[ad_1]
Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).
Restrepo-Pérez, L., Joo, C. & Dekker, C. Paving the way in which to single-molecule protein sequencing. Nat. Nanotechnol. 13, 786–796 (2018).
Callahan, N., Tullman, J., Kelman, Z. & Marino, J. Methods for growth of a next-generation protein sequencing platform. Tendencies Biochem. Sci. 45, 76–89 (2020).
Timp, W. & Timp, G. Past mass spectrometry, the subsequent step in proteomics. Sci. Adv. 6, eaax8978 (2020).
Alfaro, J. A. et al. The rising panorama of single-molecule protein sequencing applied sciences. Nat. Strategies 18, 604–617 (2021).
Swaminathan, J., Boulgakov, A. A. & Marcotte, E. M. A theoretical justification for single molecule peptide sequencing. PLoS Comput. Biol. 11, e1004080 (2015).
Yao, Y., Docter, M., van Ginkel, J., de Ridder, D. & Joo, C. Single-molecule protein sequencing by means of fingerprinting: computational evaluation. Phys. Biol. 12, 055003 (2015).
Ohayon, S., Girsault, A., Nasser, M., Shen-Orr, S. & Meller, A. Simulation of single-protein nanopore sensing exhibits feasibility for whole-proteome identification. PLoS Comput. Biol. 15, e1007067 (2019).
van Ginkel, J. et al. Single-molecule peptide fingerprinting. Proc. Natl Acad. Sci. USA 115, 3338 (2018).
Swaminathan, J. et al. Extremely parallel single-molecule identification of proteins in zeptomole-scale mixtures. Nat. Biotechnol. 36, 1076–1082 (2018).
Rosen, C. B., Rodriguez-Larrea, D. & Bayley, H. Single-molecule site-specific detection of protein phosphorylation with a nanopore. Nat. Biotechnol. 32, 179–181 (2014).
Kennedy, E., Dong, Z., Tennant, C. & Timp, G. Studying the first construction of a protein with 0.07 nm3 decision utilizing a subnanometre-diameter pore. Nat. Nanotechnol. 11, 968–976 (2016).
Restrepo-Pérez, L., Wong, C. H., Maglia, G., Dekker, C. & Joo, C. Label-free detection of post-translational modifications with a nanopore. Nano Lett. 19, 7957–7964 (2019).
Ouldali, H. et al. Electrical recognition of the twenty proteinogenic amino acids utilizing an aerolysin nanopore. Nat. Biotechnol. 38, 176–181 (2020).
Zhao, Y. et al. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling. Nat. Nanotechnol. 9, 466–473 (2014).
Ohshiro, T. et al. Detection of post-translational modifications in single peptides utilizing electron tunnelling currents. Nat. Nanotechnol. 9, 835–840 (2014).
Koussa, M. A., Halvorsen, Ok., Ward, A. & Wong, W. P. DNA nanoswitches: a quantitative platform for gel-based biomolecular interplay evaluation. Nat. Strategies 12, 123–126 (2014).
Halvorsen, Ok., Schaak, D. & Wong, W. P. Nanoengineering a single-molecule mechanical swap utilizing DNA self-assembly. Nanotechnology 22, 494005 (2011).
Yang, D., Ward, A., Halvorsen, Ok. & Wong, W. P. Multiplexed single-molecule pressure spectroscopy utilizing a centrifuge. Nat. Commun. 7, 11026 (2016).
Kim, J., Zhang, C.-Z., Zhang, X. & Springer, T. A. A mechanically stabilized receptor–ligand flex-bond vital within the vasculature. Nature 466, 992–995 (2010).
Pfitzner, E. et al. Inflexible DNA beams for high-resolution single-molecule mechanics. Angew. Chem. Int. Ed. 52, 7766–7771 (2013).
Kilchherr, F. et al. Single-molecule dissection of stacking forces in DNA. Science 353, aaf5508 (2016).
Kostrz, D. et al. A modular DNA scaffold to review protein–protein interactions at single-molecule decision. Nat. Nanotechnol. 14, 988–993 (2019).
Gosse, C., Strick, T. R. & Kostrz, D. Molecular scaffolds: when DNA turns into the {hardware} for single-molecule investigations. Curr. Opin. Chem. Biol. 53, 192–203 (2019).
Ma, X. et al. Interactions between PHD3-bromo of MLL1 and H3K4me3 revealed by single-molecule magnetic tweezers in a parallel DNA circuit. Bioconjug Chem. 30, 2998–3006 (2019).
Hatch, Ok., Danilowicz, C., Coljee, V. & Prentiss, M. Demonstration that the shear pressure required to separate quick double-stranded DNA doesn’t improve considerably with sequence size for sequences longer than 25 base pairs. Phys. Rev. E. 78, 011920 (2008).
Watson, J. D. & Crick, F. H. C. Molecular construction of nucleic acids: a construction for deoxyribose nucleic acid. Nature 171, 737–738 (1953).
Woodside, M. T. et al. Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proc. Natl Acad. Sci. USA 103, 6190–6195 (2006).
Bustamante, C., Marko, J. F., Siggia, E. D. & Smith, S. Entropic elasticity of λ-phage DNA. Science 265, 1599–1600 (1994).
Abello, N., Kerstjens, H. A. M., Postma, D. S. & Bischoff, R. Selective acylation of major amines in peptides and proteins. J. Proteome Res. 6, 4770–4776 (2007).
Zhang, X., Halvorsen, Ok., Zhang, C.-Z., Wong, W. P. & Springer, T. A. Mechanoenzymatic cleavage of the ultralarge vascular protein von Willebrand issue. Science 324, 1330–1334 (2009).
Oesterhelt, F. et al. Unfolding pathways of particular person bacteriorhodopsins. Science 288, 143–146 (2000).
Carrion-Vazquez, M. et al. The mechanical stability of ubiquitin is linkage dependent. Nat. Struct. Mol. Biol. 10, 738–743 (2003).
Oda, E. et al. Noxa, a BH3-only member of the Bcl-2 household and candidate mediator of p53-induced apoptosis. Science 288, 1053 (2000).
Czabotar, P. E. et al. Structural insights into the degradation of Mcl-1 induced by BH3 domains. Proc. Natl Acad. Sci. USA 104, 6217 (2007).
Sattler, M. et al. Construction of Bcl-xL-Bak peptide complicated: recognition between regulators of apoptosis. Science 275, 983–986 (1997).
Apweiler, R. et al. UniProt: the Common Protein knowledgebase. Nucleic Acids Res. 32, D115–D119 (2004).
Adamczyk, M., Gebler, J. C. & Wu, J. Selective evaluation of phosphopeptides inside a protein combination by chemical modification, reversible biotinylation and mass spectrometry. Speedy Commun. Mass Spectrom. 15, 1481–1488 (2001).
Meinhart, A. & Cramer, P. Recognition of RNA polymerase II carboxy-terminal area by 3′-RNA-processing elements. Nature 430, 223–226 (2004).
Phatnani, H. P. & Greenleaf, A. L. Phosphorylation and features of the RNA polymerase II CTD. Genes Dev. 20, 2922–2936 (2006).
Kim, M., Suh, H., Cho, E. J. & Buratowski, S. Phosphorylation of the yeast Rpb1 C-terminal area at serines 2, 5, and seven. J. Biol. Chem. 284, 26421–26426 (2009).
Eick, D. & Geyer, M. The RNA polymerase II carboxy-terminal area (CTD) code. Chem. Rev. 113, 8456–8490 (2013).
Knight, Z. A. et al. Phosphospecific proteolysis for mapping websites of protein phosphorylation. Nat. Biotechnol. 21, 1047–1054 (2003).
Ribeck, N. & Saleh, O. A. Multiplexed single-molecule measurements with magnetic tweezers. Rev. Sci. Instrum. 79, 094301 (2008).
De Vlaminck, I. et al. Extremely parallel magnetic tweezers by focused DNA tethering. Nano Lett. 11, 5489–5493 (2011).
Cnossen, J. P., Dulin, D. & Dekker, N. H. An optimized software program framework for real-time, high-throughput monitoring of spherical beads. Rev. Sci. Instrum. 85, 103712 (2014).
Smith, S. B., Finzi, L. & Bustamante, C. Direct mechanical measurements of the elasticity of single DNA molecules through the use of magnetic beads. Science 258, 1122 (1992).
Danilowicz, C., Greenfield, D. & Prentiss, M. Dissociation of ligand–receptor complexes utilizing magnetic tweezers. Anal. Chem. 77, 3023–3028 (2005).
Shon, M. J., Rah, S.-H. & Yoon, T.-Y. Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers. Sci. Adv. 5, eaav1697 (2019).
Sen, Y.-H., Jain, T., Aguilar, C. A. & Karnik, R. Enhanced discrimination of DNA molecules in nanofluidic channels by means of a number of measurements. Lab. Chip 12, 1094–1101 (2012).
Keyser, U. F. et al. Direct pressure measurements on DNA in a solid-state nanopore. Nat. Phys. 2, 473–477 (2006).
Mulhall, E. M. et al. Single-molecule pressure spectroscopy reveals the dynamic energy of the hair-cell tip-link connection. Nat. Commun. 12, 849 (2021).
Bustamante, C., Chemla, Y. R. & Moffitt, J. R. Excessive-resolution dual-trap optical tweezers with differential detection: instrument design. Chilly Spring Harb. 2009, pdb.ip73 (2009).
Lipfert, J., Hao, X. & Dekker, N. H. Quantitative modeling and optimization of magnetic tweezers. Biophys. J. 96, 5040–5049 (2009).
Dulin, D. et al. Excessive spatiotemporal-resolution magnetic tweezers: calibration and purposes for DNA dynamics. Biophys. J. 109, 2113–2125 (2015).
De Vlaminck, I., Henighan, T., van Loenhout, M. T. J., Burnham, D. R. & Dekker, C. Magnetic forces and DNA mechanics in multiplexed magnetic tweezers. PLoS ONE 7, e41432 (2012).
Yu, Z. et al. A pressure calibration commonplace for magnetic tweezers. Rev. Sci. Instrum. 85, 123114 (2014).
[ad_2]