein-inorganic self-assembly, and its application

Tian Jiang, Yuhui Hou, Tengjiang Zhang, Xudong Feng, Chun Li

期刊论文

Proteomics study of Mycoplasma pneumoniae pneumonia reveals the Fc fragment of the IgG-binding protein

期刊论文

Production of rhamnolipids-producing enzymes of

Kata Kiss,Wei Ting Ng,Qingxin Li

期刊论文

Mechanisms of connective tissue formation and blocks of mitogen activated protein kinase

Irina A SHURYGINA, Michael G SHURYGIN, Nataliya I AYUSHINOVA, Galina B GRANINA, Nikolay V ZELENIN

期刊论文

immune mapped protein 1 (NcIMP1) is a novel vaccine candidate against neosporosis

Xia CUI,Daoyu YANG,Tao LEI,Hui WANG,Pan HAO,Qun LIU

期刊论文

Fabrication of high-capacity cation-exchangers for protein adsorption: Comparison of grafting-from and

Ming Zhao, Run Liu, Jian Luo, Yan Sun, Qinghong Shi

期刊论文

Characterization of polyclonal antibodies against nonstructural protein 9 from the porcine reproductive

Mengmeng ZHAO,Juanjuan QIAN,Jiexiong XIE,Tiantian CUI,Songling FENG,Guoqiang WANG,Ruining WANG,Guihong ZHANG

期刊论文

Transgenic technologies in cassava for nutritional improvement and viral disease resistance: a key strategy for food security in Africa

Maliwan NACONSIE,Peng ZHANG

期刊论文

新型冠状病毒HCoV-19 S蛋白与人ACE2蛋白表面糖链和独特翻译后修饰的质谱分析

孙泽宇, 任科燚, 张兴, 陈景华, 姜正一, 江静, 季飞洋, 欧阳晓希, 李兰娟

期刊论文

Development of a new method for RMR and Q classification method to optimize support system in tunneling

Asghar RAHMATI,Lohrasb FARAMARZI,Manouchehr SANEI

期刊论文

抗白粉病基因 <i>Pm40i> 在我国“后 <i>Pm21i> 时代”小麦育种中的重要作用

唐圣雯,胡玉亭,钟胜福,罗培高

期刊论文

NiFeRuO<i>xi> nanosheets on Ni foam as an electrocatalyst for efficient

期刊论文

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