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吸附 1

基于质谱的免疫肽组学 1

患者来源肝胆肿瘤类器官 1

环状RNA 1

粗粒化计算 1

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Cystine oligomers successfully attached to peptide cysteine-rich fibrils

Christian Bortolini,Mingdong Dong

《化学科学与工程前沿（英文）》 2016年 第10卷 第1期   页码 99-102 doi: 10.1007/s11705-016-1554-6

摘要： Amyloid peptides are renowned to be related to neurodegenerative diseases, however, a fruitful avenue is to employ them as high-performance nanomaterials. These materials benefit from the intrinsic outstanding mechanical robustness of the amyloid backbone made of -strands. In this work, we exploited amyloid-like fibrils as functional material to attach pristine L-cysteine aggregates (cystine oligomers) and gold nanoparticles, without the need of templating compounds. This work will open new avenues on functional materials design and their realisation.

关键词： cysteine     peptide fibrils     gold nanoparticles     amyloids     oligomers     nanomaterials    

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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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Glucagon-like peptide-2 exhibits protective effect on hepatic ischemia-reperfusion injury in rats

null

《医学前沿（英文）》 2015年 第9卷 第3期   页码 368-373 doi: 10.1007/s11684-015-0403-1

摘要：

Glucagon-like peptide-2 (GLP-2) has potent anti-inflammatory effects and protects against experimental ischemia/reperfusion (I/R) injury in pulmonary, intestinal, and myocardial tissue. However, its protective abilities against I/R injury in the liver are unknown. We investigated the potential role of GLP-2 pretreatment on hepatic I/R injury in rats. A total of 24 rats were randomly divided into three groups (n = 8). The first group was the control group; the second group was the vehicle-treated hepatic ischemia/reperfusion (HIR, vehicle saline-treated) group; and the third group was the GLP-2 pretreated I/R (GLP2-IR) group. Each rat in the third group was intraperitoneally administered 5 μg GLP-2 for 5 d before the procedure. A portal triad was created to induce ischemia with a vascular atraumatic clamp. After 40 min, the clamp was released to initiate hepatic reperfusion for 6 h. Blood samples and tissue specimens from the liver were obtained. Alanine aminotransferase, aspartate aminotransferase, and total bilirubin levels significantly increased in the saline-treated HIR group (P<0.001), whereas GLP-2 pretreatment significantly decreased their levels (P<0.01). Our data suggested that GLP-2 pretreatment may have a protective effect on liver I/R injury. However, dose-response studies are necessary to determine the most effective dose.

关键词： ischemia/reperfusion     liver     glucagon-like peptide-2     alanine aminotransferase    

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The role of natriuretic peptide precursor A gene polymorphism in the development of coronary heart disease

Ripen NSENGA MD, Longxian CHENG PhD, Mei’an HE PhD, Tangchun WU PhD,

《医学前沿（英文）》 2009年 第3卷 第4期   页码 437-442 doi: 10.1007/s11684-009-0074-x

摘要： Natriuretic peptide precursor A (NPPA) is synthesized, stored, and released by atrial myocytes. Previous studies have shown that NPPA plays a significant role in the regulation of coronary circulation and in atherosclerosis. Rs5065 NPPA gene polymorphism leads to the translation of NPPA with two additional arginines and has been suggested to be associated with salt-sensitive hypertension. The purpose of the present study was to investigate the relationship between the rs5065 NPPA gene polymorphism and the risk of coronary heart disease (CHD) in Chinese Han population. We genotyped the single nucleotide polymorphism (SNP) rs5065 NPPA in the human NPPA gene in 1861 sex- and age-matched subjects, comprising of 904 CHD cases and 957 controls of Chinese Han population. Genotyping of SNP was performed with Taqman SNP allelic discrimination assays by means of an ABI 7900HT. Our study showed that the frequencies of rs5065 NPPA C allele in the case and the control groups were 0.012 and 0.005, respectively. There was significant difference in C allele frequency distribution between the two groups (OR=2.607, 95% CI: 1.197−5.678, =0.012). In the case group, there was significant difference between smokers and nonsmokers with subjects carrying C allele (=0.037), and no significant difference in gender, age, fasting total cholesterol (TC), triglycerides (TG), fasting plasma glucose (FPG), body mass index (BMI), and blood pressure (BP) between the cases and the controls (>0.05). Our results suggest that the C allele of rs5065 NPPA gene polymorphism may be associated with the risk of CHD.

关键词： natriuretic peptide precursor A     coronary heart disease     gene polymorphism     allelic discrimination     polymorphism     single nucleotide    

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Overcoming oral insulin delivery barriers: application of cell penetrating peptide and silica-based nanoporous

Huining HE, Junxiao YE, Jianyong SHENG, Jianxin WANG, Yongzhuo HUANG, Guanyi CHEN, Jingkang WANG, Victor C YANG

《化学科学与工程前沿（英文）》 2013年 第7卷 第1期   页码 9-19 doi: 10.1007/s11705-013-1306-9

摘要： Oral insulin delivery has received the most attention in insulin formulations due to its high patient compliance and, more importantly, to its potential to mimic the physiologic insulin secretion seen in non-diabetic individuals. However, oral insulin delivery has two major limitations: the enzymatic barrier that leads to rapid insulin degradation, and the mucosal barrier that limits insulin’s bioavailability. Several approaches have been actively pursued to circumvent the enzyme barrier, with some of them receiving promising results. Yet, thus far there has been no major success in overcoming the mucosal barrier, which is the main cause in undercutting insulin’s oral bioavailability. In this review of our group’s research, an innovative silica-based, mucoadhesive oral insulin formulation with encapsulated-insulin/cell penetrating peptide (CPP) to overcome both enzyme and mucosal barriers is discussed, and the preliminary and convincing results to confirm the plausibility of this oral insulin delivery system are reviewed. In vitro studies demonstrated that the CPP-insulin conjugates could facilitate cellular uptake of insulin while keeping insulin’s biologic functions intact. It was also confirmed that low molecular weight protamine (LMWP) behaves like a CPP peptide, with a cell translocation potency equivalent to that of the widely studied TAT. The mucoadhesive properties of the produced silica-chitosan composites could be controlled by varying both the pH and composition; the composite consisting of chitosan (25 wt-%) and silica (75 wt-%) exhibited the greatest mucoadhesion at gastric pH. Furthermore, drug release from the composite network could also be regulated by altering the chitosan content. Overall, the universal applicability of those technologies could lead to development of a generic platform for oral delivery of many other bioactive compounds, especially for peptide or protein drugs which inevitably encounter the poor bioavailability issues.

关键词： insulin     cell penetrating peptide     mucoadhesive composites     oral delivery    

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Rational Design of and Mechanism Insight into an Efficient Antifreeze Peptide for Cryopreservation

Haishan Qi,Yihang Gao,Lin Zhang,Zhongxin Cui,Xiaojie Sui,Jianfan Ma,Jing Yang,Zhiquan Shu,Lei Zhang,

《工程（英文）》 doi: 10.1016/j.eng.2023.01.015

摘要： The development of effective antifreeze peptides to control ice growth has attracted a significant amount of attention yet still remains a great challenge. Here, we propose a novel design method based on an in-depth investigation of repetitive motifs in various ice-binding proteins (IBPs) with an evolution analysis. In this way, several peptides with notable antifreeze activity were developed. In particular, a designed antifreeze peptide named AVD exhibits ideal ice recrystallization inhibition (IRI), solubility, and biocompatibility, making it suitable for use as a cryoprotective agent (CPA). A mutation analysis and molecular dynamics (MD) simulations indicated that the Thr6 and Asn8 residues of the AVD peptide are fundamental to its ice-binding capacity, while the Ser18 residue can synergistically enhance their interaction with ice, revealing the antifreeze mechanism of AVD. Furthermore, to demonstrate the cryoprotection potential of AVD, the peptide was successfully employed for the cryopreservation of various cells, which demonstrated significant post-freezing cell recovery. This work opens up a new avenue for designing antifreeze materials and provides peptide-based functional modules for synthetic biology.

关键词： Antifreeze peptides     Evolution analysis     Ice recrystallization inhibition     Molecular dynamics simulation     Cryopreservation     Synthetic biology    

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电中性固体表面上多条肽链的吸附过程——粗粒化模拟研究 Research

裘若桑, 肖杰, 陈晓东

《工程（英文）》 2020年 第6卷 第2期   页码 185-194 doi: 10.1016/j.eng.2018.12.012

摘要：

蛋白质在固体表面的吸附过程涉及诸多复杂的分子间相互作用，因此到目前为止仍然无法做到精准调控。通过模拟计算，可以获取固-液界面分子尺度的蛋白质移动机理，从而为预测蛋白质吸附和结垢现象提供可靠的理论依据。本研究通过多尺度粗粒化模型对多条疏水的丙氨酸十二肽在金表面的聚集和吸附过程进行了分析。大约有一半（46.6%）的丙氨酸十二肽可以组成聚集体。30.0%的独立肽链会被快速地吸附到固体表面。这些在表面吸附的肽链经过一段时间的爬行，其中的一些（51.0%）能与吸附在表面的或是游离在溶液中的肽链融合，从而形成吸附在表面的聚集体。这些在固-液界面吸附的肽链使得固体表面性质发生变化。这一变化可能会进一步影响之后溶液中肽链和聚集体在金表面的吸附。本研究揭示的多条肽链吸附机理有希望为进一步研究多个蛋白质分子在固体表面的吸附机理提供理论基础。

关键词： 肽链     聚集体     吸附     粗粒化计算    

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Multifunctional peptide conjugated amphiphilic cationic copolymer for enhancing ECs targeting, penetrating

Xinghong Duo, Lingchuang Bai, Jun Wang, Jintang Guo, Xiangkui Ren, Shihai Xia, Wencheng Zhang, Abraham Domb, Yakai Feng

《化学科学与工程前沿（英文）》 2020年 第14卷 第5期   页码 889-901 doi: 10.1007/s11705-020-1919-8

摘要： Gene therapy has drawn great attention in the treatments of many diseases, especially for cardiovascular diseases. However, the development of gene carriers with low cytotoxicity and multitargeting function is still a challenge. Herein, the multitargeting REDV-G-TAT-G-NLS peptide was conjugated to amphiphilic cationic copolymer poly( -caprolactone-co-3(S)-methyl-morpholine-2,5-dione)- -polyethyleneimine (PCLMD- -PEI) via a heterobifunctional orthopyridyl disulfide-poly(ethylene glycol)- -hydroxysuccinimide (OPSS-PEG-NHS) linker to prepare PCLMD- -PEI-PEG-REDV-G-TAT-G-NLS copolymers with the aim to develop the gene carriers with low cytotoxicity and high transfection efficiency. The multitargeting micelles were prepared from PCLMD- -PEI-PEG-REDV-G-TAT-G-NLS copolymers by self-assembly method and used to load pEGFP-ZNF580 plasmids (pDNA) to form gene complexes for enhancing the proliferation and migration of endothelial cells (ECs). The loading pDNA capacity was proved by agarose gel electrophoresis assay. These multitargeting gene complexes exhibited low cytotoxicity by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. The high internalization efficiency of these gene complexes was confirmed by flow cytometry. The results of transfection demonstrated that these multitargeting gene complexes possessed relatively high transfection efficiency. The rapid migration of ECs transfected by these gene complexes was verified by wound healing assay. Owing to ECs-targeting ability, cell-penetrating ability and nuclear targeting capacity of REDV-G-TAT-G-NLS peptide, the multitargeting polycationic gene carrier with low cytotoxicity and high transfection efficiency has great potential in gene therapy.

关键词： gene carriers     multitargeting function     ECs     transfection efficiency    

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Erratum to: Multifunctional peptide conjugated amphiphilic cationic copolymer for enhancing ECs targeting

Xinghong Duo, Lingchuang Bai, Jun Wang, Jintang Guo, Xiangkui Ren, Shihai Xia, Wencheng Zhang, Abraham Domb, Yakai Feng

《化学科学与工程前沿（英文）》 2021年 第15卷 第1期   页码 220-220 doi: 10.1007/s11705-020-1995-9

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Effect of ambient polycyclic aromatic hydrocarbons and nicotine on the structure of Aβ protein

《环境科学与工程前沿（英文）》 2023年 第17卷 第2期 doi: 10.1007/s11783-023-1615-2

摘要：

● B[a]P, nicotine and phenanthrene molecules altered the secondary structure of Aβ42.

关键词： Polycyclic aromatic hydrocarbons     Nicotine     toxicology     Aβ42 peptide     Alzheimer’s disease     Molecular dynamics simulations     Environmental pollution    

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Effect of salvia miltiorrhiza pretreatment on the CCK and VIP expression in hepatic ischemia-reperfusion-induced digestive tract congestion

Zhi-Yong ZHANG, Xiao-Ping CHEN, Qi-Ping LU

《医学前沿（英文）》 2010年 第4卷 第3期   页码 317-322 doi: 10.1007/s11684-010-0035-4

摘要： The inhibitory effect of different reperfusion periods 45 min following hepatic ischemia on the expression of cholecystokinin (CCK) and vasoactive intestinal peptide (VIP) in the jejunum and the effect of salvia miltiorrhiza pretreatment were investigated, and the possible mechanism and implications were explored. Eighty rats were randomly divided into four groups: normal control group (CO group), sham-operated group (SO group), ischemia/reperfusion (I/R) injury group (IR group) and salvia miltiorrhiza pretreatment group (SM group). The rat model of I/R was established by using a non-invasive artery clamp to clip (45 min) or relax the hepatic pedicle. In the SM group, saline (40 mL/kg) and salvia miltiorrhiza injection (6 g/kg) were injected via the tail vein 30 min before clipping the hepatic pedicle. In the SO group only the porta hepatis was dissected after laparotomy without clamping the hepatic pedicle. At 0, 3, 12, 24 and 72 h post-reperfusion, respectively, upper jejunum samples were taken for immunohistochemistry of CCK and VIP. It was found that 0 h after I/R, the expression of CCK and VIP in the upper jejunum was upregulated. With prolongation of the reperfusion period, the expression of CCK and VIP was also increased, reached the peak at the 24th h, and gradually returned to the normal level at the 72nd h after reperfusion. The levels of both CCK and VIP in the SM group were lower than those in the IR group. It is suggested that the digestive tract congestion injury caused by liver ischemia can upregulate the expression of CCK and VIP in the jejunum following reperfusion. Salviae pretreatment can partly reduce the increased expression of CCK and VIP in the jejunum in the same period, which might contribute to the early recovery of gastrointestinal motility.

关键词： hepatic ischemia-reperfusion     digestive tract congestion     cholecystokinin     vasoactive intestinal peptide     salvia miltiorrhiza    

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Head-to-tail cyclization 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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肿瘤特异性环状RNA来源抗原肽被证实存在于肝胆肿瘤中 Article

王文闻, 马莉丽 , 邢政, 苑廷淦, 包金霞, 朱妍静, 赵晓芳, 赵燕, 宗雅丽, 张雅妮, 莘似韵, 邱辛瑶, 杨帅, 王红阳, 高栋, 王鹏, 陈磊

《工程（英文）》 2023年 第22卷 第3期   页码 159-170 doi: 10.1016/j.eng.2022.06.008

摘要：

由于缺乏经证实具备免疫原性的多肽，基于肿瘤抗原的免疫治疗应用受到限制。在本研究中，利用肝胆肿瘤类器官分析了环状RNA（circRNA）作为肿瘤抗原肽新来源的潜力。使用RNA测序（RNA-seq）和基于算法的评分工具，预测出27 个类器官中3950 个肿瘤特异性circRNA 可翻译18 971 条抗原肽。抗原图谱显示，11 个氨基酸长度（mer）的肽和人类白细胞抗原（HLA）-A结合肽的免疫原性相关评分最高。通过对5 个类器官进行基于质谱的免疫肽组学分析，直接证实其中三个类器官的13 条抗原肽为HLA-A、HLA-B 和HLA-C（HLA-ABC）结合肽。通过流式细胞仪和酶联免疫分析发现，HLA-ABC 呈递的cricRNA来源肿瘤特异性肽可以刺激CD8 T细胞，使其CD107a 和干扰素γ（IFNγ）共表达提高、IFNγ分泌增加。细胞杀伤实验证实，经circRNA 来源免疫原性肽活化的T 细胞可杀伤类器官细胞。值得注意的是，来自circTBC1D15 的抗原肽YGFNEILKK不仅可以被HLA-ABC呈递，还能活化T细胞，显著降低肿瘤类器官活率。本研究的发现提供了一种产生肿瘤抗原的重要来源，提示肿瘤特异性circRNA 可作为抗肿瘤靶点。

关键词： 肿瘤抗原     患者来源肝胆肿瘤类器官     环状RNA     基于质谱的免疫肽组学    

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标题 作者 时间 类型 操作

Cystine oligomers successfully attached to peptide cysteine-rich fibrils

Christian Bortolini,Mingdong Dong

期刊论文

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

Glucagon-like peptide-2 exhibits protective effect on hepatic ischemia-reperfusion injury in rats

null

期刊论文

The role of natriuretic peptide precursor A gene polymorphism in the development of coronary heart disease

Ripen NSENGA MD, Longxian CHENG PhD, Mei’an HE PhD, Tangchun WU PhD,

期刊论文

Overcoming oral insulin delivery barriers: application of cell penetrating peptide and silica-based nanoporous

Huining HE, Junxiao YE, Jianyong SHENG, Jianxin WANG, Yongzhuo HUANG, Guanyi CHEN, Jingkang WANG, Victor C YANG

期刊论文

Rational Design of and Mechanism Insight into an Efficient Antifreeze Peptide for Cryopreservation

Haishan Qi,Yihang Gao,Lin Zhang,Zhongxin Cui,Xiaojie Sui,Jianfan Ma,Jing Yang,Zhiquan Shu,Lei Zhang,

期刊论文

电中性固体表面上多条肽链的吸附过程——粗粒化模拟研究

裘若桑, 肖杰, 陈晓东

期刊论文

Multifunctional peptide conjugated amphiphilic cationic copolymer for enhancing ECs targeting, penetrating

Xinghong Duo, Lingchuang Bai, Jun Wang, Jintang Guo, Xiangkui Ren, Shihai Xia, Wencheng Zhang, Abraham Domb, Yakai Feng

期刊论文

Erratum to: Multifunctional peptide conjugated amphiphilic cationic copolymer for enhancing ECs targeting

Xinghong Duo, Lingchuang Bai, Jun Wang, Jintang Guo, Xiangkui Ren, Shihai Xia, Wencheng Zhang, Abraham Domb, Yakai Feng

期刊论文

Effect of ambient polycyclic aromatic hydrocarbons and nicotine on the structure of Aβ protein

期刊论文

Effect of salvia miltiorrhiza pretreatment on the CCK and VIP expression in hepatic ischemia-reperfusion-induced digestive tract congestion

Zhi-Yong ZHANG, Xiao-Ping CHEN, Qi-Ping LU

期刊论文

Head-to-tail cyclization 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

肿瘤特异性环状RNA来源抗原肽被证实存在于肝胆肿瘤中

王文闻, 马莉丽 , 邢政, 苑廷淦, 包金霞, 朱妍静, 赵晓芳, 赵燕, 宗雅丽, 张雅妮, 莘似韵, 邱辛瑶, 杨帅, 王红阳, 高栋, 王鹏, 陈磊

期刊论文