Review

Proactive Manipulation Techniques for Protein Transport at Confined Nanoscale

  • Chaofan Ma ,
  • Wei Xu ,
  • Wei Liu ,
  • Changhui Xu ,
  • Jingjie Sha
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  • 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 date: 2023-04-20

  Online published: 2023-06-01

Supported by

National Natural Science Foundation of China(52075099); National Natural Science Foundation of China(52035003)

Abstract

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.

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 . DOI: 10.6023/A23040149

References

[1]
Thomas A.; Teicher B. A.; Hassan R. Lancet Oncol. 2016, 17, e254.
[2]
Carter P. J.; Lazar G. A. Nat. Rev. Drug Discov. 2018, 17, 197.
[3]
Strohl W. R. Protein Cell 2018, 9, 86.
[4]
Rodrigues R. C.; Berenguer-Murcia á.; Carballares D.; Morellon- Sterling R.; Fernandez-Lafuente R. Biotechnol. Adv. 2021, 52, 107821.
[5]
Rodrigues R. C.; Ortiz C.; Berenguer-Murcia á.; Torres R.; Fernández-Lafuente R. Chem. Soc. Rev. 2013, 42, 6290.
[6]
Basolo A.; Matrone A.; Elisei R.; Santini F. Semin. Cancer Biol. 2022, 79, 197.
[7]
Rizo J. Annu. Rev. Biophys. 2022, 51, 377.
[8]
Hetz C.; Soto C. CMLS, Cell. Mol. Life Sci. 2003, 60, 133.
[9]
Hofmann C.; Katus H. A.; Doroudgar S. Circulation 2019, 139, 2085.
[10]
Zhang Y.; Guo Y.; Xianyu Y.; Chen W.; Zhao Y.; Jiang X. Adv. Mater. 2013, 25, 3802.
[11]
Cohen L.; Walt D. R. Chem. Rev. 2019, 119, 293.
[12]
Vanova V.; Mitrevska K.; Milosavljevic V.; Hynek D.; Richtera L.; Adam V. Biosens. Bioelectron. 2021, 180, 113087.
[13]
Zhan K.; Li Z.; Chen J.; Hou Y.; Zhang J.; Sun R.; Bu Z.; Wang L.; Wang M.; Chen X.; Hou X. Nano Today 2020, 33, 100868.
[14]
Lu H.; Giordano F.; Ning Z. Genomics, Proteomics Bioinf. 2016, 14, 265.
[15]
Wang Y.; Zhao Y.; Bollas A.; Wang Y.; Au K. F. Nat. Biotechnol. 2021, 39, 1348.
[16]
Sha J.; Xu B.; Chen Y.; Yang Y. Acta Chim. Sinica 2017, 75, 1121. (in Chinese)
[16]
(沙菁?, 徐冰, 陈云飞, 杨颜菁, 化学学报, 2017, 75, 1121.)
[17]
Fu F.; Zhang Z.; Sun Q.; Xu B.; Sha J. Acta Chim. Sinica 2019, 77, 287. (in Chinese)
[17]
(傅方舟, 张志诚, 孙倩怡, 徐冰, 沙菁?, 化学学报, 2019, 77, 287.)
[18]
Wang Y.; Yu X.; Liu Y.; Xie X.; Cheng X.; Huang S.; Wang Z. Acta Chim. Sinica 2014, 72, 378. (in Chinese)
[18]
(王跃, 余旭丰, 刘芸芸, 谢骁, 程秀兰, 黄少铭, 王志民, 化学学报, 2014, 72, 378.)
[19]
Shendure J.; Balasubramanian S.; Church G. M.; Gilbert W.; Rogers J.; Schloss J. A.; Waterston R. H. Nature 2017, 550, 345.
[20]
Deamer D.; Akeson M.; Branton D. Nat. Biotechnol. 2016, 34, 518.
[21]
Lu S.; Wu X.; Li M.; Ying Y.; Long Y. View 2020, 1, 20200006.
[22]
Hu Z.; Huo M.; Ying Y.; Long Y. Angew. Chem., Int. Ed. 2021, 60, 14738.
[23]
Ying Y.-L.; Hu Z.-L.; Zhang S.; Qing Y.; Fragasso A.; Maglia G.; Meller A.; Bayley H.; Dekker C.; Long Y.-T. Nat. Nanotechnol. 2022, 17, 1136.
[24]
Nehra A.; Ahlawat S.; Singh K. P. Sens. Actuators, B 2019, 284, 595.
[25]
Ying Y.-L.; Zhang J.; Gao R.; Long Y.-T. Angew. Chem., Int. Ed. 2013, 52, 13154.
[26]
Zhan K.; Li Z.; Chen J.; Hou Y.; Zhang J.; Sun R.; Bu Z.; Wang L.; Wang M.; Chen X.; Hou X. Nano Today 2020, 33, 100868.
[27]
Hu R.; Rodrigues J. V.; Waduge P.; Yamazaki H.; Cressiot B.; Chishti Y.; Makowski L.; Yu D.; Shakhnovich E.; Zhao Q.; Wanunu M. ACS Nano 2018, 12, 4494.
[28]
Tripathi P.; Benabbas A.; Mehrafrooz B.; Yamazaki H.; Aksimentiev A.; Champion P. M.; Wanunu M. Proc. Natl. Acad. Sci. U.S.A. 2021, 118, e2016262118.
[29]
Waduge P.; Hu R.; Bandarkar P.; Yamazaki H.; Cressiot B.; Zhao Q.; Whitford P. C.; Wanunu M. ACS Nano 2017, 11, 5706.
[30]
Si W.; Aksimentiev A. ACS Nano 2017, 11, 7091.
[31]
Guo B.-Y.; Zeng T.; Wu H.-C. Sci. Bull. 2015, 60, 287.
[32]
Cressiot B.; Ouldali H.; Pastoriza-Gallego M.; Bacri L.; Van der Goot F. G.; Pelta J. ACS Sens. 2019, 4, 530.
[33]
Wang Y.; Gu L.-Q.; Tian K. Nanoscale 2018, 10, 13857.
[34]
Yan S.; Wang L.; Wang Y.; Cao Z.; Zhang S.; Du X.; Fan P.; Zhang P.; Chen H.; Huang S. Angew. Chem., Int. Ed. 2022, 61, e202116482.
[35]
Li F.; Fahie M. A.; Gilliam K. M.; Pham R.; Chen M. Nat. Commun. 2022, 13, 3541.
[36]
Versloot R. C. A.; Lucas F. L. R.; Yakovlieva L.; Tadema M. J.; Zhang Y.; Wood T. M.; Martin N. I.; Marrink S. J.; Walvoort M. T. C.; Maglia G. Nano Lett. 2022, 22, 5357.
[37]
Wang J.; Prajapati J. D.; Gao F.; Ying Y.-L.; Kleinekath?fer U.; Winterhalter M.; Long Y.-T. J. Am. Chem. Soc. 2022, 144, 15072.
[38]
Hu Z.; Huo M.; Ying Y.; Long Y. Angew. Chem., Int. Ed. 2021, 60, 14738.
[39]
Yin Y.-D.; Zhang L.; Leng X.-Z.; Gu Z.-Y. TrAC, Trends Anal. Chem. 2020, 133, 116091.
[40]
Ying Y.-L.; Long Y.-T. J. Am. Chem. Soc. 2019, 141, 15720.
[41]
Lucas F. L. R.; Versloot R. C. A.; Yakovlieva L.; Walvoort M. T. C.; Maglia G. Nat. Commun. 2021, 12, 5795.
[42]
Afshar Bakshloo M.; Kasianowicz J. J.; Pastoriza-Gallego M.; Mathé J.; Daniel R.; Piguet F.; Oukhaled A. J. Am. Chem. Soc. 2022, 144, 2716.
[43]
Sheng Y.; Zhou K.; Liu L.; Wu H. Angew. Chem. 2022, 134, e202200866.
[44]
Ouldali H.; Sarthak K.; Ensslen T.; Piguet F.; Manivet P.; Pelta J.; Behrends J. C.; Aksimentiev A.; Oukhaled A. Nat. Biotechnol. 2020, 38, 176.
[45]
Brinkerhoff H.; Kang A. S. W.; Liu J.; Aksimentiev A.; Dekker C. Science 2021, 374, 1509.
[46]
Xue L.; Yamazaki H.; Ren R.; Wanunu M.; Ivanov A. P.; Edel J. B. Nat. Rev. Mater. 2020, 5, 931.
[47]
Eggenberger O. M.; Ying C.; Mayer M. Nanoscale 2019, 11, 19636.
[48]
Deng T.; Li M.; Wang Y.; Liu Z. Sci. Bull. 2015, 60, 304.
[49]
Miles B. N.; Ivanov A. P.; Wilson K. A.; Do?an F.; Japrung D.; Edel J. B. Chem. Soc. Rev. 2013, 42, 15.
[50]
Sha J.; Si W.; Xu W.; Zou Y.; Chen Y. Sci. China: Technol. Sci. 2015, 58, 803.
[51]
Chen W.; Liu G.-C.; Ouyang J.; Gao M.-J.; Liu B.; Zhao Y.-D. Sci. China: Chem. 2017, 60, 721.
[52]
Arjmandi-Tash H.; Belyaeva L. A.; Schneider G. F. Chem. Soc. Rev. 2016, 45, 476.
[53]
Qiu H.; Zhou W.; Guo W. ACS Nano 2021, 15, 18848.
[54]
Su S.; Wang X.; Xue J. Mater. Horiz. 2021, 8, 1390.
[55]
Dai B.; Zhou R.; Ping J.; Ying Y.; Xie L. TrAC, Trends Anal. Chem. 2022, 154, 116658.
[56]
Hu R.; Rodrigues J. V.; Waduge P.; Yamazaki H.; Cressiot B.; Chishti Y.; Makowski L.; Yu D.; Shakhnovich E.; Zhao Q.; Wanunu M. ACS Nano 2018, 12, 4494.
[57]
Liu Y.; Pan T.; Wang K.; Wang Y.; Yan S.; Wang L.; Zhang S.; Du X.; Jia W.; Zhang P.; Chen H.-Y.; Huang S. Angew. Chem., Int. Ed. 2021, 60, 23863.
[58]
Freedman K. J.; Haq S. R.; Edel J. B.; Jemth P.; Kim M. J. Sci. Rep. 2013, 3, 1638.
[59]
Bandara Y. M. N. D. Y.; Farajpour K. J.; Freedman J. B. J. Am. Chem. Soc. 2022, 144, 3063.
[60]
Qiao L.; Slater G. W. J. Chem. Phys. 2020, 152, 144902.
[61]
Xue X.-G.; Zhao L.; Lu Z.-Y.; Li Z.-S. Phys. Lett. A 2012, 376, 290.
[62]
Polson J. M.; Hassanabad M. F.; McCaffrey A. J. Chem. Phys. 2013, 138, 024906.
[63]
Bucataru I. C.; Dragomir I.; Asandei A.; Pantazica A.-M.; Ghionescu A.; Branza-Nichita N.; Park Y.; Luchian T. Biosensors 2022, 12, 596.
[64]
Pandey D.; Bhattacharyya S. Appl. Math. Model. 2022, 111, 471.
[65]
Saharia J.;Bandara, Y. M. N. D. Y.; Karawdeniya, B. I.; Hammond, C.; Alexandrakis, G.; Kim, M. J. RSC Adv. 2021, 11, 24398.
[66]
Velasco A. E.; Friedman S. G.; Pevarnik M.; Siwy Z. S.; Taborek P. Phys. Rev. E 2012, 86, 025302.
[67]
Dabhade A.; Chauhan A.; Chaudhury S. ChemPhysChem 2022, 24, e202200666.
[68]
Fahie M. A.; Chen M. J. Phys. Chem. B 2015, 119, 10198.
[69]
Liu Y.; Deng Y.; Yang Y.; Qu Y.; Zhang C.; Li Y.-Q.; Zhao M.; Li W. Nanoscale Adv. 2021, 3, 5941.
[70]
Chinappi M.; Yamaji M.; Kawano R.; Cecconi F. ACS Nano 2020, 14, 15816.
[71]
Asandei A.; Schiopu I.; Chinappi M.; Seo C. H.; Park Y.; Luchian T. ACS Appl. Mater. Interfaces 2016, 8, 13166.
[72]
Firnkes M.; Pedone D.; Knezevic J.; D?blinger M.; Rant U. Nano Lett. 2010, 10, 2162.
[73]
Niu H.; Li M.-Y.; Ying Y.-L.; Long Y.-T. Chem. Sci. 2022, 13, 2456.
[74]
Li J.; Hu R.; Li X.; Tong X.; Yu D.; Zhao Q. Electrophoresis 2017, 38, 1130.
[75]
Saharia J.;Bandara, Y. M. N. D. Y.; Kim, M. J. Electrophoresis 2022, 43, 785.
[76]
Zhang Y.; Zhao J.; Si W.; Kan Y.; Xu Z.; Sha J.; Chen Y. Small Methods 2020, 4, 1900893.
[77]
Huang G.; Willems K.; Soskine M.; Wloka C.; Maglia G. Nat. Commun. 2017, 8, 935.
[78]
Ouldali H.; Sarthak K.; Ensslen T.; Piguet F.; Manivet P.; Pelta J.; Behrends J. C.; Aksimentiev A.; Oukhaled A. Nat. Biotechnol. 2020, 38, 176.
[79]
Wang X.; Thomas T.-M.; Ren R.; Zhou Y.; Zhang P.; Li J.; Cai S.; Liu K.; Ivanov A. P.; Herrmann A.; Edel J. B. J. Am. Chem. Soc. 2023, 145, 6371.
[80]
Sze J. Y. Y.; Ivanov A. P.; Cass A. E. G.; Edel J. B. Nat. Commun. 2017, 8, 1552.
[81]
Zhang X.; Luo D.; Zheng Y.-W.; Li X.-Q.; Song J.; Zhao W.-W.; Chen H.-Y.; Xu J.-J. ACS Nano 2022, 16, 15108.
[82]
Wang Z.; Hu R.; Zhu R.; Lu W.; Wei G.; Zhao J.; Gu Z.; Zhao Q. Small Methods 2022, 6, 2200743.
[83]
Lu B.; Hoogerheide D. P.; Zhao Q.; Zhang H.; Tang Z.; Yu D.; Golovchenko J. A. Nano Lett. 2013, 13, 3048.
[84]
Leong I. W.; Tsutsui M.; Yokota K.; Taniguchi M. Anal. Chem. 2021, 93, 16700.
[85]
Asandei A.; Di Muccio G.; Schiopu I.; Mereuta L.; Dragomir I. S.; Chinappi M.; Luchian T. Small Methods 2020, 4, 1900595.
[86]
Bell N. A. W.; Keyser U. F. J. Am. Chem. Soc. 2015, 137, 2035.
[87]
Liu W.; Yang Z.-L.; Yang C.-N.; Ying Y.-L.; Long Y.-T. Chem. Sci. 2022, 13, 4109.
[88]
Hwang H.-J.; Kim J.-S.; Lee J.; Min J. S.; Jeong K.-B.; Kim E.; Lee M.-K.; Chi S.-W. Anal. Chem. 2022, 94, 7449.
[89]
Wei R.; Gatterdam V.; Wieneke R.; Tampé R.; Rant U. Nat. Nanotechnol. 2012, 7, 257.
[90]
Yusko E. C.; Bruhn B. R.; Eggenberger O. M.; Houghtaling J.; Rollings R. C.; Walsh N. C.; Nandivada S.; Pindrus M.; Hall A. R.; Sept D.; Li J.; Kalonia D. S.; Mayer M. Nat. Nanotechnol. 2017, 12, 360.
[91]
Houghtaling J.; Ying C.; Eggenberger O. M.; Fennouri A.; Nandivada S.; Acharjee M.; Li J.; Hall A. R.; Mayer M. ACS Nano 2019, 13, 5231.
[92]
Lynch C. I.; Klesse G.; Rao S.; Tucker S. J.; Sansom M. S. P. ACS Nano 2021, 15, 19098.
[93]
Trick J. L.; Wallace E. J.; Bayley H.; Sansom M. S. P. ACS Nano 2014, 8, 11268.
[94]
Powell M. R.; Cleary L.; Davenport M.; Shea K. J.; Siwy Z. S. Nat. Nanotechnol. 2011, 6, 798.
[95]
Klesse G.; Tucker S. J.; Sansom M. S. P. ACS Nano 2020, 14, 10480.
[96]
Lucas F. L. R.; Sarthak K.; Lenting E. M.; Coltan D.; van der Heide N. J.; Versloot R. C. A.; Aksimentiev A.; Maglia G. ACS Nano 2021, 15, 9600.
[97]
Si W.; Yang H.; Wu G.; Zhang Y.; Sha J. Nanoscale 2021, 13, 15352.
[98]
Versloot R. C. A.; Lucas F. L. R.; Yakovlieva L.; Tadema M. J.; Zhang Y.; Wood T. M.; Martin N. I.; Marrink S. J.; Walvoort M. T. C.; Maglia G. Nano Lett. 2022, 22, 5357.
[99]
Li M.-Y.; Wang Y.-Q.; Ying Y.-L.; Long Y.-T. Chem. Sci. 2019, 10, 10400.
[100]
Willems K.; Rui? D.; Biesemans A.; Galenkamp N. S.; Van Dorpe P.; Maglia G. ACS Nano 2019, 13, 9980.
[101]
Liu S.-C.; Ying Y.-L.; Li W.-H.; Wan Y.-J.; Long Y.-T. Chem. Sci. 2021, 12, 3282.
[102]
Schmid S.; St?mmer P.; Dietz H.; Dekker C. Nat. Nanotechnol. 2021, 16, 1244.
[103]
Wen C.; Bertosin E.; Shi X.; Dekker C.; Schmid S. Nano Lett. 2022, 23, 788.
[104]
Pérez-Mitta G.; Burr L.; Tuninetti J. S.; Trautmann C.; Toimil-Molares M. E.; Azzaroni O. Nanoscale 2016, 8, 1470.
[105]
Spiering A.; Getfert S.; Sischka A.; Reimann P.; Anselmetti D. Nano Lett. 2011, 11, 2978.
[106]
Wu Y.; Chuah K.; Gooding J. J. Biosens. Bioelectron. 2020, 165, 112434.
[107]
Shang J.; Li Z.; Liu L.; Xi D.; Wang H. ACS Sens. 2018, 3, 512.
[108]
Hu R.; Lu W.; Wei G.; Nan H.; Li J.; Zhao Q. Adv. Mater. Technol. 2022, 7, 2200018.
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