Zephyrnet Logo

Full-length single-molecule protein fingerprinting – Nature Nanotechnology

Date:

  • Aebersold, R. et al. How many human proteoforms are there? Nat. Chem. Biol. 14, 206–214 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, H. K., Pham, M. H. C., Ko, K. S., Rhee, B. D. & Han, J. Alternative splicing isoforms in health and disease. Pflügers Arch. 470, 995–1016 (2018).

  • Paronetto, M. P., Passacantilli, I. & Sette, C. Alternative splicing and cell survival: from tissue homeostasis to disease. Cell Death Differ. 23, 1919–1929 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lin, H. & Caroll, K. S. Introduction: posttranslational protein modification. Chem. Rev. 118, 887–888 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Carbonara, K., Andonovski, M. & Coorssen, J. R. Proteomes are of proteoforms: embracing the complexity. Proteomes 9, 38 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Benson, M. D., Ngo, D., Ganz, P. & Gerszten, R. E. Emerging affinity reagents for high throughput proteomics: trust, but verify. Circulation 140, 1610–1612 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yang, Y. et al. Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity. Nat. Commun. 7, 13397 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Čaval, T., Tian, W., Yang, Z., Clausen, H. & Heck, A. J. R. Direct quality control of glycoengineered erythropoietin variants. Nat. Commun. 9, 3342 (2018).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Siuti, N. & Kelleher, N. L. Decoding protein modifications using top-down mass spectrometry. Nat. Methods 410, 817–821 (2007).

    Article 

    Google Scholar
     

  • Wang, Y., Zhao, Y., Bollas, A., Wang, Y. & Au, K. F. Nanopore sequencing technology, bioinformatics and applications. Nat. Biotechnol. 39, 1348–1365 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ardui, S., Ameur, A., Vermeesch, J. R. & Hestand, M. S. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res. 46, 2159–2168 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Restrepo-Pérez, L., Joo, C. & Dekker, C. Paving the way to single-molecule protein sequencing. Nat. Nanotechnol. 13, 786–796 (2018).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Alfaro, J. A. et al. The emerging landscape of single-molecule protein sequencing technologies. Nat. Methods 18, 604–617 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Floyd, B. M. & Marcotte, E. M. Protein sequencing, one molecule at a time. Annu. Rev. Biophys. 51, 181–200 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Timp, W. & Timp, G. Beyond mass spectrometry, the next step in proteomics. Sci. Adv. 6, eaax8978 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Swaminathan, J., Boulgakov, A. A. & Marcotte, E. M. A theoretical justification for single molecule peptide sequencing. PLoS Comput. Biol. 11, e1004080 (2015).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rodriques, S. G., Marblestone, A. H. & Boyden, E. S. A theoretical analysis of single molecule protein sequencing via weak binding spectra. PLoS ONE 14, e0212868 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yao, Y., Docter, M., Van Ginkel, J., De Ridder, D. & Joo, C. Single-molecule protein sequencing through fingerprinting: computational assessment. Phys. Biol. 12, 10–16 (2015).

    Article 

    Google Scholar
     

  • de Lannoy, C. V. et al. Evaluation of FRET X for single-molecule protein fingerprinting. iScience 24, 103239 (2021).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

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

  • van Ginkel, J. et al. Single-molecule peptide fingerprinting. Proc. Natl Acad. Sci. USA 115, 3338–3343 (2018).

  • Swaminathan, J. et al. Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures. Nat. Biotechnol. 36, 1076–1082 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Shrestha, P. et al. Single-molecule mechanical fingerprinting with DNA nanoswitch calipers. Nat. Nanotechnol. 16, 1362–1370 (2021).

  • Filius, M., Kim, S. H., Severins, I. & Joo, C. High-resolution single-molecule FRET via DNA exchange (FRET X). Nano Lett. 21, 3295–3301 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Filius, M., van Wee, R. & Joo, C. in Single Molecule Analysis: Methods and Protocols (eds Heller, I. et al.) 203–213 (Springer, 2024).

  • Van Wee, R., Filius, M. & Joo, C. Completing the canvas: advances and challenges for DNA-PAINT super-resolution imaging. Trends Biochem. Sci. 11, 918–930 (2021).


    Google Scholar
     

  • Schnitzbauer, J., Strauss, M. T., Schlichthaerle, T., Schueder, F. & Jungmann, R. Super-resolution microscopy with DNA-PAINT. Nat. Protoc. 12, 1198–1228 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shi, X. et al. Quantitative fluorescence labeling of aldehyde-tagged proteins for single-molecule imaging. Nat. Methods 9, 499–503 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schuler, B. & Hofmann, H. Single-molecule spectroscopy of protein folding dynamics—expanding scope and timescales. Curr. Opin. Struct. Biol. 23, 36–47 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yang, X. & Qian, K. Protein O-GlcNAcylation: emerging mechanisms and functions. Nat. Rev. Mol. Cell Biol. 18, 452–465 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vellosillo, P. & Minguez, P. A global map of associations between types of protein posttranslational modifications and human genetic diseases. iScience 24, 102917 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mauri, T. et al. O-GlcNAcylation prediction: an unattained objective. Adv. Appl. Bioinform. Chem. 14, 87–102 (2021).

  • Shi, J., Ruijtenbeek, R. & Pieters, R. J. Demystifying O-GlcNAcylation: hints from peptide substrates. Glycobiology 28, 814–824 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shen, D. L. et al. Catalytic promiscuity of O-GlcNAc transferase enables unexpected metabolic engineering of cytoplasmic proteins with 2-azido-2-deoxy-glucose. ACS Chem. Biol. 12, 206–213 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mayer, A., Gloster, T. M., Chou, W. K., Vocadlo, D. J. & Tanner, M. E. 6′-Azido-6′-deoxy-UDP-N-acetylglucosamine as a glycosyltransferase substrate. Bioorg. Med. Chem. Lett. 21, 1199–1201 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Macdonald, J. I., Munch, H. K., Moore, T. & Francis, M. B. One-step site-specific modification of native proteins with 2-pyridinecarboxyaldehydes. Nat. Chem. Biol. 11, 326–331 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, S. et al. S100A8/A9 in inflammation. Front. Immunol. 9, 1298 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vijayan, A. L. et al. Procalcitonin: a promising diagnostic marker for sepsis and antibiotic therapy. J. Intensive Care 5, 51 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Senior, A. W. et al. Improved protein structure prediction using potentials from deep learning. Nature 577, 706–710 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jungmann, R. et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat. Methods 11, 313–318 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Erickson, H. P. Size and shape of protein molecules at the nanometer level determined by sedimentation, gel filtration, and electron microscopy. Biol. Proced. Online 11, 32–51 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ree, R., Varland, S. & Arnesen, T. Spotlight on protein N-terminal acetylation. Exp. Mol. Med. 50, 1–13 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bloom, S. et al. Decarboxylative alkylation for site-selective bioconjugation of native proteins via oxidation potentials. Nat. Chem. 10, 205–211 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ramirez, D. H. et al. Engineering a proximity-directed O-GlcNAc transferase for selective protein O-GlcNAcylation in cells. ACS Chem. Biol. 15, 1059–1066 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yang, Y.-Y., Ascano, J. M. & Hang, H. C. Bioorthogonal chemical reporters for monitoring protein acetylation. J. Am. Chem. Soc. 132, 3640–3641 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Westcott, N. P., Fernandez, J. P., Molina, H. & Hang, H. C. Chemical proteomics reveals ADP-ribosylation of small GTPases during oxidative stress. Nat. Chem. Biol. 13, 302–308 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rabuka, D., Hubbard, S. C., Laughlin, S. T., Argade, S. P. & Bertozzi, C. R. A chemical reporter strategy to probe glycoprotein fucosylation. J. Am. Chem. Soc. 128, 12078–12079 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Boeggeman, E. et al. Direct identification of nonreducing GlcNAc residues on N-glycans of glycoproteins using a novel chemoenzymatic method. Bioconjugate Chem. 18, 806–814 (2007).

    Article 
    CAS 

    Google Scholar
     

  • van Geel, R. et al. Chemoenzymatic conjugation of toxic payloads to the globally conserved N-glycan of native mAbs provides homogeneous and highly efficacious antibody–drug conjugates. Bioconjugate Chem. 26, 2233–2242 (2015).

    Article 

    Google Scholar
     

  • Tate, E. W., Kalesh, K. A., Lanyon-Hogg, T., Storck, E. M. & Thinon, E. Global profiling of protein lipidation using chemical proteomic technologies. Curr. Opin. Chem. Biol. 24, 48–57 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Anderson, N. L. & Anderson, N. G. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteom. 1, 845–867 (2002).

    Article 
    CAS 

    Google Scholar
     

  • Han, X., Aslanian, A. & Yates, J. R. Mass spectrometry for proteomics. Curr. Opin. Chem. Biol. 12, 483–490 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Filius, M. et al. High-speed super-resolution imaging using protein-assisted DNA-PAINT. Nano Lett. 20, 2264–2270 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, S. H., Kim, H., Jeong, H. & Yoon, T. Y. Encoding multiple virtual signals in DNA barcodes with single-molecule FRET. Nano Lett. 21, 1694–1701 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • McCann, J. J., Choi, U. B., Zheng, L., Weninger, K. & Bowen, M. E. Optimizing methods to recover absolute FRET efficiency from immobilized single molecules. Biophys. J. 99, 961–970 (2010).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cristianini, N. & Shawe-Taylor, J. An Introduction to Support Vector Machines and Other Kernel-based Learning Methods (Cambridge University Press, 2000).

  • Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).

    MathSciNet 

    Google Scholar
     

  • Pabst, M. et al. A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium. ISME J. 16, 346–357 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chuh, K. N., Zaro, B. W., Piller, F., Piller, V. & Pratt, M. R. Changes in metabolic chemical reporter structure yield a selective probe of O-GlcNAc modification. J. Am. Chem. Soc. 136, 12283–12295 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • spot_img

    Latest Intelligence

    spot_img