Laffeber, C., Koning, Okay. D., Kanaar, R. & Lebbink, J. H. G. Experimental proof for enhanced receptor binding by quickly spreading SARS-CoV-2 variants. J. Mol. Biol. 433, 167058–167058 (2021).
Barton, M. I. et al. Results of widespread mutations within the SARS-CoV-2 spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. eLife 10, e70658 (2021).
Majumdar, P. & Niyogi, S. SARS-CoV-2 mutations: the organic trackway in direction of viral health. Epidemiol. Infect. 149, E110 (2021).
Bayarri-Olmos, R. et al. The alpha/B.1.1.7 SARS-CoV-2 variant displays considerably increased affinity for ACE-2 and requires decrease inoculation doses to trigger illness in K18-hACE2 mice. eLife 10, e70002 (2021).
Hill, D. B. et al. Pressure technology and dynamics of particular person cilia beneath exterior loading. Biophys. J. 98, 57–66 (2010).
Wu, C.-T. et al. SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming. Cell 186, 112–130.e20 (2023).
Milles, L. F., Schulten, Okay., Gaub, H. E. & Bernardi, R. C. Molecular mechanism of maximum mechanostability in a pathogen adhesin. Science 359, 1527–1533 (2018).
Alsteens, D. et al. Nanomechanical mapping of first binding steps of a virus to animal cells. Nat. Nanotechnol. 12, 177–183 (2017).
Koehler, M., Delguste, M., Sieben, C., Gillet, L. & Alsteens, D. Preliminary step of virus entry: virion binding to cell-surface glycans. Annu. Rev. Virol. 7, 143–165 (2020).
Sokurenko, E. V., Vogel, V. & Thomas, W. E. Catch-bond mechanism of force-enhanced adhesion: counterintuitive, elusive, however…widespread? Cell Host Microbe 4, 314–323 (2008).
Tian, F. et al. N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. eLife 10, e69091 (2021).
Zheng, Bin, et al. S373P mutation stabilizes the receptor-binding area of the spike protein in omicron and promotes binding. JACS Au https://doi.org/10.1021/jacsau.3c00142 (2023).
Koehler, M. et al. Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. Nat. Commun. 12, 6977 (2021).
Yang, J. et al. Molecular interplay and inhibition of SARS-CoV-2 binding to the ACE2 receptor. Nat. Commun. 11, 4541 (2020).
Cao, W. et al. Biomechanical characterization of SARS-CoV-2 spike RBD and human ACE2 protein-protein interplay. Biophys. J. 120, 1011–1019 (2021).
Zhang, X. et al. Pathogen-host adhesion between SARS-CoV-2 spike proteins from totally different variants and human ACE2 studied at single-molecule and single-cell ranges. Rising Microbes Infect. 11, 2658–2669 (2022).
Zhu, R. et al. Pressure-tuned avidity of spike variant-ACE2 interactions considered on the single-molecule stage. Nat. Commun. 13, 7926 (2022).
Bauer, M. S. et al. A tethered ligand assay to probe SARS-CoV-2:ACE2 interactions. Proc. Natl Acad. Sci. USA 119, e2114397119 (2022).
Bauer, M. S. et al. A tethered ligand assay to probe the SARS-CoV-2 ACE2 interplay beneath fixed power. Preprint at biorxiv https://doi.org/10.1101/2020.09.27.315796 (2020).
Löf, A. et al. Multiplexed protein power spectroscopy reveals equilibrium protein folding dynamics and the low-force response of von Willebrand issue. Proc. Natl Acad. Sci. USA 116, 18798–18807 (2019).
Lansdorp, B. M. & Saleh, O. A. Energy spectrum and Allan variance strategies for calibrating single-molecule video-tracking devices. Rev. Sci. Instrum. 83, 025115 (2012).
Velthuis, A. J. W. T., Kerssemakers, J. W. J., Lipfert, J. & Dekker, N. H. Quantitative tips for power calibration by means of spectral evaluation of magnetic tweezers knowledge. Biophys. J. 99, 1292–1302 (2010).
Neuman, Okay. C. & Nagy, A. Single-molecule power spectroscopy: optical tweezers, magnetic tweezers and atomic power microscopy. Nat. Strategies 5, 491–505 (2008).
Lipfert, J., Hao, X. & Dekker, N. H. Quantitative modeling and optimization of magnetic tweezers. Biophys. J. 96, 5040–5049 (2009).
Ott, W. et al. Elastin-like polypeptide linkers for single-molecule power spectroscopy. ACS Nano 11, 6346–6354 (2017).
Kim, J., Zhang, C. Z., Zhang, X. & Springer, T. A. A mechanically stabilized receptor-ligand flex-bond necessary within the vasculature. Nature 466, 992–995 (2010).
Shrestha, P. et al. Single-molecule mechanical fingerprinting with DNA nanoswitch calipers. Nat. Nanotechnol. 16, 1362–1370 (2021).
Yang, D., Ward, A., Halvorsen, Okay. & Wong, W. P. Multiplexed single-molecule power spectroscopy utilizing a centrifuge. Nat. Commun. 7, 11026 (2016).
Kilchherr, F. et al. Single-molecule dissection of stacking forces in DNA. Science 353, aaf5508 (2016).
Le, S., Yu, M. & Yan, J. Direct single-molecule quantification reveals unexpectedly excessive mechanical stability of vinculin—talin/α-catenin linkages. Sci. Adv. 5, eaav2720 (2019).
Halvorsen, Okay., Schaak, D. & Wong, W. P. Nanoengineering a single-molecule mechanical change utilizing DNA self-assembly. Nanotechnology 22, 494005 (2011).
Kostrz, D. et al. A modular DNA scaffold to review protein-protein interactions at single-molecule decision. Nat. Nanotechnol. 14, 988–993 (2019).
Gong, S. Y. et al. Contribution of single mutations to chose SARS-CoV-2 rising variants spike antigenicity. Virology 563, 134–145 (2021).
Rajah, M. M. et al. SARS‐CoV‐2 Alpha, Beta, and Delta variants show enhanced spike‐mediated syncytia formation. EMBO J. 40, e108944 (2021).
Gobeil, S. M. C. et al. Impact of pure mutations of SARS-CoV-2 on spike construction, conformation, and antigenicity. Science 373, eabi6226 (2021).
Ren, W. et al. Characterization of SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by cell entry and immune evasion. mBio 13, e00099–00022 (2022).
McCallum, M. et al. Molecular foundation of immune evasion by the Delta and Kappa SARS-CoV-2 variants. Science 374, 1621–1626 (2021).
Albrecht, C. et al. DNA: a programmable power sensor. Science 301, 367–370 (2003).
Gruber, S. et al. Designed anchoring geometries decide lifetimes of biotin–streptavidin bonds beneath fixed load and allow ultra-stable coupling. Nanoscale 12, 21131–21137 (2020).
Webb, B. & Sali, A. Comparative protein construction modeling utilizing MODELLER. Curr. Protoc. Bioinform 54, 5.6.1–5.6.37 (2016).
Phillips, J. C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130 (2020).
Melo, M. C. R., Bernardi, R. C., Fuente-Nunez, C. D. L. & Luthey-Schulten, Z. Generalized correlation-based dynamical community evaluation: a brand new high-performance method for figuring out allosteric communications in molecular dynamics trajectories. J. Chem. Phys. 153, 134104 (2020).
Schoeler, C. et al. Mapping mechanical power propagation by means of biomolecular complexes. Nano Lett. 15, 7370–7376 (2015).
Lan, J. et al. Construction of the SARS-CoV-2 spike receptor-binding area certain to the ACE2 receptor. Nature 581, 215–220 (2020).
Liu, H. et al. The idea of a extra contagious 501Y.V1 variant of SARS-CoV-2. Cell Res. 31, 720–722 (2021).
Han, P. et al. Receptor binding and sophisticated constructions of human ACE2 to spike RBD from Omicron and Delta SARS-CoV-2. Cell 185, 630–640.e610 (2022).
Dulin, D., Lipfert, J., Moolman, M. C. & Dekker, N. H. Finding out genomic processes on the single-molecule stage: introducing the instruments and purposes. Nat. Rev. Genet. 14, 9–22 (2013).
Shang, J. et al. Cell entry mechanisms of SARS-CoV-2. Proc. Natl Acad. Sci. USA 117, 11727–11734 (2020).
V’kovski, P., Kratzel, A., Steiner, S, Stalder, H. & Thiel, V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat. Rev. Microbiol. 19, 155–170 (2020).
Michaud, W. A., Boland, G. M. & Rabi, S. A. The SARS-CoV-2 spike mutation D614G will increase entry health throughout a variety of ACE2 ranges, instantly outcompetes the wild kind, and is preferentially integrated into trimers. Preprint at bioRxiv https://doi.org/10.1101/2020.08.25.267500 (2020).
Jackson, C. B., Farzan, M., Chen, B. & Choe, H. Mechanisms of SARS-CoV-2 entry into cells. Nat. Rev. Mol. Cell Biol. 23, 3–20 (2022).
Harvey, W. T. et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat. Rev. Microbiol. 19, 409–424 (2021).
Escalera, A. et al. Mutations in SARS-CoV-2 variants of concern hyperlink to elevated spike cleavage and virus transmission. Cell Host Microbe 30, 373–387.e377 (2022).
Ulrich, L. et al. Enhanced health of SARS-CoV-2 variant of concern Alpha however not Beta. Nature 602, 307–313 (2022).
Buss, L. F. et al. Three-quarters assault fee of SARS-CoV-2 within the Brazilian Amazon throughout a largely unmitigated epidemic. Science 371, 288–292 (2021).
Solar, Okay. et al. SARS-CoV-2 transmission, persistence of immunity, and estimates of Omicron’s affect in South African inhabitants cohorts. Sci. Transl. Med. 14, eabo7081 (2022).
Starr, T. N. et al. Deep mutational scanning of SARS-CoV-2 receptor binding area reveals constraints on folding and ACE2 binding. Cell 182, 1295–1310.e1220 (2020).
Liu, C. et al. The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to different variants. Cell Host Microbe 30, 53–68.e12 (2022).
Bayarri-Olmos, R. et al. Useful results of receptor-binding area mutations of SARS-CoV-2 B.1.351 and P.1 variants. Entrance. Immunol. 12, 757197 (2021).
Mlcochova, P. et al. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 599, 114–119 (2021).
Hu, J. et al. Elevated immune escape of the brand new SARS-CoV-2 variant of concern Omicron. Cell Mol. Immunol. 19, 293–295 (2022).
Ju, B. et al. Immune escape by SARS-CoV-2 Omicron variant and structural foundation of its efficient neutralization by a broad neutralizing human antibody VacW-209. Cell Res. 32, 491–494 (2022).
Fan, Y. et al. SARS-CoV-2 Omicron variant: current progress and future views. Sig. Transduct. Goal Ther. 7, 141 (2022).
Planas, D. et al. Appreciable escape of SARS-CoV-2 Omicron to antibody neutralization. Nature 602, 671–675 (2022).
Li, B. et al. Viral an infection and transmission in a big, well-traced outbreak attributable to the SARS-CoV-2 Delta variant. Nat. Commun. 13, 460 (2022).
Komatsu, T. et al. Molecular cloning, mRNA expression and chromosomal localization of mouse angiotensin-converting enzyme-related carboxypeptidase (mACE2). DNA Sequence 13, 217–220 (2002).
Marra, M. A. et al. The genome sequence of the SARS-associated coronavirus. Science 300, 1399–1404 (2003).
Li, F., Li, W., Farzan, M. & Harrison, S. C. Construction of SARS coronavirus spike receptor-binding area complexed with receptor. Science 309, 1864–1868 (2005).
Milles, L. F. & Gaub, H. E. Is mechanical receptor ligand dissociation pushed by unfolding or unbinding? Preprint at bioRxiv https://doi.org/10.1101/593335 (2019).
Wu, F. et al. A brand new coronavirus related to human respiratory illness in China. Nature 579, 265–269 (2020).
Walker, P. U., Vanderlinden, W. & Lipfert, J. Dynamics and vitality panorama of DNA plectoneme nucleation. Phys. Rev. E 98, 042412 (2018).
van Loenhout, M. T., Kerssemakers, J. W., De Vlaminck, I. & Dekker, C. Non-bias-limited monitoring of spherical particles, enabling nanometer decision at low magnification. Biophys. J. 102, 2362–2371 (2012).
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).
Lipfert, J. et al. Strategies and protocols. Strategies Mol. Biol. 582, 71–89 (2009).
Yu, Z. et al. A power calibration customary for magnetic tweezers. Rev. Sci. Instrum. 85, 123114 (2014).
De Vlaminck, I., Henighan, T., van Loenhout, M. T., Burnham, D. R. & Dekker, C. Magnetic forces and DNA mechanics in multiplexed magnetic tweezers. PLoS ONE 7, e41432 (2012).
Zimmermann, J. L., Nicolaus, T., Neuert, G. & Clean, Okay. Thiol-based, site-specific and covalent immobilization of biomolecules for single-molecule experiments. Nat. Protoc. 5, 975–985 (2010).
Yin, J., Lin, A. J., Golan, D. E. & Walsh, C. T. Web site-specific protein labeling by Sfp phosphopantetheinyl transferase. Nat. Protoc. 1, 280–285 (2006).
Chen, I., Dorr, B. M. & Liu, D. R. A common technique for the evolution of bond-forming enzymes utilizing yeast show. Proc. Natl Acad. Sci. USA 108, 11399–11404 (2011).
Durner, E., Ott, W., Nash, M. A. & Gaub, H. E. Submit-translational sortase-mediated attachment of high-strength power spectroscopy handles. ACS Omega 2, 3064–3069 (2017).
Humphrey, W., Dalke, A. & Schulten, Okay. VMD: visible molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).
Ribeiro, J. V. et al. QwikMD—integrative molecular dynamics toolkit for novices and consultants. Sci. Rep. 6, 26536 (2016).
Bernardi, R. C. et al. Mechanisms of nanonewton mechanostability in a protein complicated revealed by molecular dynamics simulations and single-molecule power spectroscopy. J. Am. Chem. Soc. 141, 14752–14763 (2019).
Finest, R. B. et al. Optimization of the additive CHARMM all-atom protein power subject focusing on improved sampling of the spine ϕ, ψ and side-chain χ1 and χ2 dihedral angles. J. Chem. Principle Comput. 8, 3257–3273 (2012).
MacKerell, A. D. et al. All-atom empirical potential for molecular modeling and dynamics research of proteins. J. Phys. Chem. B 102, 3586–3616 (1998).
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 (1998).
Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an N⋅log(N) methodology for Ewald sums in giant methods. J. Chem. Phys. 98, 10089–10092 (1993).
Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005).
Efron, B. & Tibshirani, R. J. An Introduction to the Bootstrap 372–391 (CRC Press, 1994).
Virtanen, P. et al. SciPy 1.0: basic algorithms for scientific computing in Python. Nat. Strategies 17, 261–272 (2020).
Pedregosa, F. et al. Scikit-learn: machine studying in Python. J. Mach. Study. Res. 12, 2825–2830 (2011).
Hagberg, A. A., Schult, D. A. & Swart, P. J. ExplorkX. In Proc. seventh Python in Science Convention https://www.osti.gov/servlets/purl/960616 (2008).
Hunter, J. D. Matplotlib: a 2D graphics surroundings. Comput. Sci. Eng. 9, 90–95 (2007).