Elucidation of the effect of aptamer immobilization strategies on the interaction between cell and its aptamer using atomic force spectroscopy

The immobilization strategy of cell‐specific aptamers is of great importance for studying the interaction between a cell and its aptamer. However, because of the difficulty of studying living cell, there have not been any systematic reports about the effect of immobilization strategies on the binding ability of an immobilized aptamer to its target cell. Because atomic force spectroscopy (AFM) could not only be suitable for the investigation of living cell under physiological conditions but also obtains information reflecting the intrinsic properties of individuals, the effect of immobilization strategies on the interaction of aptamer/human hepatocarcinoma cell Bel‐7404 was successively evaluated using AFM here. Two different immobilization methods, including polyethylene glycol immobilization method and glutaraldehyde immobilization method were used, and the factors, such as aptamer orientation, oligodeoxythymidine spacers and dodecyl spacers, were investigated. Binding events measured by AFM showed that a similar unbinding force was obtained regardless of the change of the aptamer orientation, the immobilization method, and spacers, implying that the biophysical characteristics of the aptamer at the molecular level remain undisturbed. However, it showed that the immobilization orientation, immobilization method, and spacers could alter the binding probability of aptamer/Bel‐7404 cell. Presumably, these factors may affect the accessibility of the aptamer toward its target cell. These results may provide valuable information for aptamer sensor platforms including ultrasensitive biosensor design. Copyright © 2015 John Wiley & Sons, Ltd.     

Investigation of the interactions between aptamer and misfolded proteins: From monomer and oligomer to fibril by single‐molecule force spectroscopy

Increasing knowledge on the understanding interactions of aptamer with misfolded proteins (including monomer, oligomer, and amyloid fibril) is crucial for development of aggregation inhibitors and diagnosis of amyloid diseases. Herein, the interactions of lysozyme monomer–, oligomer‐, and amyloid fibril–aptamer were investigated using single‐molecule force spectroscopy. The results revealed that the aptamer screened against lysozyme monomer could also bind to oligomer and amyloid fibril, in spite of the recognition at a lower binding probability. It may be attributed to the inherent structural differences of misfolded proteins and the flexible conformation of aptamer. In addition, dynamic force spectra showed that there were similar dissociation paths in the dissociation process of lysozyme monomer–, oligomer‐, and amyloid fibril–aptamer complexes. It showed that the dissociation only passed 1 energy barrier from the binding state to the detachment. However, the dynamic parameters suggested that the oligomer‐ and amyloid fibril–aptamer were more stable than lysozyme monomer–aptamer. The phenomena may result from the exposure of aptamer‐recognized sequences on the surface and the electrostatic interactions. This work demonstrated that single‐molecule force spectroscopy could be a powerful tool to study the binding behavior of the aptamer with misfolded proteins at single‐molecule level, providing abundant information for researches and comprehensive applications of aptamer probes in diagnosis of amyloid diseases.     

通过毕赤酵母表达系统获得高纯度的重组人血管内皮生长因子 (rhVEGF165)

血管内皮生长因子 (Vascular endothelial growth factor,VEGF165) 是一种高度特异性的促血管内皮细胞生长因子,高纯度的VEGF165对于抗肿瘤药物和生物标志物研发检测试剂必不可少。目前关于VEGF165的异源表达方法,纯化步骤多且产物纯度不高。以毕赤酵母表达系统为基础,构建人血管内皮生长因子 (VEGF165) 多拷贝的表达载体。按照酵母密码子偏好性优化人血管内皮生长因子基因 (vegf165) 的密码子,在毕赤酵母BBPB表达载体基础上,用Biobrick生物积块的方法,构建以Pgap为启动子的五拷贝rhVEGF165表达载体,同时添加组氨酸标签。利用His标签和VEGF165自身的肝素结合结构域,仅用两步亲和层析纯化得到纯度高于98%的rhVEGF165蛋白。rhVEGF165纯化后浓度为0.45 mg/mL,且具有生物学活性。该异源表达策略简化了rhVEGF165的纯化步骤,rhVEGF165具有天然VEGF165的生物学活性,且纯度达到目前文献报道的最高水平。     

原子力显微镜单分子力谱研究生物分子间相互作用

原子力显微镜单分子力谱是近年来发展起来的能在单分子水平研究生物分子相互作用的新工具。本文综述了单分子力谱的测定原理、方法及其在研究蛋白．蛋白、蛋白-DNA相互作用,蛋白质去折叠和活细胞上配体／受体结合中的应用进展。     

Probing the interaction between p53 and the bacterial protein azurin by single molecule force spectroscopy

p53 is a human tumour suppressor which regulates multiple cellular processes, including cell growth, genomic stability and cell death. Recent works have demonstrated the bacterial redox protein azurin to enter cancer cells and induce apoptosis through p53 stabilization, resulting in a tumour growth regression. Azurin has been shown to bind p53 although many details of the complex formed by these two proteins are still poorly characterized. Here, we get insight into the kinetics of this complex formation, by exploring the interaction between p53 and azurin in their environment by single molecule force spectroscopy. To this aim, azurin has been linked to the atomic force microscope tip, whereas p53 has been immobilized onto a gold substrate. Therefore, by performing force-distance cycles we have detected specific recognition events between p53 and azurin, displaying unbinding forces of around 70 pN for an applied loading rate of 3 nN s(-1). The specificity of these events has been assessed by the significant reduction of their frequency observed after blocking the p53 sample by an azurin solution. Moreover, by measuring the rupture force as a function of the loading rate we have determined the dissociation rate constant of this complex to be approximately 0.1 s(-1). Our findings are here discussed in connection with results obtained in bulk experiments, with the aim of clarifying some molecular details of the p53-azurin complex that may help designing new anticancer strategy.     

Detection of metal binding sites on functional S-layer nanoarrays using single molecule force spectroscopy

Crystalline bacterial cell surface layers (S-layers) show the ability to recrystallize into highly regular pattern on solid supports. In this study, the genetically modified S-layer protein SbpA of Lysinibacillus sphaericus CCM 2177, carrying a hexa-histidine tag (His₆-tag) at the C-terminus, was used to generate functionalized two-dimensional nanoarrays on a silicon surface. Atomic force microscopy (AFM) was applied to explore the topography and the functionality of the fused His₆-tags. The accessibility of the His₆-tags was demonstrated by in-situ anti-His-tag antibody binding to the functional S-layer array. The metal binding properties of the His₆-tag was investigated by single molecule force microscopy. For this purpose, newly developed tris–NTA was tethered to the AFM tips via a flexible polyethylene glycol (PEG) linker. The functionalized tips showed specific interactions with S-layer containing His₆-tags in the presence of nickel ions. Thus the His₆-tag is located at the outer surface of the S-layer and can be used for stable but reversible attachment of functional tris–NTA derivatives.     

Culture of endothelial cells by transfection with plasmid harboring vascular endothelial growth factor

Vascular endothelial cells (ECs) are usually difficult to culture in a large scale because of their complicated requirements for cell growth. As the vascular endothelial growth factor (VEGF) is a key growth factor in the EC culture, we transfected human umbilical vein endothelial cells (HUVEC) using a plasmid containing VEGF gene and let them grow in a culture medium eliminated an important supplement, endothelail cell growth supplement (ECGS). The expression of VEGF by HUVEC tansfected with VEGF gene was not enough to stimulate the growth of HUVEC, only 40% of maximum cell density obtainable in the presence of ECGS., However, when the culture medium was supplied with 2.5 ng/mL of basic fibroblast growth factor (bFGF), a synergistic effect of VEGF and bFGF was observed. In this case, the final cell density was recovered up to about 78% of maxium value.     

Human single chain antibody to vascular endothelial growth factor:gene cloning, high-level expression, affinity maturation and bioactivity

Using antibody phage display technique,a human single chain antibody to vascular endothelial growth factor (VEGF) has been cloned.The antibody expression reached 45% of the total bacterial proteins.The purification and refolding of the antibody were completed in one step by using gel filtration chromatograph.ELISA analysis showed that the antibody not only specifically bound to human VEGF,but also competitively inhibited VEGF reacting with its receptors.In order to raise the affinity of the single chain antibody,its heavy chain variable region was randomly mutated using error-prone PCR and an antibody mutant library was constructed,from which a mutant with higher affinity was screened out.The three-dimensional structure and binding affinity of wild type and mutant antibody were compared.Our study provided a potential reagent for tumor angiogenic therapy and a significant model for antibody high-level expression and affinity maturation.     

Immunochemical and single molecule force spectroscopy studies of specific interaction between the laminin binding protein and the West Nile virus surface glycoprotein E domain II

ELISA and Western blot immunochemical data attest an effective and highly specific interaction of the surface glycoprotein E domain II (DII) of the tick born encephalitis and Dengue viruses with the laminin binding protein (LBP). Based on a highly conservative structure of the DII in different flaviviruses we propose a similarly effective interaction between the LBP and the DII of the surface glycoprotein E of the West Nile virus. We report the results of studies of this interaction by immunochemical and single molecule force spectroscopy methods. The specific binding between these species is confirmed by both methods.     

血小板活化因子对大鼠黄体细胞孕酮分泌及血管内皮生长因子表达的作用

本文旨在研究血小板活化因子(platelet-activating factor,PAF)对大鼠黄体细胞孕酮分泌及血管内皮生长因子(vascularendothelial growth factor,VEGF)mRNA表达的作用.将未成年(25～28 d)Sprague-Dawley雌性大鼠颈部皮下注射50 IU孕马血清促性腺激素(pregnant mare serum gonadotrophin,PMSG),48 h后注射25 IU人绒毛膜促性腺激素(human chorionicgonadotrophin.hCG)诱导卵泡发育和黄体生成,第6天(hCG注射日为第1天)收集卵巢黄体细胞,体外培养24 h后,不加或加入不同剂量(0.1 μg/mL、1 μg/mL、10 μg/mL)PAF,37℃、5%CO2培养箱内培养24 h.用放射免疫方法测定培养液中孕酮的含量,流式细胞仪和RT-PCR方法检测黄体细胞凋亡以及VEGF mRNA的表达.结果显示,PAF促进黄体细胞孕酮分泌,1 μg/mL PAF作用最强(P<0.05);PAF促进黄体细胞凋亡无明显剂量依赖性,但10 μg/mL PAF显著促进大鼠黄体细胞凋亡(P<0.05):PAF刺激黄体细胞VEGF mRNA表达,1 μg/mL PAF效果最显著(P<0.01).结果提示,PAF可通过调节黄体细胞孕酮的分泌和VEGF mRNA的表达来促进黄体形成.     

Human single chain antibody to vascular endothelial growth factor: gene cloning, high-level expression, affinity maturation and bioactivity

Using antibody phage display technique, a human single chain antibody to vascular endothelial growth factor (VEGF) has been cloned. The antibody expression reached 45% of the total bacterial proteins. The purification and refolding of the antibody were completed in one step by using gel filtration chromatograph. ELISA analysis showed that the antibody not only specifically bound to human VEGF, but also competitively inhibited VEGF reacting with its receptors. In order to raise the affinity of the single chain antibody, its heavy chain variable region was randomly mutated using error-prone PCR and an antibody mutant library was constructed, from which a mutant with higher affinity was screened out. The three-dimensional structure and binding affinity of wild type and mutant antibody were compared. Our study provided a potential reagent for tumor angiogenic therapy and a significant model for antibody high-level expression and affinity maturation.     

Circulating and exhaled vascular endothelial growth factor in asthmatic pregnancy

Context: Vascular endothelial growth factor (VEGF) plays a role in asthma and pathological pregnancies.

Objective: This is the first study assessing plasma and exhaled breath condensate VEGF levels in asthmatic pregnancy.

Material and methods: Thirty-one asthmatic pregnant, 29 asthmatic nonpregnant, 28 healthy pregnant and 22 healthy nonpregnant women were enrolled. Plasma was collected in all subjects, EBC in 57 volunteers for VEGF measurements.

Results: Plasma VEGF decreased in both pregnant groups (p < 0.01), without any differences between the asthmatic and the respective nonasthmatic groups (p > 0.05). VEGF was undetectable in EBC.

Conclusion: Concomitant asthma does not affect plasma VEGF during pregnancy.     

血管内皮生长因子特异性鼠源单链抗体的人源化

以抗体阻断血管生成信号来治疗实体肿瘤显示了很好的前景,但鼠源抗体首先必须经人源化改造以降低其免疫原性才能应用于人体。本研究以同源模建预测了一体人血管内皮生长因子（VEGF）特异性鼠源单链抗体E11的三维结构,以结构数据为基础并采取单个最相似框架区替代法对其进行人源化设计;合成并组装了人源化单链抗体基因并在大肠杆菌中表达,包含体形式的产物以凝胶柱色谱法复性,经ELISA检测表明,人源化后的单链抗体保持了与天然VEGF结合的活性,表明采取的人源化路线具有可行性。     

Salt dependent binding of T4 gene 32 protein to single and double-stranded DNA: single molecule force spectroscopy measurements

Bacteriophage T4 gene 32 protein (gp32) is a well-studied representative of the large family of single-stranded DNA (ssDNA) binding proteins, which are essential for DNA replication, recombination and repair. Surprisingly, gp32 has not previously been observed to melt natural dsDNA. At the same time, *I, a truncated version of gp32 lacking its C-terminal domain (CTD), was shown to decrease the melting temperature of natural DNA by about 50 deg. C. This profound difference in the duplex destabilizing ability of gp32 and *I is especially puzzling given that the previously measured binding of both proteins to ssDNA was similar. Here, we resolve this apparent contradiction by studying the effect of gp32 and *I on the thermodynamics and kinetics of duplex DNA melting. We use a previously developed single molecule technique for measuring the non-cooperative association constants (K(ds)) to double-stranded DNA to determine K(ds) as a function of salt concentration for gp32 and *I. We then develop a new single molecule method for measuring K(ss), the association constant of these proteins to ssDNA. Comparing our measured binding constants to ssDNA for gp32 and *I we see that while they are very similar in high salt, they strongly diverge at [Na+] < 0.2 M. These results suggest that intact protein must undergo a conformational rearrangement involving the CTD that is in pre-equilibrium to its non-cooperative binding to both dsDNA and ssDNA. This lowers the effective concentration of protein available for binding, which in turn lowers the rate at which it can destabilize dsDNA. For the first time, we quantify the free energy of this CTD unfolding, and show it to be strongly salt dependent and associated with sodium counter-ion condensation on the CTD.     

AFM force spectroscopy reveals how subtle structural differences affect the interaction strength between Candida albicans and DC‐SIGN

The fungus Candida albicans is the most common cause of mycotic infections in immunocompromised hosts. Little is known about the initial interactions between Candida and immune cell receptors, such as the C‐type lectin dendritic cell‐specific intracellular cell adhesion molecule‐3 (ICAM‐3)‐grabbing non‐integrin (DC‐SIGN), because a detailed characterization at the structural level is lacking. DC‐SIGN recognizes specific Candida‐associated molecular patterns, that is, mannan structures present in the cell wall of Candida. The molecular recognition mechanism is however poorly understood. We postulated that small differences in mannan‐branching may result in considerable differences in the binding affinity. Here, we exploit atomic force microscope‐based dynamic force spectroscopy with single Candida cells to gain better insight in the carbohydrate recognition capacity of DC‐SIGN. We demonstrate that slight differences in the N‐mannan structure of Candida, that is, the absence or presence of a phosphomannan side chain, results in differences in the recognition by DC‐SIGN as follows: (i) it contributes to the compliance of the outer cell wall of Candida, and (ii) its presence results in a higher binding energy of 1.6 k_BT. The single‐bond affinity of tetrameric DC‐SIGN for wild‐type C. albicans is ~10.7 k_BT and a dissociation constant k_D of 23 μM, which is relatively strong compared with other carbohydrate–protein interactions described in the literature. In conclusion, this study shows that DC‐SIGN specifically recognizes mannan patterns on C. albicans with high affinity. Knowledge on the binding pocket of DC‐SIGN and its pathogenic ligands will lead to a better understanding of how fungal‐associated carbohydrate structures are recognized by receptors of the immune system and can ultimately contribute to the development of new anti‐fungal drugs. Copyright © 2015 John Wiley & Sons, Ltd.     

一种具有人VEGF结合活性的人源单一重链可变区的克隆与表达

为避免一种来自五特征转基因小鼠的全人VEGF单克隆IgM抗体分子量大的不足,本研究探讨了该抗体单一重链可变区的功能特性。首先,PCR获得该抗体的重链可变区,将该序列克隆至pET28a表达载体内,在大肠杆菌中进行了诱导表达。通过变性纯化和复性等方法获得了具有生物学活性的16kDa重组抗体片段——rhVVH。体外结合实验表明,rhVVH保留有完整免疫球蛋白的人VEGF结合活性。人脐静脉内皮细胞(HUVEC)增殖抑制实验表明:rhVVH可以剂量依赖性的抑制HUVEC的增殖。上述结果揭示了该抗体单一重链可变区保留有完整抗体的部分功能,为进一步开展全人源VEGF单克隆IgM抗体小型化研究奠定了基础。     

Refinement of the solution structure of the heparin-binding domain of vascular endothelial growth factor using residual dipolar couplings

Previous NMR structural studies of the heparin-binding domain of vascular endothelial growth factor (VEGF₁₆₅) revealed a novel fold comprising two subdomains, each containing two disulfide bridges and a short two-stranded antiparallel -sheet. The mutual orientation of the two subdomains was poorly defined by the NMR data. Heteronuclear relaxation data suggested that this disorder resulted from a relative lack of experimental restraints due to the limited size of the interface, rather than inherent high-frequency flexibility. Refinement of the structure using ¹H^N-¹⁵N residual dipolar coupling restraints results in significantly improved definition of the relative subdomain orientations.