{"id":352,"date":"2025-10-02T15:52:13","date_gmt":"2025-10-02T19:52:13","guid":{"rendered":"https:\/\/sites.nd.edu\/gtimp-lab\/?page_id=352"},"modified":"2025-10-26T10:35:15","modified_gmt":"2025-10-26T14:35:15","slug":"protein-sequencing-with-solid-state-nanopores","status":"publish","type":"page","link":"https:\/\/sites.nd.edu\/gtimp-lab\/?page_id=352","title":{"rendered":"Protein Sequencing with Solid State Nanopores"},"content":{"rendered":"
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\"\"<\/figure>\n<\/div>\n\n\n

MD simulations of the translocation of A\u03b21-42<\/sub> through a sub<\/em>-nanopore in silica are shown above. <\/strong>Visual molecular dynamics (VMD) snapshots are shown depicting three amino acid residues, arginine (R), aspartic acid (D) and glycine (G) translocating through a sub<\/em>-nanopore. The sub<\/em>-nanopore spanned a 4.0 nm<\/em> thick membrane with a bi-conical topography defined by a cone angle of q<\/em>1<\/sub> = 10\u00b0 and a 0.4 nm<\/em> diameter at the waist.  The pore is ghosted in the figure; only the water molecules, the peptide fragments and the Na<\/em>+<\/sup> (yellow\/green) and Cl<\/em>–<\/sup> (blue) ions are represented. -Courtesy of Archith Rayabharam and Narayana Aluru<\/p>\n\n\n\n

Paul A, Rayabharam A, Almonte L, Rigo E, Joseph J, Kumar A, Dong Z, Aluru N, and Timp G, “Peptide Sequencing With Single Acid Resolution Using a Sub-Nanometer Diameter Pore” Adv. Funct. Mater. 2025, e15800 e15800, DOI: 10.1002\/adfm.202515800 Link to publication.<\/a><\/p>\n\n\n\n

Timp W, and Timp G, “Beyond Mass Spectrometry, the Next Step in Proteomics” Science Advances, published online 10 January 2020. doi: 10.1126\/sciadv.aax8978. Link to publication.<\/a><\/p>\n\n\n\n

Rigo E, Dong Z, Park JH, Kennendy E, Hokmabadi M, Almonte-Garcia L, Ding L, Aluru N, and Timp G, “Measurements of the Size and Correlations between Ions using an Electrolytic Point Contact” Nature Communications, published online 30 May 2019. doi: 10.1038\/s41467-019-10265-2. Link to publication.<\/a><\/p>\n\n\n\n

Dong Z, Kennedy E, Hokmabadi M, and Timp G, “Discriminating Residue Substitutions in a Single Protein Molecule Using a Sub-nanopore” ACS Nano, published online 24 May 2017. doi: 10.1021\/acsnano.6b08452. Link to publication.<\/a><\/p>\n\n\n\n

Kennedy E, Dong Z, Tennant C, and Timp G, “Reading the primary structure of a protein with 0.07 nm3<\/sup> resolution using a subnanometre-diameter pore” Nature Nanotechnology, published online 25 July 2016. doi: 10.1038\/NNANO.2016.120. Link to publication.<\/a><\/p>\n\n\n\n

Eisenstein M, “Teaching nanopores to speak protein” Nature Methods 13, 715 (2016) doi: 10.1038\/nmeth.3988. Link to publication.<\/a><\/p>\n\n\n\n

Kolmogorov M, Kennedy E, Dong Z, Timp G, Pevzner P, “Single-Molecule Protein Identification by Sub-Nanopore Sensors” PLOS Computational Biology doi: https:\/\/doi.org\/10.1371\/hournal.pcbi.1005356. Link to publication.<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

MD simulations of the translocation of A\u03b21-42 through a sub-nanopore in silica are shown above. Visual molecular dynamics (VMD) snapshots are shown depicting three amino acid residues, arginine (R), aspartic acid (D) and glycine (G) translocating through a sub-nanopore. The sub-nanopore spanned a 4.0 nm thick membrane with a bi-conical topography defined by a cone … Continue reading “Protein Sequencing with Solid State Nanopores”<\/span><\/a><\/p>\n","protected":false},"author":5046,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_monsterinsights_skip_tracking":false,"footnotes":""},"class_list":["post-352","page","type-page","status-publish","hentry"],"yoast_head":"\nProtein Sequencing with Solid State Nanopores - TIMP NANO-BIO LAB<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sites.nd.edu\/gtimp-lab\/?page_id=352\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Protein Sequencing with Solid State Nanopores - TIMP NANO-BIO LAB\" \/>\n<meta property=\"og:description\" content=\"MD simulations of the translocation of A\u03b21-42 through a sub-nanopore in silica are shown above. 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