Möller, L., Regnier, G., Labro, A. J., Blunck, R. & Snyders, D. J. Figuring out the right stoichiometry of Kv2.1/Kv6.4 heterotetramers, purposeful in a number of stoichiometrical configurations. Proc. Natl Acad. Sci. USA 117, 9365–9376 (2020).
Wieczorek, M. et al. Uneven molecular structure of the human γ-tubulin ring complicated. Cell 180, 165–175 (2020).
Hofmann, S. et al. Conformation area of a heterodimeric ABC exporter underneath turnover circumstances. Nature 571, 580–583 (2019).
Zhang, D. et al. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature 594, 454–458 (2021).
Lemmens, L. J. et al. Designed uneven protein meeting on a symmetric scaffold. Angew. Chem. Int. Ed. 59, 12113–12121 (2020).
Cordeiro, S. et al. Conotoxin kappaM-RIIIJ, a software concentrating on uneven heteromeric Kv1 channels. Proc. Natl Acad. Sci. USA 116, 1059–1064 (2019).
Su, Q. et al. Structural foundation for Ca2+ activation of the heteromeric PKD1L3/PKD2L1 channel. Nat. Commun. 12, 4871 (2021).
Laverty, D. et al. Cryo-EM construction of the human α1β3γ2 GABAA receptor in a lipid bilayer. Nature 565, 516–520 (2019).
Emiri et al. The IgM pentamer is an uneven pentagon with an open groove that binds the AIM protein. Sci. Adv. 4, eaau1199 (2018).
Rullo-Tubau, J. et al. Construction and mechanisms of transport of human Asc1/CD98hc amino acid transporter. Nat. Commun. 15, 2986 (2024).
Pavlenok, M., Yu, L., Herrmann, D., Wanunu, M. & Niederweis, M. Management of subunit stoichiometry in single-chain MspA nanopores. Biophys. J. 121, 742–754 (2022).
Kasianowicz, J. J., Brandin, E., Branton, D. & Deamer, D. W. Characterization of particular person polynucleotide molecules utilizing a membrane channel. Proc. Natl Acad. Sci. USA 93, 13770–13773 (1996).
Ying, Y.-L. et al. Nanopore-based applied sciences past DNA sequencing. Nat. Nanotechnol. 17, 1136–1146 (2022).
Branton, D. et al. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26, 1146–1153 (2008).
Manrao, E. A. et al. Studying DNA at single-nucleotide decision with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotechnol. 30, 349–353 (2012).
Steffensen, M. B., Rotem, D. & Bayley, H. Single-molecule evaluation of chirality in a multicomponent response community. Nat. Chem. 6, 603–607 (2014).
Shi, W. et al. Nanopore sensing. Anal. Chem. 89, 157–188 (2016).
Koch, C. et al. Nanopore sequencing of DNA-barcoded probes for extremely multiplexed detection of microRNA, proteins and small biomarkers. Nat. Nanotechnol. 18, 1483–1491 (2023).
Thakur, A. Ok. & Movileanu, L. Actual-time measurement of protein–protein interactions at single-molecule decision utilizing a organic nanopore. Nat. Biotechnol. 37, 96–101 (2019).
Galenkamp, N. S., Biesemans, A. & Maglia, G. Directional conformer change in dihydrofolate reductase revealed by single-molecule nanopore recordings. Nat. Chem. 12, 481–488 (2020).
Liu, Y. et al. Allosteric switching of calmodulin in a Mycobacterium smegmatis porin A (MspA) nanopore-trap. Angew. Chem. Int. Ed. 60, 23863–23870 (2021).
Xing, Y. et al. Extremely shape- and size-tunable membrane nanopores made with DNA. Nat. Nanotechnol. 17, 708–713 (2022).
Li, F., Gilliam, Ok., Pham, R. & Chen, M. Mapping the conformational power panorama of Abl kinase utilizing ClyA nanopore tweezers. Nat. Commun. 13, 3541 (2022).
Sutherland, T. C. et al. Construction of peptides investigated by nanopore evaluation. Nano Lett. 4, 1273–1277 (2004).
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).
Shimizu, Ok. et al. De novo design of a nanopore for single-molecule detection that comes with a β-hairpin peptide. Nat. Nanotechnol. 17, 67–75 (2022).
Xin, Ok. L. et al. 3D blockage mapping for figuring out familial level mutations in single amyloid-β peptides with a nanopore. Angew. Chem. Int. Ed. 61, e202209970 (2022).
Zhang, Y. et al. Peptide sequencing based mostly on host–visitor interaction-assisted nanopore sensing. Nat. Strategies 21, 102–109 (2024).
Cao, C. et al. Discrimination of oligonucleotides of various lengths with a wild-type aerolysin nanopore. Nat. Nanotechnol. 11, 713–718 (2016).
Liu, L. & Wu, H. C. DNA-based nanopore sensing. Angew. Chem. Int. Ed. 55, 15216–15222 (2016).
Workman, R. E. et al. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nat. Strategies 16, 1297–1305 (2019).
Boersma, A. J. & Bayley, H. Steady stochastic detection of amino acid enantiomers with a protein nanopore. Angew. Chem. Int. Ed. 124, 9744–9747 (2012).
Wang, J. et al. Identification of single amino acid chiral and positional isomers utilizing an electrostatically uneven nanopore. J. Am. Chem. Soc. 144, 15072–15078 (2022).
Ramsay, W. J. & Bayley, H. Single-molecule dedication of the isomers of d-glucose and d-fructose that bind to boronic acids. Angew. Chem. Int. Ed. 57, 2841–2845 (2018).
Cheley, S., Braha, O., Lu, X., Conlan, S. & Bayley, H. A purposeful protein pore with a ‘retro’ transmembrane area. Protein Sci. 8, 1257–1267 (1999).
Zhang, S. et al. A nanopore-based saccharide sensor. Angew. Chem. Int. Ed. 61, e202203769 (2022).
Howorka, S., Cheley, S. & Bayley, H. Sequence-specific detection of particular person DNA strands utilizing engineered nanopores. Nat. Biotechnol. 19, 636–639 (2001).
Zeid, L. A. et al. Separation of multiphosphorylated cyclopeptides and their positional isomers by hydrophilic interplay liquid chromatography (HILIC) coupled to electrospray ionization mass spectrometry (ESI-MS). J. Chromatogr. B 1177, 122792 (2023).
Tsuzuki, S. et al. Origin of attraction and directionality of the π/π interplay: mannequin chemistry calculations of benzene dimer interplay. J. Am. Chem. Soc. 124, 104–112 (2002).
Thakuria, R., Nath, N. Ok. & Saha, B. Ok. The character and purposes of π–π interactions: a perspective. Cryst. Development Des. 19, 523–528 (2019).
Burley, S. Ok. & Petsko, G. A. Fragrant–fragrant interplay: a mechanism of protein construction stabilization. Science 229, 23–28 (1985).
McGaughey, G. B., Gagne, M. & Rappe, A. Ok. π-stacking interactions: alive and effectively in proteins. J. Biol. Chem. 273, 15458–15463 (1998).
Li, M.-Y., Wang, Y.-Q., Lu, Y., Ying, Y.-L. & Lengthy, Y.-T. Single molecule examine of hydrogen bond interactions between single oligonucleotide and aerolysin sensing interface. Entrance. Chem. 7, 528 (2019).
Ouldali, H. et al. Electrical recognition of the twenty proteinogenic amino acids utilizing an aerolysin nanopore. Nat. Biotechnol. 38, 176–181 (2020).
Wu, X.-Y. et al. Exact building and tuning of an aerolysin single-biomolecule interface for single-molecule sensing. CCS Chem. 1, 304–312 (2019).
Liu, W. et al. Profiling single-molecule response kinetics underneath nanopore confinement. Chem. Sci. 13, 4109–4114 (2022).
Liu, W. et al. Observing confined native oxygen-induced reversible thiol/disulfide cycle with a protein nanopore. Angew. Chem. Int. Ed. 62, e202304023 (2023).
Jiang, J. et al. Protein nanopore reveals the renin–angiotensin system crosstalk with single-amino-acid decision. Nat. Chem. 15, 578–586 (2023).
Zhong C.-B. et al. Dice-SmartNano. Zenodo https://zenodo.org/data/11609574 (2024).
Zhang, L-L. et al. Excessive-throughput single biomarker identification utilizing droplet nanopore. Chem. Sci. 15, 8355–8362 (2024).
Li, M.-Y. et al. Revisiting the origin of nanopore present blockage for quantity distinction sensing on the atomic degree. JACS Au 1, 967–976 (2021).
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparability of easy potential features for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).
Humphrey, W., Dalke, A. & Schulten, Ok. VMD: Visible Molecular Dynamics. J. Mol. Graph. 14, 33–38 (1996).
Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005).
Finest, R. B. et al. Optimization of the additive CHARMM all-atom protein pressure subject concentrating on improved sampling of the spine ϕ, ψ and side-chain χ1 and χ2 dihedral angles. J. Chem. Principle Comput. 8, 3257–3273 (2012).
Vanommeslaeghe, Ok. et al. CHARMM normal pressure subject: a pressure subject for drug-like molecules suitable with the CHARMM all-atom additive organic pressure fields. J. Comput. Chem. 31, 671–690 (2010).
Feller, S. E., Zhang, Y., Pastor, R. W. & Brooks, B. R. Fixed stress molecular dynamics simulation: the Langevin piston technique. J. Chem. Phys. 103, 4613–4621 (1995).
York, D. M., Darden, T. A. & Pedersen, L. G. The impact of long-range electrostatic interactions in simulations of macromolecular crystals: a comparability of the Ewald and truncated listing strategies. J. Chem. Phys. 99, 8345–8348 (1993).
Allen, M. P. & Tildesley, D. J. Pc Simulation of Liquids (Oxford Univ. Press, 2017).
Case, D. A. et al. AmberTools. J. Chem. Inf. Mannequin. 63, 6183–6191 (2023).
Case, D. A. et al. Amber 2023 (Univ. California, San Francisco, 2023).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. CryoSPARC: algorithms for speedy unsupervised cryo-EM construction dedication. Nat. Strategies 14, 290–296 (2017).
Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Strategies 17, 1214–1221 (2020).
Rosenthal, P. B. & Henderson, R. Optimum dedication of particle orientation, absolute hand, and distinction loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory analysis and evaluation. J. Comput. Chem. 25, 1605–1612 (2004).
Liu, S.-C. & Lengthy, Y.-T. PyNanoLab. Zenodo https://doi.org/10.5281/zenodo.11383973 (2019).
Liu, W. et al. Single-molecule sensing inside stereo- and regio-defined hetero-nanopores. Zenodo https://zenodo.org/data/11371804 (2024).