受限纳尺度下蛋白质输运的主动操纵技术

doi:10.6023/A23040149

化学学报 ›› 2023, Vol. 81 ›› Issue (7): 857-868.DOI: 10.6023/A23040149 上一篇

综述

受限纳尺度下蛋白质输运的主动操纵技术

马超凡^a^,^b, 徐伟^a^,^b, 刘巍^a^,^b, 徐昌晖^a^,^b, 沙菁㛃^a^,^b^,^*()

a 东南大学机械工程学院南京 211189
b 东南大学江苏省微纳生物医学仪器设计与制造重点实验室南京 211189

投稿日期:2023-04-20 发布日期:2023-05-31

作者简介:

马超凡, 男, 东南大学机械工程学院博士研究生. 主要从事生物纳米孔蛋白质检测与构象分析的研究.

沙菁㛃, 女, 东南大学机械工程学院设计工程系, 教授, 博士生导师. 主要研究方向为微纳流体系统、微纳传感器设计. 先后主持或完成包括4项国家自然科学基金(其中一项优秀结题)、参与1项973计划、1项国家自然科学基金重点项目. 近几年, 在JACS、ACS Nano、Small、Nanoscale、Analytical Chemistry、ACS Sensors、Nanotechnology、Appl. Phys. Lett.等微纳领域权威国际期刊发表SCI论文50余篇(含JCR一区、二区论文近50篇, 影响因子超10.0论文6篇). 申请发明专利18项, 已经获得授权13项. 中国机械工程学会高级会员、ASME会员、长期担任《Lab on a Chip》、《Nanotechnology》、《BIOTECHNOLOGY AND BIOENGINEERING》、《中国科学》等期刊的审稿人.

基金资助:
国家自然科学基金(52075099); 国家自然科学基金(52035003)

Proactive Manipulation Techniques for Protein Transport at Confined Nanoscale

Chaofan Ma^a^,^b, Wei Xu^a^,^b, Wei Liu^a^,^b, Changhui Xu^a^,^b, Jingjie Sha^a^,^b()

a School of Mechanical Engineering, Southeast University, Nanjing 211189
b Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University,Nanjing 211189

Received:2023-04-20 Published:2023-05-31
Contact: *E-mail: major212@seu.edu.cn
Supported by:
National Natural Science Foundation of China(52075099); National Natural Science Foundation of China(52035003)

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摘要/Abstract

蛋白质是人体细胞、组织的重要组成部分, 与众多代谢活动密切相关, 它们的一些微小改变就可能引发人体的重大疾病. 因此, 蛋白质检测是生物化学领域的重要课题. 纳米孔技术能够在单分子水平甚至单氨基酸水平上实时检测蛋白质, 有望成为最低成本和最高效的蛋白质检测方法之一. 然而, 使用纳米孔检测蛋白质时, 由于实验条件和检测策略的原因, 使得蛋白质在纳米孔中驻留时间过短, 无法从蛋白质捕获的电信号中清晰地反映更多的生物细节信息. 解决这一问题的关键在于控制蛋白质通过纳米孔时的输运速度, 满足传感器件带宽的要求. 本综述从外部力场竞争、内部力场相互作用、亲疏水相互作用、空间位阻效应等角度综述了蛋白质在纳米孔中输运的主动操纵技术, 目的是提高纳米孔对蛋白质的捕获频率, 延长蛋白质在纳米孔内的驻留时间, 以实现高分辨率的蛋白质检测, 充分揭示蛋白质分子的构象变化机制、反应动力学, 甚至实现蛋白质测序等. 最后对纳米孔传感技术在蛋白质检测方面存在的巨大挑战和发展趋势进行了详细展望和总结阐述.

关键词: 蛋白质检测, 纳米孔, 操纵方法, 捕获时间, 纳尺度输运

Proteins are important components of human cells and tissues and are closely related to numerous metabolic activities, and some small changes in them may trigger major diseases in the human body. Therefore, protein detection is an important topic in the field of biochemistry. Nanopore technology is capable of real-time protein detection at the single molecule level or even at the single amino acid level, and is expected to be one of the lowest costs and most efficient protein detection methods. However, when using nanopores to detect proteins, the experimental conditions and detection strategy make the protein residence time in the nanopore too short to clearly reflect more detailed biological information from the electrical signal captured by the protein. The critical solution to this problem lies in controlling the transport rate of proteins through the nanopore to meet the bandwidth of the sensor device. In this paper, the active manipulation techniques of protein transport in nanopores are reviewed from the perspectives of external force field competition, internal force field interaction, hydrophilic interaction, and spatial resistance effect, with the aim of improving the capture frequency of proteins by nanopores and prolonging the residence time of proteins in nanopores to achieve high-resolution protein detection, fully reveal the conformational change mechanism of protein molecules, reaction kinetics, and even realize protein sequencing, etc. Finally, the great challenges and development trends of nanopore sensing technology for protein detection are described in detail.

Key words: protein detection, nanopore, manipulation method, residence time, nanoscale transport

引用此文

马超凡, 徐伟, 刘巍, 徐昌晖, 沙菁㛃. 受限纳尺度下蛋白质输运的主动操纵技术[J]. 化学学报, 2023, 81(7): 857-868.

Chaofan Ma, Wei Xu, Wei Liu, Changhui Xu, Jingjie Sha. Proactive Manipulation Techniques for Protein Transport at Confined Nanoscale[J]. Acta Chimica Sinica, 2023, 81(7): 857-868.

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图/表 6

图1. 通过改变溶液pH、定点突变、施加其他力场来调节蛋白质在纳米孔内的力场竞争机制. (a)生物纳米孔系统的pH调节, 增强的电渗流可以将多肽短暂束缚在α-HL纳米孔的管腔或前庭[71]. (b)固态纳米孔的pH调节, 电渗效应在亲和素蛋白的过孔输运中占主导, 甚至可以逆转电泳主导的输运[72]. (c)修改纳米孔壁面电荷, N226Q/S228K突变AeL纳米孔的正电荷修饰获得了一个更大的电渗流速度, 导致非均匀带电多肽的频率最大增加8倍[73]. (d)施加压力梯度力, 通过对压力和电压的微调, 抑肽蛋白的捕获率比传统的电压驱动方法提高了5倍以上[74]. (e)施加浓度梯度力, 离子浓度富集和电渗、电泳共同作用, 决定了蛋白质能否被捕获[75]

Figure 1. Regulating the force field competition mechanism of proteins within nanopores by changing solution pH, targeted mutations, and applying other force fields. (a) pH regulation of biological nanopore systems, enhanced electroosmotic flow can transiently bind peptides in the lumen or vestibule of α-HL nanopores[71]. (b) pH regulation of solid nanopores, where electroosmotic effects dominate the transport of avidin proteins and can even reverse the electrophoretic force dominated transport[72]. (c) Nanopore surface charge modification, positive charge modification of N226Q/S228K mutant AeL nanopores results in a greater electroosmotic flow rate, leading to a maximum 8-fold increase in the frequency of non-uniformly charged peptides[73]. (d) By applying pressure gradient force, the capture rate of protein can be increased by more than 5 times compared to the conventional voltage driven method by fine-tuning the pressure and voltage[74]. (e) Application of concentration gradient forces, ion concentration enrichment and electroosmosis and electrophoresis work together to determine whether proteins can be captured[75]

图2. 通过对待测蛋白质的化学修饰来调节蛋白质在纳米孔内的力场竞争机制. (a)分别将20种天然氨基酸与7个带正电的精氨酸连接起来, 操纵不同的氨基酸被AeL纳米孔捕获, 并将时间分辨率提高到足以区分20种天然氨基酸的程度[78]. (b)待测蛋白质修饰SUP, 由于带正电的SUPs与纳米孔表面的静电相互作用, 可以大大减缓目标蛋白的输运[79]. (c)待测蛋白质修饰双链DNA运载体, 能够通过纳米孔捕获事件的中的次峰值电流的特征变化来区分个体蛋白质的大小[80]. (d)待测蛋白质修饰功能性DNA纳米结构, 利用TDN-apt将AChE的代表性靶点运载通过纳米孔, 实现了AChE的单分子蛋白质检测[81]. (e)基于金属有机笼PCC-57与生物分子的内在相互作用, 提高固体纳米孔的灵敏度和选择性[82]

Figure 2. Modulating the force field competition mechanism of proteins within nanopores by chemical modification of target proteins. (a) The 20 natural amino acids were linked to 7 positively charged arginines, respectively, and the different amino acids were manipulated to be captured by the AeL nanopores and the temporal resolution was increased enough to distinguish the 20 natural amino acids[78]. (b) The targeted protein is modified with SUPs, which can greatly slow down the transport of the target protein due to the electrostatic interaction between the positively charged SUPs and the nanopore surface[79]. (c) The targeted protein modifies double-stranded DNA carriers and is able to distinguish the size of individual proteins by characteristic changes in the sub-peak currents in the nanopore capture event[80]. (d) Functional DNA nanostructures modified with the targeted protein, and single-molecule protein detection of AChE by TDN-apt transporting a representative target of AChE through the nanopore[81]. (e) Improved sensitivity and selectivity of solid nanopores based on the intrinsic interaction of metal-organic cage PCC-57 with biomolecules[82]

图3. 调节蛋白质与纳米孔之间的内部力场相互作用来操纵蛋白质的输运行为. (a)含硫醇肽(R1-R5)作为反应物与半胱氨酸突变气溶素(AeL)纳米孔结合, 研究蛋白质的单分子反应动力学[87]. (b) Bak-BH3多肽偶联OmpG纳米孔, 用于研究Bcl-xL和Bak-BH3之间的相互作用, 以及它被一种小分子抑制剂抑制的效果[88]. (c)固态氮化硅纳米孔涂敷金膜, 以实现自组装硫醇单分子层的功能化[89]. (d)磷脂双分子层修饰的固态纳米孔, 蛋白拴链被嵌入脂质双分子层, 拴链的灵活性和长度允许蛋白质在孔中自由旋转[90]. (e)固态纳米孔修饰磷脂的无栓连方法[91]

Figure 3. Modulating internal force field interactions between proteins and nanopores to manipulate protein transport behavior. (a) Thiol-containing peptides (R1-R5) as reactants bound to cysteine mutant AeL nanopore to study the kinetics of single-molecule reactions of proteins[87]. (b) Bak-BH3 peptide coupled to OmpG nanopores for studying the interaction between Bcl-xL and Bak-BH3 and its inhibition by a small molecule inhibitor[88]. (c) Solid silicon nitride nanopores coated with gold films for functionalization of self-assembled thiol monomolecular layers[89]. (d) Solid-state nanopores modified with lipid bilayers in which protein tethers are embedded in the lipid bilayer and the flexibility and length of the tethers allow the protein to rotate freely in the pore[90]. (e) Solid-state nanopore modification of lipids without tethers[91]

图4. 调节纳米孔壁面的亲疏水性来操纵蛋白质的输运行为. (a)疏水壁面纳米孔构筑的门控系统[92??-95]. (b)在α-螺旋FraC纳米孔腔内的精确位置引入疏水性的芳香族氨基酸, 可以增加多肽的捕获频率, 并在很大程度上提高了相似大小的多肽之间的区分能力[96]. (c)含有更多疏水残基的多肽通过二硫化钼纳米孔的渗透速度较慢, 特别是对苯类残基的结合亲和力非常显著[97]. (d)高离子强度和低pH值条件下, 在其收缩处使用带有苯丙氨酸的纳米孔可以识别亲水性多肽[98]

Figure 4. Modulating the hydrophobicity of nanopore surface to manipulate protein transport behavior. (a) Gating system constructed by hydrophobic surface nanopores[92??-95]. (b) The introduction of hydrophobic aromatic amino acids at precise locations within the α-helical FraC nanopore cavity increases the capture frequency of peptides and largely improves the ability to distinguish between similarly sized peptides[96]. (c) Slower penetration of peptides containing more hydrophobic residues through molybdenum disulfide nanopores, especially with significant binding affinity for benzene residues[97]. (d) Recognition of hydrophilic peptides by using nanopores with phenylalanine at their constriction under high ionic strength and low pH conditions[98]

图5. 利用纳米孔内部结构的空间位阻效应操纵蛋白质输运行为 (a) α-HL纳米孔结构示意图. (b) MspA纳米孔结构示意图. (c)在入口和出口端的双重能量势垒的ClyA纳米孔, 其中空间位阻引起的能垒最为显著[100]. (d) α-HL纳米孔的入口出口端能垒和一个内部能垒, 多肽分别在β-桶或前庭结构域被捕获, 揭示了关于纳米孔内肽的随机运动的方向和速率的丰富的动力学细节[71]. (e)用biotin将链霉亲和素(mSA)与一段β发卡肽连接起来, 对待测蛋白的过孔进行卡位[101]. (f) NEOtrap捕获大质量蛋白质, 能够根据大小和形状敏感地区分蛋白质, 并区分核苷酸依赖的蛋白质构象[102-103]

Figure 5. Manipulation of protein transport behavior by spatial resistance effect of nanopore internal structure. (a) Schematic diagram of α-HL nanopore structure. (b) Schematic diagram of MspA nanopore structure. (c) ClyA nanopores with dual energy barriers at the entrance and exit ends, where the energy barriers due to spatial resistance are the most significant[100]. (d) Energy barriers at the entrance exit end of α-HL nanopores and an internal energy barrier where peptides are trapped in the β-barrel or vestibular structural domain, respectively, reveal rich kinetic details about the direction and rate of stochastic motion of peptides within the nanopore[71]. (e) The streptavidin was linked to a segment of β hairpin peptide using biotin to latch onto the perforation of the target protein[101]. (f) NEOtrap captures large mass proteins, enables sensitive differentiation of proteins based on size and shape, and distinguishes nucleotide-dependent protein conformations[102-103]

图6. 操纵蛋白质在纳米孔内输运的间接方法. (a)、(b)通过光镊和电场(纳米孔力谱学)研究连接到双链DNA上的单个蛋白质分子的输运动力学[105]. (c)纳米孔检测hOGG1的活性的间接策略, 利用DNA底物的酶催化裂解反应探测人的8-氧鸟嘌呤DNA糖化酶(hOGG1)的活性[107]. (d)抗体修饰的磁性纳米颗粒被用于在受控的电磁铁作用下将从样品中提取的待测分析物递送到抗体修饰的纳米孔阵列中[106]. (e)使用酶作为分子马达来控制生物分子通过纳米孔的速度, 实现蛋白质测序[45]

Figure 6. Indirect methods for manipulating protein transport within nanopores. (a), (b) Study of transport dynamics of individual protein molecules attached to double-stranded DNA by optical tweezers and electric fields (nanopore force spectroscopy)[105]. (c) Indirect strategy for nanopore detection of hOGG1 activity, using enzyme-catalyzed cleavage of DNA substrates to detect human 8-oxoguanine DNA glycosylase (hOGG1) activity[107]. (d) Antibody-modified magnetic nanoparticles are used to deliver the analyte to be measured from the sample into the antibody-modified nanopore array under the action of a controlled electromagnet[106]. (e) Using enzymes as molecular motors to control the speed of biomolecules through nanopores for protein sequencing[45]

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受限纳尺度下蛋白质输运的主动操纵技术

Proactive Manipulation Techniques for Protein Transport at Confined Nanoscale

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