15.3 C
Canberra
Wednesday, October 22, 2025

Full-length protein classification by way of cysteine fingerprinting in solid-state nanopores


  • Singh, A. In direction of resolving proteomes in single cells. Nat. Strategies 18, 856 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bennett, H. M., Stephenson, W., Rose, C. M. & Darmanis, S. Single-cell proteomics enabled by next-generation sequencing or mass spectrometry. Nat. Strategies 20, 363–374 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • MacCoss, M. J. et al. Sampling the proteome by rising single-molecule and mass spectrometry strategies. Nat. Strategies 20, 339–346 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alfaro, J. A. et al. The rising panorama of single-molecule protein sequencing applied sciences. Nat. Strategies 18, 604–617 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ouldali, H. et al. Electrical recognition of the twenty proteinogenic amino acids utilizing an aerolysin nanopore. Nat. Biotechnol. 38, 176–181 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yusko, E. C. et al. Actual-time form approximation and fingerprinting of single proteins utilizing a nanopore. Nat. Nanotechnol. 12, 360–367 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jiang, J. et al. Protein nanopore reveals the renin–angiotensin system crosstalk with single-amino-acid decision. Nat. Chem. 15, 578–586 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Martin-Baniandres, P. et al. Enzyme-less nanopore detection of post-translational modifications inside lengthy polypeptides. Nat. Nanotechnol. 18, 1335–1340 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Reed, B. D. et al. Actual-time dynamic single-molecule protein sequencing on an built-in semiconductor machine. Science 378, 186–192 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Swaminathan, J. et al. Extremely parallel single-molecule identification of proteins in zeptomole-scale mixtures. Nat. Biotechnol. 36, 1076–1091 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Brinkerhoff, H., Kang, A. S. W., Liu, J., Aksimentiev, A. & Dekker, C. A number of rereads of single proteins at single-amino acid decision utilizing nanopores. Science 374, 1509–1513 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ohayon, S. et al. Full‐size single protein molecules monitoring and counting in skinny silicon channels. Adv. Mater. 36, 2314319 (2024).

    Article 
    CAS 

    Google Scholar
     

  • Filius, M. et al. Full-length single-molecule protein fingerprinting. Nat. Nanotechnol. 5, 652–659 (2024).

    Article 

    Google Scholar
     

  • Wang, Ok. et al. Unambiguous discrimination of all 20 proteinogenic amino acids and their modifications by nanopore. Nat. Strategies 21, 92–101 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Zhang, M. et al. Actual-time detection of 20 amino acids and discrimination of pathologically related peptides with functionalized nanopore. Nat. Strategies 21, 609–618 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yu, L. et al. Unidirectional single-file transport of full-length proteins by means of a nanopore. Nat. Biotechnol. 41, 1130–1139 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Soni, N., Freundlich, N., Ohayon, S., Huttner, D. & Meller, A. Single-file translocation dynamics of SDS-denatured, complete proteins by means of sub-5 nm solid-state nanopores. ACS Nano 16, 11405–11414 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sauciuc, A., Morozzo della Rocca, B., Tadema, M. J., Chinappi, M. & Maglia, G. Translocation of linearized full-length proteins by means of an engineered nanopore below opposing electrophoretic drive. Nat. Biotechnol. 42, 1275–1281 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Restrepo-Pérez, L., John, S., Aksimentiev, A., Joo, C. & Dekker, C. SDS-assisted protein transport by means of solid-state nanopores. Nanoscale 9, 11685–11693 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Motone, Ok. et al. Multi-pass, single-molecule nanopore studying of lengthy protein strands. Nature 633, 662–669 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sauciuc, A. & Maglia, G. Managed translocation of proteins by means of a organic nanopore for single-protein fingerprint identification. Nano. Lett. 24, 14118–14124 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Qing, Y., Ionescu, S. A., Pulcu, G. S. & Bayley, H. Directional management of a processive molecular hopper. Science 361, 908–912 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Thakur, M. et al. Wafer-scale fabrication of nanopore gadgets for single-molecule DNA biosensing utilizing MoS2. Small Strategies 4, 2000072 (2020).

    Article 
    CAS 

    Google Scholar
     

  • De Vreede, L. J. et al. Wafer-scale fabrication of fused silica chips for low-noise recording of resistive pulses by means of nanopores. Nanotechnology 30, 265301 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Leitao, S. M. et al. Spatially multiplexed single-molecule translocations by means of a nanopore at managed speeds. Nat. Nanotechnol. 18, 1078–1084 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Liu, H., Zhou, Q., Wang, W., Fang, F. & Zhang, J. Strong-state nanopore array: manufacturing and functions. Small 19, 2205680 (2023).

    Article 
    CAS 

    Google Scholar
     

  • Kim, M. J., Wanunu, M., Bell, D. C. & Meller, A. Fast fabrication of uniformly sized nanopores and nanopore arrays for parallel DNA evaluation. Adv. Mater. 18, 3149–3153 (2006).

    Article 
    CAS 

    Google Scholar
     

  • Yuan, Z., Lei, X. & Wang, C. Controllable fabrication of strong state nanopores array by electron beam shrinking. Int. J. Mach. Instruments Manuf. 159, 103623 (2020).

    Article 

    Google Scholar
     

  • Verschueren, D. V., Yang, W. & Dekker, C. Lithography-based fabrication of nanopore arrays in freestanding SiN and graphene membranes. Nanotechnology 29, 145302 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dela Torre, R., Larkin, J., Singer, A. & Meller, A. Fabrication and characterization of solid-state nanopore arrays for high-throughput DNA sequencing. Nanotechnology 23, 385308 (2012).

    Article 
    PubMed Central 

    Google Scholar
     

  • Zvuloni, E., Zrehen, A., Gilboa, T. & Meller, A. Quick and deterministic fabrication of sub-5 nanometer solid-state pores by feedback-controlled laser processing. ACS Nano 15, 12189–12200 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Giannopoulos, I., Mochi, I., Vockenhuber, M., Ekinci, Y. & Kazazis, D. Excessive ultraviolet lithography reaches 5 nm decision. Nanoscale 16, 15533–15543 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wanunu, M., Sutin, J., McNally, B., Chow, A. & Meller, A. DNA translocation ruled by interactions with solid-state nanopores. Biophys. J. 95, 4716–4725 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Soni, N., Chandra Verma, N., Talor, N. & Meller, A. Over 30-fold enhancement in DNA translocation dynamics by means of nanoscale pores coated with an anionic surfactant. Nano Lett. 23, 4609–4616 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wells, D. B., Abramkina, V. & Aksimentiev, A. Exploring transmembrane transport by means of α-hemolysin with grid-steered molecular dynamics. J. Chem. Phys. 127, 125101 (2007).

    Article 
    PubMed 

    Google Scholar
     

  • Kowalczyk, S. W., Grosberg, A. Y., Rabin, Y. & Dekker, C. Modeling the conductance and DNA blockade of solid-state nanopores. Nanotechnology 22, 315101 (2011).

    Article 
    PubMed 

    Google Scholar
     

  • Mohapatra, S., Teherpuria, H., Mogurampelly, S., Downton, M. & Kannam, S. Ok. Ionic circulate by means of partially blocked nanopores. Phys. Chem. Chem. Phys. 26, 26911–26920 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sadasivan, H., Stiffler, D., Tirumala, A., Israeli, J. & Narayanasamy, S. Accelerated dynamic time warping on GPU for selective nanopore sequencing. J. Biotechnol. Biomed. 07, 137–148 (2024).

    Article 

    Google Scholar
     

  • Chesnokov, M. S. et al. Shift in VEGFA isoform stability in the direction of extra angiogenic variants is related to tumor stage and differentiation of human hepatocellular carcinoma. PeerJ 2018, e4915 (2018).

    Article 

    Google Scholar
     

  • Wanunu, M., Morrison, W., Rabin, Y., Grosberg, A. Y. & Meller, A. Electrostatic focusing of unlabelled DNA into nanoscale pores utilizing a salt gradient. Nat. Nanotechnol. 5, 160–165 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Comer, J., Dimitrov, V., Zhao, Q., Timp, G. & Aksimentiev, A. Microscopic mechanics of hairpin DNA translocation by means of artificial nanopores. Biophys. J. 96, 593–608 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zrehen, A., Gilboa, T. & Meller, A. Actual-time visualization and sub-diffraction restrict localization of nanometer-scale pore formation by dielectric breakdown. Nanoscale 9, 16437–16445 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Phillips, J. C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huang, J. & Mackerell, A. D. CHARMM36 all-atom additive protein drive discipline: validation primarily based on comparability to NMR knowledge. J. Comput. Chem. 34, 2135–2145 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yoo, J. & Aksimentiev, A. New methods for outdated canine: enhancing the accuracy of biomolecular drive fields by pair-specific corrections to non-bonded interactions. Phys. Chem. Chem. Phys. 20, 8432–8449 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparability of straightforward potential capabilities for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).

    Article 
    CAS 

    Google Scholar
     

  • Miyamoto, S. & Kollman, P. A. SETTLE: an analytical model of the SHAKE and RATTLE algorithm for inflexible water fashions. J. Comput. Chem. 13, 952–962 (1992).

    Article 
    CAS 

    Google Scholar
     

  • Andersen, H. C. RATTLE: a ‘velocity’ model of the SHAKE algorithm for molecular dynamics calculations. J. Comput. Phys. 52, 24–34 (1983).

    Article 
    CAS 

    Google Scholar
     

  • Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an Nlog(N) technique for Ewald sums in massive methods. J. Chem. Phys. 98, 10089–10092 (1993).

    Article 
    CAS 

    Google Scholar
     

  • Martyna, G. J., Tobias, D. J. & Klein, M. L. Fixed stress molecular dynamics algorithms. J. Chem. Phys. 101, 4177–4189 (1994).

    Article 
    CAS 

    Google Scholar
     

  • Aksimentiev, A. & Schulten, Ok. Imaging α-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map. Biophys. J. 88, 3745–3761 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Humphrey, W., Dalke, A. & Schulten, Ok. VMD: visible molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Permyakov, E. A. & Berliner, L. J. α-Lactalbumin: construction and performance. FEBS Lett. 473, 269–274 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Vanommeslaeghe, Ok., Raman, E. P. & MacKerell, A. D. Automation of the CHARMM Normal Power Discipline (CGenFF) II: project of bonded parameters and partial atomic fees. J. Chem. Inf. Mannequin 52, 3155–3168 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schmid, S., Stömmer, P., Dietz, H. & Dekker, C. Nanopore electro-osmotic lure for the label-free research of single proteins and their conformations. Nat. Nanotechnol. 16, 1244–1250 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Soni, N., Verma, N. C. & Meller, A. Full-length protein classification by way of cysteine fingerprinting in solid-state nanopores: supply knowledge and codes. Zenodo https://doi.org/10.5281/zenodo.16789170 (2025).

  • Related Articles

    LEAVE A REPLY

    Please enter your comment!
    Please enter your name here

    [td_block_social_counter facebook="tagdiv" twitter="tagdivofficial" youtube="tagdiv" style="style8 td-social-boxed td-social-font-icons" tdc_css="eyJhbGwiOnsibWFyZ2luLWJvdHRvbSI6IjM4IiwiZGlzcGxheSI6IiJ9LCJwb3J0cmFpdCI6eyJtYXJnaW4tYm90dG9tIjoiMzAiLCJkaXNwbGF5IjoiIn0sInBvcnRyYWl0X21heF93aWR0aCI6MTAxOCwicG9ydHJhaXRfbWluX3dpZHRoIjo3Njh9" custom_title="Stay Connected" block_template_id="td_block_template_8" f_header_font_family="712" f_header_font_transform="uppercase" f_header_font_weight="500" f_header_font_size="17" border_color="#dd3333"]
    - Advertisement -spot_img

    Latest Articles