| Sonstiges: |
- Nachgewiesen in: MEDLINE
- Sprachen: English
- Publication Type: Journal Article; Review
- Language: English
- [Nat Protoc] 2024 Jun; Vol. 19 (6), pp. 1779-1806. <i>Date of Electronic Publication: </i>2024 Mar 11.
- MeSH Terms: Proteins* / chemistry ; Proteins* / metabolism ; Single Molecule Imaging / methods ; Magnetics / methods ; Nanotechnology / methods ; Protein Conformation ; Protein Folding
- References: Swift, J. et al. Nuclear lamin-A scales with tissue stiffness and enhances matrix-directed differentiation. Science 341, 1240104 (2013). (PMID: 23990565397654810.1126/science.1240104) ; De Belly, H., Paluch, E. K. & Chalut, K. J. Interplay between mechanics and signalling in regulating cell fate. Nat. Rev. Mol. Cell Biol. 23, 465–480 (2022). (PMID: 3536581610.1038/s41580-022-00472-z) ; Iskratsch, T., Wolfenson, H. & Sheetz, M. P. Appreciating force and shape—the rise of mechanotransduction in cell biology. Nat. Rev. Mol. Cell Biol. 15, 825–833 (2014). (PMID: 25355507933922210.1038/nrm3903) ; Paul, C. D., Mistriotis, P. & Konstantopoulos, K. Cancer cell motility: lessons from migration in confined spaces. Nat. Rev. Cancer 17, 131–140 (2017). (PMID: 2790933910.1038/nrc.2016.123) ; Dumortier, J. G. et al. Hydraulic fracturing and active coarsening position the lumen of the mouse blastocyst. Science 365, 465–468 (2019). (PMID: 3137160810.1126/science.aaw7709) ; Mongera, A. et al. A fluid-to-solid jamming transition underlies vertebrate body axis elongation. Nature 561, 401–405 (2018). (PMID: 30185907614838510.1038/s41586-018-0479-2) ; Pesce, M. et al. Cardiac fibroblasts and mechanosensation in heart development, health and disease. Nat. Rev. Cardiol. 20, 309–324 (2022). (PMID: 3637643710.1038/s41569-022-00799-2) ; Kefauver, J. M., Ward, A. B. & Patapoutian, A. Discoveries in structure and physiology of mechanically activated ion channels. Nature 587, 567–576 (2020). (PMID: 33239794847743510.1038/s41586-020-2933-1) ; Huse, M. Mechanical forces in the immune system. Nat. Rev. Immunol. 17, 679–690 (2017). (PMID: 28757604631270510.1038/nri.2017.74) ; Romani, P., Valcarcel-Jimenez, L., Frezza, C. & Dupont, S. Crosstalk between mechanotransduction and metabolism. Nat. Rev. Mol. Cell Biol. 22, 22–38 (2021). (PMID: 3318827310.1038/s41580-020-00306-w) ; Romani, P. et al. Mitochondrial fission links ECM mechanotransduction to metabolic redox homeostasis and metastatic chemotherapy resistance. Nat. Cell Biol. 24, 168–180 (2022). (PMID: 35165418761574510.1038/s41556-022-00843-w) ; Jaalouk, D. E. & Lammerding, J. Mechanotransduction gone awry. Nat. Rev. Mol. Cell Biol. 10, 63–73 (2009). (PMID: 19197333266895410.1038/nrm2597) ; Chemla, Y. R. et al. Mechanism of force generation of a viral DNA packaging motor. Cell 122, 683–692 (2005). (PMID: 1614310110.1016/j.cell.2005.06.024) ; Ranade, S. S., Syeda, R. & Patapoutian, A. Mechanically activated ion channels. Neuron 87, 1162–1179 (2015). (PMID: 26402601458260010.1016/j.neuron.2015.08.032) ; Neuman, K. C. & Nagy, A. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat. Methods 5, 491–505 (2008). (PMID: 18511917339740210.1038/nmeth.1218) ; Krieg, M. et al. Atomic force microscopy-based mechanobiology. Nat. Rev. Phys. 1, 41–57 (2018). (PMID: 10.1038/s42254-018-0001-7) ; Bustamante, C. J., Chemla, Y. R., Liu, S. & Wang, M. D. Optical tweezers in single-molecule biophysics. Nat. Rev. Methods Prim. 1, 25 (2021). (PMID: 10.1038/s43586-021-00021-6) ; Popa, I., Kosuri, P., Alegre-Cebollada, J., Garcia-Manyes, S. & Fernandez, J. M. Force dependency of biochemical reactions measured by single-molecule force-clamp spectroscopy. Nat. Protoc. 8, 1261–1276 (2013). (PMID: 23744288467694110.1038/nprot.2013.056) ; Li, H. et al. Reverse engineering of the giant muscle protein titin. Nature 418, 998–1002 (2002). (PMID: 1219855110.1038/nature00938) ; Echelman, D. J., Lee, A. Q. & Fernandez, J. M. Mechanical forces regulate the reactivity of a thioester bond in a bacterial adhesin. J. Biol. Chem. 292, 8988–8997 (2017). (PMID: 28348083544813010.1074/jbc.M117.777466) ; Milles, L. F., Schulten, K., Gaub, H. E. & Bernardi, R. C. Molecular mechanism of extreme mechanostability in a pathogen adhesin. Science 359, 1527–1533 (2018). (PMID: 29599244645193210.1126/science.aar2094) ; Mora, M., Stannard, A. & Garcia-Manyes, S. The nanomechanics of individual proteins. Chem. Soc. Rev. 49, 6816–6832 (2020). (PMID: 3292943610.1039/D0CS00426J) ; Dudko, O. K., Hummer, G. & Szabo, A. Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proc. Natl Acad. Sci. USA 105, 15755–15760 (2008). (PMID: 18852468257292110.1073/pnas.0806085105) ; Cecconi, C., Shank, E. A., Bustamante, C. & Marqusee, S. Direct observation of the three-state folding of a single protein molecule. Science 309, 2057–2060 (2005). (PMID: 1617947910.1126/science.1116702) ; Stigler, J., Ziegler, F., Gieseke, A., Gebhardt, J. C. & Rief, M. The complex folding network of single calmodulin molecules. Science 334, 512–516 (2011). (PMID: 2203443310.1126/science.1207598) ; Neupane, K., Manuel, A. P. & Woodside, M. T. Protein folding trajectories can be described quantitatively by one-dimensional diffusion over measured energy landscapes. Nat. Phys. 12, 700–703 (2016). (PMID: 10.1038/nphys3677) ; Woodside, M. T. & Block, S. M. Reconstructing folding energy landscapes by single-molecule force spectroscopy. Annu. Rev. Biophys. 43, 19–39 (2014). (PMID: 24895850460957310.1146/annurev-biophys-051013-022754) ; Kaiser, C. M., Goldman, D. H., Chodera, J. D., Tinoco, I. Jr. & Bustamante, C. The ribosome modulates nascent protein folding. Science 334, 1723–1727 (2011). (PMID: 22194581417236610.1126/science.1209740) ; Lipfert, J., Kerssemakers, J. W., Jager, T. & Dekker, N. H. Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments. Nat. Methods 7, 977–980 (2010). (PMID: 2095317310.1038/nmeth.1520) ; Ding, F. et al. Single-molecule mechanical identification and sequencing. Nat. Methods 9, 367–372 (2012). (PMID: 22406857352817610.1038/nmeth.1925) ; Hodeib, S. et al. Single molecule studies of helicases with magnetic tweezers. Methods 105, 3–15 (2016). (PMID: 2737112110.1016/j.ymeth.2016.06.019) ; Lionnet, T. et al. Magnetic trap construction. Cold Spring Harb. Protoc. 2012, 133–138 (2012). (PMID: 2219426010.1101/pdb.prot067496) ; Rivas-Pardo, J. A. et al. Work done by titin protein folding assists muscle contraction. Cell Rep. 14, 1339–1347 (2016). (PMID: 26854230486525510.1016/j.celrep.2016.01.025) ; Chen, H. et al. Dynamics of equilibrium folding and unfolding transitions of titin immunoglobulin domain under constant forces. J. Am. Chem. Soc. 137, 3540–3546 (2015). (PMID: 25726700444671110.1021/ja5119368) ; Bauer, M. S. et al. A tethered ligand assay to probe SARS-CoV-2:ACE2 interactions. Proc. Natl Acad. Sci. USA 119, e2114397119 (2022). (PMID: 35312342916851410.1073/pnas.2114397119) ; Yao, M. et al. The mechanical response of talin. Nat. Commun. 7, 11966 (2016). (PMID: 27384267494105110.1038/ncomms11966) ; Popa, I. et al. A HaloTag anchored ruler for week-long studies of protein dynamics. J. Am. Chem. Soc. 138, 10546–10553 (2016). (PMID: 27409974551059810.1021/jacs.6b05429) ; Lof, A. et al. Multiplexed protein force spectroscopy reveals equilibrium protein folding dynamics and the low-force response of von Willebrand factor. Proc. Natl Acad. Sci. USA 116, 18798–18807 (2019). (PMID: 31462494675458310.1073/pnas.1901794116) ; Zhao, X., Zeng, X., Lu, C. & Yan, J. Studying the mechanical responses of proteins using magnetic tweezers. Nanotechnology 28, 414002 (2017). (PMID: 2876650610.1088/1361-6528/aa837e) ; Choi, H. K. et al. Watching helical membrane proteins fold reveals a common N-to-C-terminal folding pathway. Science 366, 1150–1156 (2019). (PMID: 31780561738237010.1126/science.aaw8208) ; Choi, H. K. et al. Evolutionary balance between foldability and functionality of a glucose transporter. Nat. Chem. Biol. 18, 713–723 (2022). (PMID: 35484435761294510.1038/s41589-022-01002-w) ; Choi, H. K., Kim, H. G., Shon, M. J. & Yoon, T. Y. High-resolution single-molecule magnetic tweezers. Annu. Rev. Biochem. 91, 33–59 (2022). (PMID: 3528747210.1146/annurev-biochem-032620-104637) ; Smith, S. B., Finzi, L. & Bustamante, C. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258, 1122–1126 (1992). (PMID: 143981910.1126/science.1439819) ; Strick, T. R., Allemand, J. F., Bensimon, D., Bensimon, A. & Croquette, V. The elasticity of a single supercoiled DNA molecule. Science 271, 1835–1837 (1996). (PMID: 859695110.1126/science.271.5257.1835) ; Gosse, C. & Croquette, V. Magnetic tweezers: micromanipulation and force measurement at the molecular level. Biophys. J. 82, 3314–3329 (2002). (PMID: 12023254130211910.1016/S0006-3495(02)75672-5) ; Maier, B., Bensimon, D. & Croquette, V. Replication by a single DNA polymerase of a stretched single-stranded DNA. Proc. Natl Acad. Sci. USA 97, 12002–12007 (2000). (PMID: 110502321728410.1073/pnas.97.22.12002) ; Dekker, N. H. et al. The mechanism of type IA topoisomerases. Proc. Natl Acad. Sci. USA 99, 12126–12131 (2002). (PMID: 1216766812940910.1073/pnas.132378799) ; Crut, A., Koster, D. A., Seidel, R., Wiggins, C. H. & Dekker, N. H. Fast dynamics of supercoiled DNA revealed by single-molecule experiments. Proc. Natl Acad. Sci. USA 104, 11957–11962 (2007). (PMID: 17623785192454310.1073/pnas.0700333104) ; England, C. G., Luo, H. & Cai, W. HaloTag technology: a versatile platform for biomedical applications. Bioconjug. Chem. 26, 975–986 (2015). (PMID: 25974629448233510.1021/acs.bioconjchem.5b00191) ; Zakeri, B. et al. Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proc. Natl Acad. Sci. USA 109, E690–E697 (2012). (PMID: 22366317331137010.1073/pnas.1115485109) ; Tapia-Rojo, R., Eckels, E. C. & Fernandez, J. M. Ephemeral states in protein folding under force captured with a magnetic tweezers design. Proc. Natl Acad. Sci. USA 116, 7873–7878 (2019). (PMID: 30936303647543110.1073/pnas.1821284116) ; Stannard, A. et al. Molecular fluctuations as a ruler of force-induced protein conformations. Nano Lett. 21, 2953–2961 (2021). (PMID: 33765390761071410.1021/acs.nanolett.1c00051) ; Tapia-Rojo, R., Alonso-Caballero, A. & Fernandez, J. M. Direct observation of a coil-to-helix contraction triggered by vinculin binding to talin. Sci. Adv. 6, eaaz4707 (2020). (PMID: 32494739724431110.1126/sciadv.aaz4707) ; Franz, F. et al. Allosteric activation of vinculin by talin. Nat. Commun. 14, 4311 (2023). (PMID: 374638951035420210.1038/s41467-023-39646-4) ; Tapia-Rojo, R. et al. Enhanced statistical sampling reveals microscopic complexity in the talin mechanosensor folding energy landscape. Nat. Phys. 19, 52–60 (2023). (PMID: 3666016410.1038/s41567-022-01808-4) ; Austen, K. et al. Extracellular rigidity sensing by talin isoform-specific mechanical linkages. Nat. Cell Biol. 17, 1597–1606 (2015). (PMID: 26523364466288810.1038/ncb3268) ; Riveline, D. et al. Focal contacts as mechanosensors: externally applied local mechanical force induces growth of focal contacts by an mDia1-dependent and ROCK-independent mechanism. J. Cell Biol. 153, 1175–1186 (2001). (PMID: 11402062219203410.1083/jcb.153.6.1175) ; Grashoff, C. et al. Measuring mechanical tension across vinculin reveals regulation of focal adhesion dynamics. Nature 466, 263–266 (2010). (PMID: 20613844290188810.1038/nature09198) ; Garcia-Manyes, S. et al. Single-molecule force spectroscopy predicts a misfolded, domain-swapped conformation in human γD-crystallin protein. J. Biol. Chem. 291, 4226–4235 (2016). (PMID: 2670347610.1074/jbc.M115.673871) ; Mora, M. et al. A single-molecule strategy to capture non-native intramolecular and intermolecular protein disulfide bridges. Nano Lett. 22, 3922–3930 (2022). (PMID: 35549281913692110.1021/acs.nanolett.2c00043) ; Petrosyan, R., Patra, S., Rezajooei, N., Garen, C. R. & Woodside, M. T. Unfolded and intermediate states of PrP play a key role in the mechanism of action of an antiprion chaperone. Proc. Natl Acad. Sci. USA 118, e2010213118 (2021). (PMID: 33619087793634210.1073/pnas.2010213118) ; Gupta, A. N. et al. Pharmacological chaperone reshapes the energy landscape for folding and aggregation of the prion protein. Nat. Commun. 7, 12058 (2016). (PMID: 27346148493125210.1038/ncomms12058) ; Sen Mojumdar, S. et al. Partially native intermediates mediate misfolding of SOD1 in single-molecule folding trajectories. Nat. Commun. 8, 1881 (2017). (PMID: 29192167570942610.1038/s41467-017-01996-1) ; Yao, M. et al. Force-dependent conformational switch of alpha-catenin controls vinculin binding. Nat. Commun. 5, 4525 (2014). (PMID: 2507773910.1038/ncomms5525) ; Dahal, N., Sharma, S., Phan, B., Eis, A. & Popa, I. Mechanical regulation of talin through binding and history-dependent unfolding. Sci. Adv. 8, eabl7719 (2022). (PMID: 3585749110.1126/sciadv.abl7719) ; Kemmerich, F. E. et al. Simultaneous single-molecule force and fluorescence sampling of DNA nanostructure conformations using magnetic tweezers. Nano Lett. 16, 381–386 (2016). (PMID: 2663202110.1021/acs.nanolett.5b03956) ; Ivanov, I. E. et al. Multimodal measurements of single-molecule dynamics using FluoRBT. Biophys. J. 114, 278–282 (2018). (PMID: 2924815010.1016/j.bpj.2017.11.017) ; Tapia-Rojo, R., Alonso-Caballero, A. & Fernandez, J. M. Talin folding as the tuning fork of cellular mechanotransduction. Proc. Natl Acad. Sci. USA 117, 21346–21353 (2020). (PMID: 32817549747463510.1073/pnas.2004091117) ; Alonso-Caballero, A. et al. Protein folding modulates the chemical reactivity of a Gram-positive adhesin. Nat. Chem. 13, 172–181 (2021). (PMID: 3325788710.1038/s41557-020-00586-x) ; Guo, H. A simple algorithm for fitting a gaussian function. In Streamlining Digital Signal Processing 297–305 (John Wiley & Sons, 2012). ; Fonnum, G., Johansson, C., Molteberg, A., Mørup, S. & Aksnes, E. Characterisation of Dynabeads® by magnetization measurements and Mössbauer spectroscopy. J. Magn. Magn. Mater. 293, 41–47 (2005). (PMID: 10.1016/j.jmmm.2005.01.041) ; Ostrofet, E., Papini, F. S. & Dulin, D. Correction-free force calibration for magnetic tweezers experiments. Sci. Rep. 8, 15920 (2018). (PMID: 30374099620602210.1038/s41598-018-34360-4) ; Buschow, K. H. J., Long, G. J. & Grandjean, F. High Density Digital Recording (Springer, 1993). ; Liu, R., Garcia-Manyes, S., Sarkar, A., Badilla, C. L. & Fernandez, J. M. Mechanical characterization of protein L in the low-force regime by electromagnetic tweezers/evanescent nanometry. Biophys. J. 96, 3810–3821 (2009). (PMID: 19413987271140610.1016/j.bpj.2009.01.043) ; Valle-Orero, J. et al. Proteins breaking bad: a free energy perspective. J. Phys. Chem. Lett. 8, 3642–3647 (2017). (PMID: 28723106595754110.1021/acs.jpclett.7b01509) ; Alegre-Cebollada, J., Badilla, C. L. & Fernandez, J. M. Isopeptide bonds block the mechanical extension of pili in pathogenic Streptococcus pyogenes. J. Biol. Chem. 285, 11235–11242 (2010). (PMID: 20139067285700110.1074/jbc.M110.102962) ; Schlierf, M., Li, H. & Fernandez, J. M. The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques. Proc. Natl Acad. Sci. USA 101, 7299–7304 (2004). (PMID: 1512381640991310.1073/pnas.0400033101) ; Evans, E. & Ritchie, K. Dynamic strength of molecular adhesion bonds. Biophys. J. 72, 1541–1555 (1997). (PMID: 9083660118435010.1016/S0006-3495(97)78802-7) ; Zhang, Y., Jiao, J. & Rebane, A. A. Hidden Markov modeling with detailed balance and its application to single protein folding. Biophys. J. 111, 2110–2124 (2016). (PMID: 27851936511295110.1016/j.bpj.2016.09.045) ; McKinney, S. A., Joo, C. & Ha, T. Analysis of single-molecule FRET trajectories using hidden Markov modeling. Biophys. J. 91, 1941–1951 (2006). (PMID: 16766620154430710.1529/biophysj.106.082487) ; Dudko, O. K., Hummer, G. & Szabo, A. Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys. Rev. Lett. 96, 108101 (2006). (PMID: 1660579310.1103/PhysRevLett.96.108101) ; Bullerjahn, J. T., Sturm, S. & Kroy, K. Theory of rapid force spectroscopy. Nat. Commun. 5, 4463 (2014). (PMID: 2507991110.1038/ncomms5463)
- Grant Information: 212218 United Kingdom WT_ Wellcome Trust; RL 2016-015 Leverhulme Trust; BB/V003518/1 RCUK | Biotechnology and Biological Sciences Research Council (BBSRC); RSWF/R3/183006 Royal Society
- Substance Nomenclature: 0 (Proteins)
- Entry Date(s): Date Created: 20240312 Date Completed: 20240611 Latest Revision: 20240611
- Update Code: 20240612
|
