Single-molecule biotechnology for protein researches

doi:10.1016/j.cjche.2020.10.031

中国化学工程学报 ›› 2021, Vol. 29 ›› Issue (2): 212-224.DOI: 10.1016/j.cjche.2020.10.031

• Bioseparations and Analysis • 上一篇下一篇

Single-molecule biotechnology for protein researches

Xiaoyan Zhuang^1,2, Qian Wu^1,2, Aihui Zhang^1,2, Langxing Liao^1,2, Baishan Fang^1,2,3

1 Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China;
2 The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China;
3 The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen 361005, China

收稿日期:2020-08-20 修回日期:2020-10-27 出版日期:2021-02-28 发布日期:2021-05-15
通讯作者: Aihui Zhang, Baishan Fang
基金资助:
This work was financially supported by the National Natural Science Foundation of China (No. 21978245) and National Postdoctoral Program for Innovative Talents (No. BX20200197).

Single-molecule biotechnology for protein researches

Xiaoyan Zhuang^1,2, Qian Wu^1,2, Aihui Zhang^1,2, Langxing Liao^1,2, Baishan Fang^1,2,3

1 Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China;
2 The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China;
3 The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen 361005, China

Received:2020-08-20 Revised:2020-10-27 Online:2021-02-28 Published:2021-05-15
Contact: Aihui Zhang, Baishan Fang
Supported by:
This work was financially supported by the National Natural Science Foundation of China (No. 21978245) and National Postdoctoral Program for Innovative Talents (No. BX20200197).

摘要/Abstract

摘要： Cells employ proteins to perform metabolic functions and maintain active physiological state through charge transfer and energy conversion. These processes are carried out in a narrow space precisely and rapidly, which, no doubt, bring great difficulty for their detection and dissection. Fortunately, in recent years, the development and expansion of single-molecule technique in protein research make monitoring the dynamical changes of protein at single-molecule level a reality, which also provides a powerful tool for the further exploration of new phenomena and new mechanisms of life activities. This paper aims to summarize the working principle and essential achievements of single-molecule technique in protein research in recent five years. We focus on not only dissecting the difference of nanopores, atomic force microscope, scanning tunneling microscope, and optical tweezers technique, but also discussing the great significance of these single-molecule techniques in investigating intramolecular and intermolecular interactions, electron transport, and conformational changes. Finally, the opportunities and challenges of the single-molecule technique in protein research are discussed, which provide a new door for single-molecule protein research.

关键词: Single-molecule protein, Enzyme, Nanopore, Atomic force microscope, Scanning tunneling microscope, Optical tweezers, Biotechnology, Imaging

Abstract: Cells employ proteins to perform metabolic functions and maintain active physiological state through charge transfer and energy conversion. These processes are carried out in a narrow space precisely and rapidly, which, no doubt, bring great difficulty for their detection and dissection. Fortunately, in recent years, the development and expansion of single-molecule technique in protein research make monitoring the dynamical changes of protein at single-molecule level a reality, which also provides a powerful tool for the further exploration of new phenomena and new mechanisms of life activities. This paper aims to summarize the working principle and essential achievements of single-molecule technique in protein research in recent five years. We focus on not only dissecting the difference of nanopores, atomic force microscope, scanning tunneling microscope, and optical tweezers technique, but also discussing the great significance of these single-molecule techniques in investigating intramolecular and intermolecular interactions, electron transport, and conformational changes. Finally, the opportunities and challenges of the single-molecule technique in protein research are discussed, which provide a new door for single-molecule protein research.

Key words: Single-molecule protein, Enzyme, Nanopore, Atomic force microscope, Scanning tunneling microscope, Optical tweezers, Biotechnology, Imaging

Xiaoyan Zhuang, Qian Wu, Aihui Zhang, Langxing Liao, Baishan Fang. Single-molecule biotechnology for protein researches[J]. 中国化学工程学报, 2021, 29(2): 212-224.

Xiaoyan Zhuang, Qian Wu, Aihui Zhang, Langxing Liao, Baishan Fang. Single-molecule biotechnology for protein researches[J]. Chinese Journal of Chemical Engineering, 2021, 29(2): 212-224.

参考文献

[1] Q.K. Li, Q. Chen, P.C. Klauser, M.Y. Li, F. Zheng, N.X. Wang, X.Y. Li, Q.B. Zhang, X.M. Fu, Q. Wang, Y. Xu, L. Wang, Developing covalent protein drugs via proximity-enabled reactive therapeutics, Cell 182 (2020) 85–97.
[2] A. Pandey, M. Mann, Proteomics to study genes and genomes, Nature 405 (6788) (2000) 837–846.
[3] L.J. Sweetlove, A.R. Fernie, The role of dynamic enzyme assemblies and substrate channelling in metabolic regulation, Nat. Commun. 9 (2018) 2136.
[4] L.T. Zhai, L.L. Feng, L. Xia, H.Y. Yin, S. Xiang, Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease-causing mutations, Nat. Commun. 7 (2016) 11229.
[5] M. Onizawa, S. Oshima, U. Schulze-Topphoff, J.A. Oses-Prieto, T. Lu, R. Tavares, T. Prodhomme, B. Duong, M.I. Whang, R. Advincula, A. Agelidis, J. Barrera, H. Wu, A. Burlingame, B.A. Malynn, S.S. Zamvil, A. Ma, The ubiquitin-modifying enzyme A20 restricts ubiquitination of the kinase RIPK3 and protects cells from necroptosis, Nat. Immunol. 16 (618) (2015) 837–846.
[6] N. Walter, C. Huang, A. Manzo, M. Sobhy, Do-it-yourself guide: How to use the modern single-molecule toolkit, Nat. Methods 5 (6) (2008) 475–478.
[7] M. Baaske, M. Foreman, F. Vollmer, Single-molecule nucleic acid interactions monitored on a label-free microcavity biosensor platform, Nat. Nanotechnol. 9 (11) (2014) 933–939.
[8] S. Howorka, Z. Siwy, Nanopore analytics: Sensing of single molecules, Chem. Soc. Rev. 38 (8) (2009) 2360–2384.
[9] C Tang, Y.X. Tang, Y.L Ye, Z.W. Yan, Z.X. Chen, L.J. Chen, L.Y. Zhang, J.Y Liu, J. Shi, H.P. Xia, W.J. Hong, Identifying the conformational isomers of singlemolecule cyclohexane at room temperature, Chem 6 (10) (2020) 2770–2781.
[10] C.C. Huang, A.V. Rudnev, W.J. Hong, Break junction under electrochemical gating: Testbed for single-molecule electronics, Chem. Soc. Rev. 44 (4) (2015) 889–901.
[11] K. Bavishi, N.S. Hatzakis, Shedding light on protein folding, structural and functional dynamics by single molecule studies, Molecules 19 (12) (2014) 19407–19434.
[12] G. Huang, K. Willems, M. Soskine, C. Wloka, G. Maglia, Electro-osmotic capture and ionic discrimination of peptide and protein biomarkers with FraC nanopores, Nat. Commun. 8 (2017) 935.
[13] S.W. Hla, K.H. Rieder, STM control of chemical reactions: Single-molecule synthesis, Rev. Phys. Chem. 54 (2003) 307–330.
[14] M. Rief, M. Gautel, F. Oesterhelt, J.M. Fernandez, H.E. Gaub, Reversible unfolding of individual titin immunoglobulin domains by AFM, Science 276 (5315) (1997) 1109–1112.
[15] N. Hacohen, C.J.X. Ip, R. Gordon, Analysis of egg white protein composition with double nanohole optical tweezers, ACS Omega 3 (5) (2018) 5266–5272.
[16] Y.J. Yang, H.L. Dong, X.W. Qiang, H. Fu, E.C. Zhou, C. Zhang, X.F. Chen, F.C. Jia, L. Dai, Z.J. Tan, X.H. Zhang, Cytosine methylation enhances dna condensation revealed by equilibrium measurements using magnetic tweezers, J. Am. Chem. Soc. 142 (2020) 9203–9209.
[17] Y.H. Luo, L.L. Wu, J. Tu, Z.H. Lu, Application of solid-state nanopore in protein detection, Int. J. Mol. Sci. 21 (8) (2020) 2808.
[18] E. Neher, B. Sakmann, Single-channel currents recorded from membrane of denervated frog muscle fibres, Nature 260 (5554) (1976) 799–802.
[19] J. Li, D. Stein, C. McMullan, D. Branton, M.J. Aziz, J.A. Golovchenko, Ion-beam sculpting at nanometre length scales, Nature 412 (6843) (2001) 166–169.
[20] O.K. Zahid, F. Wang, J.A. Ruzicka, E.W. Taylor, A.R. Hall, Sequence-specific recognition of microRNAs and other short nucleic acids with solid-state nanopores, Nano Lett. 16 (3) (2016) 2033–2039.
[21] G. Perez-Mitta, M.E. Toimil-Molares, C. Trautmann, W.A. Marmisolle, O. Azzaroni, Molecular design of solid-state nanopores: Fundamental concepts and applications, Adv. Mater. 31 (37) (2019) 1901483.
[22] M. Waugh, K. Briggs, D. Gunn, M. Gibeault, S. King, Q. Ingram, A.M. Jimenez, S. Berryman, D. Lomovtsev, L. Andrzejewski, V. Tabard-Cossa, Solid-state nanopore fabrication by automated controlled breakdown, Nat. Protoc. 15 (1) (2020) 122–143.
[23] O.M. Eggenberger, C.F. Ying, M. Mayer, Surface coatings for solid-state nanopores, Nanoscale 11 (2019) 19636–19657.
[24] K. Chuah, Y.F. Wu, S.R.C. Vivekchand, K. Gaus, P.J. Reece, A.P. Micolich, J.J. Gooding, Nanopore blockade sensors for ultrasensitive detection of proteins in complex biological samples, Nat. Commun. 10 (2019) 2109.
[25] J.J. Sha, W. Si, B. Xu, S. Zhang, K. Li, K.B. Lin, H.J. Shi, Y.F. Chen, Identification of spherical and nonspherical proteins by a solid-state nanopore, Anal. Chem. 90 (23) (2018) 13826–13831.
[26] E.C. Yusko, B.R. Bruhn, O.M. Eggenberger, J. Houghtaling, R.C. Rollings, N.C. Walsh, S. Nandivada, M. Pindrus, A.R. Hall, D. Sept, J.L. Li, D.S. Kalonia, M. Mayer, Real-time shape approximation and fingerprinting of single proteins using a nanopore, Nat. Nanotechnol. 12 (4) (2017) 360–367.
[27] J. Houghtaling, C.F. Ying, O.M. Eggenberger, A. Fennouri, S. Nandivada, M. Acharjee, J.L. Li, A.R. Hall, M. Mayer, D. Sept, Estimation of shape, volume, and dipole moment of individual proteins freely transiting a synthetic nanopore, ACS Nano 13 (5) (2019) 5231–5242.
[28] X.Y. Wang, M.D. Wilkinson, X.Y. Lin, R. Ren, K.R. Willison, A.P. Ivanov, J. Baum, J.B. Edel, Single-molecule nanopore sensing of actin dynamics and drug binding, Chem. Sci. 11 (4) (2020) 970–979.
[29] C.C. Chau, S.E. Radford, E.W. Hewitt, P. Actis, Macromolecular crowding enhances the detection of DNA and proteins by a solid-state nanopore, Nano Lett. 20 (7) (2020) 5553–5561.
[30] L. Restrepo-Perez, C. Joo, C. Dekker, Paving the way to single-molecule protein sequencing, Nat. Nanotechnol. 13 (2018) 786–796.
[31] C. Plesa, S.W. Kowalczyk, R. Zinsmeester, A.Y. Grosberg, Y. Rabin, C. Dekker, Fast translocation of proteins through solid state nanopores, Nano Lett. 13 (2013) 658–663.
[32] L. Restrepo-Perez, G. Huang, P.R. Bohlander, N. Worp, R. Eelkema, G. Maglia, C. Joo, C. Dekker, Resolving chemical modifications to a single amino acid within a peptide using a biological nanopore, ACS Nano 13 (12) (2019) 13668–13676.
[33] V. Van Meervelt, M. Soskine, S. Singh, G.K. Schuurman-Wolters, H.J. Wijma, B. Poolman, G. Maglia, Real-time conformational changes and controlled orientation of native proteins inside a protein nanoreactor, J. Am. Chem. Soc. 139 (51) (2017) 18640–18646.
[34] F.Z. Hu, B. Angelov, S. Li, N. Li, X.B. Lin, A.H. Zou, Single-molecule study of peptides with the same amino acid composition but different sequences by using an aerolysin nanopore, ChemBioChem 21 (17) (2020) 2467–2473.
[35] S. Wang, J. Cao, W.D. Jia, W.M. Guo, S.H. Yan, Y.Q. Wang, P.K. Zhang, H.Y. Chen, S. Huang, Single molecule observation of hard–soft-acid–base (HSAB) interaction in engineered Mycobacterium smegmatis porin A (MspA) nanopores, Chem. Sci. 11 (3) (2020) 879.
[36] E.L. Bonome, F. Cecconi, M. Chinappi, Translocation intermediates of ubiquitin through an a-hemolysin nanopore: implications for detection of posttranslational modifications, Nanoscale 11 (2019) 9920.
[37] D.P. Hoogerheide, P.A. Gurnev, T.K. Rostovtseva, S.M. Bezrukov, Effect of a post-translational modification mimic on protein translocation through a nanopore, Nanoscale 12 (2020) 11070.
[38] W.Q. Zhou, H. Qiu, Y.F. Guo, W.L. Guo, Molecular insights into distinct detection properties of a-Hemolysin, MspA, CsgG, and aerolysin nanopore sensors, J. Phys. Chem. B 124 (9) (2020) 1611–1618.
[39] G. Huang, A. Voet, G. Maglia, FraC nanopores with adjustable diameter identify the mass of opposite-charge peptides with 44 dalton resolution, Nat Commun. 10 (2019) 835.
[40] L. Restrepo-Perez, C.H. Wong, G. Maglia, C. Dekker, C. Joo, Label-free detection of post-translational modifications with a nanopore, Nano Lett. 19 (11) (2019) 7957–7964.
[41] K. Willems, D. Ruic, A. Biesemans, N.S. Galenkamp, P. Van Dorpe, G. Maglia, Engineering and modeling the electrophoretic trapping of a single protein inside a nanopore, ACS Nano 13 (9) (2019) 9980–9992.
[42] N.S. Galenkamp, M. Soskine, J. Hermans, C. Wloka, G. Maglia, Direct electrical quantification of glucose and asparagine from bodily fluids using nanopores, Nat. Commun. 9 (2018) 4085.
[43] C. Wloka, V. Van Meervelt, D. van Gelder, N. Danda, N. Jager, C.P. Williams, G. Maglia, Label-free and real-time detection of protein ubiquitination with a biological nanopore, ACS Nano 11 (5) (2017) 4387–4394.
[44] N.S. Galenkamp, A. Biesemans, G. Maglia, Directional conformer exchange in dihydrofolate reductase revealed by single-molecule nanopore recordings, Nat. Chem. 12 (5) (2020) 481–488.
[45] C. Cao, N. Cirauqui, M.J. Marcaida, E. Buglakova, A. Duperrex, A. Radenovic, M. Dal Peraro, Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores, Nat. Commun. 10 (2019) 4918.
[46] H. Ouldali, K. Sarthak, T. Ensslen, F. Piguet, P. Manivet, J. Pelta, J.C. Behrends, A. Aksimentiev, A. Oukhaled, Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore, Nat. Biotechnol. 38 (2) (2020) 176– 181.
[47] K. Sun, Y. Ju, C. Chen, P. Zhang, E. Sawyer, Y.F. Luo, J. Geng, Single-molecule interaction of peptides with a biological nanopore for identification of protease activity, Small Methods (2020) 1900892.
[48] G.K. Binnig, H. Rohrer, Scanning tunneling microscopy-from birth to adolescence, Rev. Mod. Phys. 59 (615) (1987) 615–625.
[49] G. Binnig, C.F. Quate, C.H. Gerber, Atomic force microscope, Phys. Rev. Lett. 56 (9) (1986) 930–933.
[50] Q.J. Chi, O. Farver, J. Ulstrup, Long-range protein electron transfer observed at the single-molecule level: In situ mapping of redox-gated tunneling resonance, Proc. Natl. Acad. Sci. 102 (45) (2005) 16203–16208.
[51] N.J. Tao, Probing potential-tuned resonant tunneling through redox molecules with scanning tunneling microscopy, Phys. Rev. Lett. 76 (21) (1996) 4066–4069.
[52] M.S. Inkpen, T. Albrecht, Probing electron transport in proteins at room temperature with single-molecule precision, ACS Nano 6 (1) (2012) 13–16.
[53] R.J. Sha, L.M. Xiang, C.R. Liu, A. Balaeff, Y.Q. Zhang, P. Zhang, Y.Q. Li, D.N. Beratan, N.J. Tao, N.C. Seeman, Charge splitters and charge transport junctions based on guanine quadruplexes, Nat. Nanotechnol. 13 (4) (2018) 316–321.
[54] X.Y. Xiao, B.Q. Xu, N.J. Tao, Changes in the conductance of single peptide molecules upon metal-ion binding, Angew. Chem. Int. Edit. 43 (45) (2004) 6148–6152.
[55] X.Y. Zhang, J. Shao, S.X. Jiang, B. Wang, Y. Zheng, Structure-dependent electrical conductivity of protein: its differences between alpha domain and beta-domain structures, Nanotechnology 26 (12) (2015) 125702.
[56] J.M. Brisendine, S. Refaely-Abramson, Z.F. Liu, J. Cui, F. Ng, J.B. Neaton, R.L. Koder, L. Venkataraman, Probing charge transport through peptide bonds, J. Phys. Chem. Lett. 9 (4) (2018) 763–767.
[57] A.C. Aragonès, E. Medina, M. Ferrer-Huerta, N. Gimeno, M. Teixidó, J.L. Palma, N.J. Tao, J.M. Ugalde, E. Giralt, I. Díez-Pérez, V. Mujica, Measuring the spinpolarization power of a single chiral molecule, Small 13 (2) (2017) 1602519.
[58] X.Y. Zhuang, A.H. Zhang, S.Y. Qiu, C. Tang, S.Q. Zhao, H.C. Li, Y.H. Zhang, Y.L. Wang, B.J. Wang, B.S. Fang, W.J. Hong, Coenzyme coupling boosts charge transport through single bioactive enzyme junctions, iScience, 23 (4) (2020) 101001.
[59] L. Venkataraman, J.E. Klare, C. Nuckolls, M.S. Hybertsen, M.L. Steigerwald, Dependence of single-molecule junction conductance on molecular conformation, Nature 442 (7105) (2006) 904–907.
[60] S. Huang, J. He, S.A. Chang, P.M. Zhang, F. Liang, S.Q. Li, M. Tuchband, A. Fuhrmann, R. Ros, S. Lindsay, Identifying single bases in a DNA oligomer with electron tunnelling, Nat. Nanotechnol. 5 (12) (2010) 868–873.
[61] B.Q. Xu, X.Y. Xiao, X.M. Yang, L. Zang, N.J. Tao, Large gate modulation in the current of a room temperature single molecule transistor, J. Am. Chem. Soc. 127 (8) (2005) 2386.
[62] F. Chen, J. He, C. Nuckolls, T. Roberts, J.E. Klare, S. Lindsay, A molecular switch based on potential-induced changes of oxidation state, Nano Lett. 5 (3) (2005) 503.
[63] J.M. Artés, I. Díez-Pérez, F. Sanz, P. Gorostiz, Direct measurement of electron transfer distance decay constants of single redox proteins by electrochemical tunneling spectroscopy, ACS Nano 5 (3) (2011) 2060–2066.
[64] M.P. Ruiz, A.C. Aragones, N. Camarero, J.G.M. Ortega, L.A. Zotti, R. Perez, J.C. Cuevas, P. Gorostiza, I. Diez-Perez, Bioengineering a single-protein junction, J. Am. Chem. Soc. 139 (43) (2017) 15337–15346.
[65] B.T. Zhang, H.Q. Deng, S. Mukherjee, W.S. Song, X. Wang, S. Lindsay, Engineering an enzyme for direct electrical monitoring of activity, ACS Nano 14 (2) (2020) 1360–1368.
[66] B.T. Zhang, W.S. Song, P. Pang, Y.N. Zhao, P.M. Zhang, I. Csabai, G. Vattay, S. Lindsay, Observation of giant conductance fluctuations in a protein, Nano Futures 1 (3) (2017) 035002.
[67] B.T. Zhang, W.S. Song, P. Pang, H.F. Lai, Q. Chen, P.M. Zhang, S. Lindsay, Role of contacts in long-range protein conductance, Proc. Natl. Acad. Sci. USA 116 (13) (2019) 5886–5891.
[68] B.T. Zhang, S. Lindsay, Electronic decay length in a protein molecule, Nano Lett. 19 (6) (2019) 4017–4022.
[69] B.T. Zhang, W.S. Song, J. Brown, R. Nemanich, S. Lindsay, Electronic conductance resonance in non-redox-active proteins, J. Am. Chem. Soc. 142 (13) (2020) 6432–6438.
[70] B. Voigtländer, Scanning probe microscopy: Atomic force microscopy and scanning tunneling microscopy, Springer, US, 2015.
[71] F.J. Giessibl, Atomic-resolution of the silicon (111)-(7x7) surface by atomicforce microscopy, Science 267 (5194) (1995) 68–71.
[72] H.B. Li, P. Zheng, Single molecule force spectroscopy: A new tool for bioinorganic chemistry, Curr. Opin. Chem. Biol. 43 (2018) 58–67.
[73] Y. Bao, Z.L. Luo, S.X. Cui, Environment-dependent single-chain mechanicsof synthetic polymers and biomacromolecules byatomic force microscopybased single-moleculeforce spectroscopy and the implications foradvanced polymer materials, Chem. Soc. Rev. 49 (2020) 2799.
[74] S. Ramachandran, F. Teran Arce, R. Lal, Potential role of atomic force microscopy in systems biology, Wires. Syst. Biol. Med. 3 (6) (2011) 702–716.
[75] F. Rico, L. Gonzalez, I. Casuso, M. Puig-Vidal, S. Scheuring, High-speed force spectroscopy unfolds titin at the velocity of molecular dynamics simulations, Science 342 (6159) (2013) 741–743.
[76] S. Lv, D.M. Dudek, Y. Cao, M.M. Balamurali, J. Gosline, H.B. Li, Designed biomaterials to mimic the mechanical properties of muscles, Nature 465 (7294) (2010) 69–73.
[77] B. Knoops, S. Becker, M.A. Poncin, J. Glibert, S. Derclaye, A. Clippe, D. Alsteens, Specific interactions measured by AFM on living cells between peroxiredoxin-5 and TLR4: Relevance for mechanisms of innate immunity, Cell Chem. Biol. 25 (5) (2018) 550–559.
[78] A. Sumino, T. Sumikama, T. Uchihashi, S. Oiki, High-speed AFM reveals accelerated binding of agitoxin-2 to a K+ channel by induced fit, Sci. Adv., 5 (2019) eaax0495.
[79] M.V. Sukhanova, S. Abrakhi, V. Joshi, D. Pastre, M.M. Kutuzov, R.O. Anarbaev, P.A. Curmi, L. Hamon, O.I. Lavrik, Single molecule detection of PARP1 and PARP2 interaction with DNA strand breaks and their poly(ADPribosyl)ation using high-resolution AFM imaging, Nucleic Acids Res. 44 (6) (2016) e60.
[80] E.L. Florin, V.T. Moy, H.E. Gaub, Adhesion forces between individual ligandreceptor pairs, Science 264 (5157) (1994) 415–417.
[81] D.H. Kim, J.E. Lee, Z.Y. Xu, K.R. Geem, Y. Kwon, J.W. Park, I. Hwang, Cytosolic targeting factor AKR2A captures chloroplast outer membrane-localized client proteins at the ribosome during translation, Nat. Commun. 6 (2015) 6843.
[82] R. Zhu, S. Howorka, J. Proll, F. Kienberger, J. Preiner, J. Hesse, A. Ebner, V.P. Pastushenko, H.J. Gruber, P. Hinterdorfer, Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns, Nat. Nanotechnol. 5 (11) (2010) 788–791.
[83] A.E.M. Beedle, A. Lezamiz, G. Stirnemann, S. Garcia-Manyes, The mechanochemistry of copper reports on the directionality of unfolding in model cupredoxin proteins, Nat. Commun. 6 (2015) 7894.
[84] J.H. Xia, J.C. Zuo, H.B. Li, Single molecule force spectroscopy reveals that the oxidation state of cobalt ions plays an important role in enhancing the mechanical stability of proteins, Nanoscale 11 (42) (2019) 19791–19796.
[85] R.C. Bernardi, E. Durner, C. Schoeler, K.H. Malinowska, B.G. Carvalho, E.A. Bayer, Z. Luthey-Schulten, H.E. Gaub, M.A. Nash, Mechanisms of nanonewton mechanostability in a protein complex revealed by molecular dynamics simulations and single-molecule force spectroscopy, J. Am. Chem. Soc. 141 (37) (2019) 14752–14763.
[86] J.A. Rivas-Pardo, J. Alegre-Cebollada, C.A. Ramirez-Sarmiento, J.M. Fernandez, V. Guixe, Identifying sequential substrate binding at the single-molecule level by enzyme mechanical stabilization, ACS Nano 9 (4) (2015) 3996–4005.
[87] A. Ashkin, J.M. Dziedzic, J.E. Bjorkholm, S. Chu, Observation of a single-beam gradient force optical trap for dielectric particles, Opt. Lett. 11 (5) (1986) 288– 290.
[88] K. Svoboda, C.F. Schmidt, B.J. Schnapp, S.M. Block, Direct observation of kinesin stepping by optical trapping interferometry, Nature 365 (6448) (1993) 721–727.
[89] J.T. Finer, R.M. Simmons, J.A. Spudich, Single myosin molecule mechanicspiconewton forces and nanometer steps, Nature 368 (6467) (1994) 113–119.
[90] D.B. Ritchie, M.T. Woodside, Probing the structural dynamics of proteins and nucleic acids with optical tweezers, Curr. Opin. Struc. Biol. 34 (2015) 43–51.
[91] K. Svoboda, S.M. Block, Biological applications of optical forces, Annu. Rev. Biophys. Biomol. Struct. 23 (1994) 247–285.
[92] Z. Ganim, M. Rief, Mechanically switching single-molecule fluorescence of GFP by unfolding and refolding, Proc. Natl. Acad. Sci. USA 114 (42) (2017) 11052–11056.
[93] E.M. Patrick, J.D. Slivka, B. Payne, M.J. Comstock, J.C. Schmidt, Observation of processive telomerase catalysis using high-resolution optical tweezers, Nat. Chem. Biol. 16 (2020) 801–812.
[94] M.D. Wang, H. Yin, R. Landick, J. Gelles, S.M. Block, Stretching DNA with optical tweezers, Biophys. J. 72 (3) (1997) 1335–1346.
[95] M. Caldarini, P. Sonar, I. Valpapuram, D. Tavella, C. Volonté, V. Pandini, M.A. Vanoni, A. Aliverti, R.A. Broglia, G. Tiana, C. Cecconi, The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer singlemolecule experiments and molecular dynamics simulations, Biophys. Chem. 195 (2014) 32–42.
[96] H. Wang, X.Q. Gao, X.D. Hu, X.T. Hu, C.G. Hu, H.B. Li, Mechanical unfolding and folding of a complex slipknot protein probed by using optical tweezers, Biochemistry 58 (47) (2019) 4751–4760.
[97] C.Z. He, S. Li, X.Q. Gao, A. Xiao, C.G. Hu, X.D. Hu, X.T. Hua, H.B. Li, Direct observation of the fast and robust folding of a slipknotted protein by optical tweezers, Nanoscale 11 (2019) 3945–3951.
[98] Y.X. Hao, C. Canavan, S.S. Taylor, R.A. Maillard, Integrated method to attach DNA handles and functionally select proteins to study folding and proteinligand interactions with optical tweezers, Sci. Rep. 7 (2017) 10843.
[99] B. Pelz, G. Zoldak, F. Zeller, M. Zacharias, M. Rief, Subnanometre enzyme mechanics probed by single-molecule force spectroscopy, Nat. Commun. 7 (2016) 10848.
[100] H. Wang, X.Q. Gao, H.B. Li, Single molecule force spectroscopy reveals the mechanical design governing the efficient translocation of the bacterial toxin protein RTX, J. Am. Chem. Soc. 141 (51) (2019) 20498–20506.
[101] D. Kostrz, H.K. Wayment-Steele, J.L. Wang, M. Follenfant, V.S. Pande, T.R. Strick, C. Gosse, A modular DNA scaffold to study protein-protein interactions at single-molecule resolution, Nat. Nanotechnol. 14 (2019) 988–993.
[102] M. Di Antonio, A. Ponjavic, A. Radzevicius, R.T. Ranasinghe, M. Catalano, X.Y. Zhang, J.Z. Shen, L.M. Needham, S.F. Lee, D. Klenerman, S. Balasubramanian, Single-molecule visualization of DNA G-quadruplex formation in live cells, Nat. Chem. 12 (2020) 832–837.
[103] L. Mejia, I. Franco, Force-conductance spectroscopy of a single-molecule reaction, Chem. Sci. 10 (11) (2019) 3249–3256.
[104] A. Pirrotta, L. De Vico, G.C. Solomon, I. Franco, Single-molecule forceconductance spectroscopy of hydrogen-bonded complexes, J. Chem. Phys. 146 (9) (2017) 092329.
[105] R.B. Zhou, B.R. Han, C.L. Xia, X.W. Zhuang, Membrane-associated periodic skeleton is a signaling platform for RTK transactivation in neurons, Science 365 (6456) (2019) 929–934.
[106] X.Y. Lin, A.P. Ivanov, J.B. Edel, Selective single molecule nanopore sensing of proteins using DNA aptamer- functionalised gold nanoparticles, Chem. Sci. 8 (5) (2017) 3905–3912.
[107] L. Restrepo-Perez, C. Joo, C. Dekker, Paving the way to single-molecule protein sequencing, Nat. Nanotechnol. 13 (9) (2018) 786–796.

Single-molecule biotechnology for protein researches

Single-molecule biotechnology for protein researches

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

本文评价

[1]	Xiaohong Zhou, Wenfeng Zhou, Wei Zhuang, Chenjie Zhu, Hanjie Ying, Hongman Zhang. Enhanced production of cytidine 5'-monophosphate using biocatalysis of di-enzymes immobilized on amino-functionalized sepharose[J]. 中国化学工程学报, 2023, 58(6): 40-52.
[2]	Xueying Zhu, Zhaoyang Zhang, Bin Jia, Yingjin Yuan. Current advances of biocontainment strategy in synthetic biology[J]. 中国化学工程学报, 2023, 56(4): 141-151.
[3]	Dahai Jiang, Zhidi Min, Jing Leng, Huanqing Niu, Yong Chen, Dong Liu, Chenjie Zhu, Ming Li, Wei Zhuang, Hanjie Ying. Characterization of two halophilic adenylate cyclases from Thermobifida halotolerans and Haloactinopolyspora alba[J]. 中国化学工程学报, 2023, 53(1): 56-62.
[4]	Xiaobo Ruan, Sheng Zhang, Wei Song, Jia Liu, Xiulai Chen, Liming Liu, Jing Wu. Efficient synthesis of tyrosol from L-tyrosine via heterologous Ehrlich pathway in Escherichia coli[J]. 中国化学工程学报, 2022, 47(7): 18-30.
[5]	Chunyu Zhang, Yan Sun, Xiaoyan Dong. Conjugation of a zwitterionic polymer with dimethyl chains to lipase significantly increases the enzyme activity and stability[J]. 中国化学工程学报, 2022, 47(7): 48-53.
[6]	Vladimir S. Derevschikov, Janna V. Veselovskaya, Anton S. Shalygin, Dmitry A. Yatsenko, Andrey Z. Sheshkovas, Oleg N. Martyanov. Operating limits and features of direct air capture on K₂CO₃/ZrO₂ composite sorbent[J]. 中国化学工程学报, 2022, 46(6): 11-20.
[7]	Yang Gui, Kai Cheng, Ruojiao Wang, Sirui Liu, Chenyang Zhao, Rui Zhang, Ming Wang, Zhen Cheng, Meng Yang. Photoacoustic detection of follicular thyroid carcinoma using targeted Nano-Au-Tripods[J]. 中国化学工程学报, 2022, 44(4): 1-7.
[8]	Ziheng Cui, Shiding Zhang, Shengyu Zhang, Biqiang Chen, Yushan Zhu, Tianwei Tan. Green biomanufacturing promoted by automatic retrobiosynthesis planning and computational enzyme design[J]. 中国化学工程学报, 2022, 41(1): 6-21.
[9]	Yumeng Zhang, Yingying Zhang, Xueling Pan, Yao Qin, Jiawei Deng, Shanshan Wang, Qingwei Gao, Yudan Zhu, Zhuhong Yang, Xiaohua Lu. Molecular insights on Ca²⁺/Na⁺ separation via graphene-based nanopores: The role of electrostatic interactions to ionic dehydration[J]. 中国化学工程学报, 2022, 41(1): 220-229.
[10]	Siyuan Gao, Yuanke Guo, Chen Ma, Ding Ma, Kequan Chen, Pingkai Ouyang, Xin Wang. Characterization and application of a recombinant dopa decarboxylase from Harmonia axyridis for the efficient biosynthesis of dopamine[J]. 中国化学工程学报, 2022, 41(1): 449-456.
[11]	Mingjie Wei, Yong Wang. Structure and dynamics of water in TiO₂ nano slits: The influence of interfacial interactions and pore sizes[J]. 中国化学工程学报, 2021, 29(3): 67-74.
[12]	Yanfeng Liu, Xiaomin Dong, Bin Wang, Rongzhen Tian, Jianghua Li, Long Liu, Guocheng Du, Jian Chen. Food synthetic biology-driven protein supply transition: From animal-derived production to microbial fermentation[J]. 中国化学工程学报, 2021, 29(2): 29-36.
[13]	Wenqiang Li, Wentao Sun, Chun Li. Engineered microorganisms and enzymes for efficiently synthesizing plant natural products[J]. 中国化学工程学报, 2021, 29(2): 62-73.
[14]	Huiling Wei, Mengyue Wu, Aili Fan, Haijia Su. Recombinant protein production in the filamentous fungus Trichoderma[J]. 中国化学工程学报, 2021, 29(2): 74-81.
[15]	Bekir Engin Eser, Yan Zhang, Li Zong, Zheng Guo. Self-sufficient Cytochrome P450s and their potential applications in biotechnology[J]. 中国化学工程学报, 2021, 29(2): 121-135.