Proactive Manipulation Techniques for Protein Transport at Confined Nanoscale

doi:10.6023/A23040149

Acta Chimica Sinica ›› 2023, Vol. 81 ›› Issue (7): 857-868.DOI: 10.6023/A23040149 Previous Articles

Review

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)

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

Cite this article

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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Fig. & Tab. 6

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]

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]

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]

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]

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]

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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