Fully Atomistic Simulations of Protein Unfolding in Low Speed Atomic Force Microscope and Force Clamp Experiments with the Help of Boxed Molecular Dynamics

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Booth, JJ; Shalashilin, DV;
(2016)
  • Publisher: American Chemical Society
  • Subject:
    arxiv: Quantitative Biology::Biomolecules
    mesheuropmc: biological sciences

The results of Boxed Dynamics (BXD) fully atomistic simulations of protein unfolding by Atomic Force Microscope (AFM), in both force clamp (FC) and velocity clamp (VC) modes are reported. In AFM experiments the unfolding occurs on time scale which is too long for standa... View more
  • References (93)
    93 references, page 1 of 10

    (1) Brockwell, D. J. Probing the mechanical stability of proteins using the atomic force microscope. Biochem. Soc. Trans. 2007, 35, 1564− 1568.

    (2) Hedberg, C.; Toledo, G.; Gustafsson, C.; Larson, G.; Oldfors, A.; Macao, B. Hereditary myopathy with early respiratory failure is associated with misfolding of the titin fibronectin III 119 subdomain.

    Neuromusc. Disord. 2014, 24, 373−379.

    (3) Marszalek, P. E.; Lu, H.; Li, H. B.; Carrion-Vazquez, M.; Oberhauser, A. F.; Schulten, K.; Fernandez, J. M. Mechanical unfolding intermediates in titin modules. Nature 1999, 402, 100−103.

    (4) Crampton, N.; Brockwell, D. J. Unravelling the design principles for single protein mechanical strength. Curr. Opin. Struct. Biol. 2010, 20, 508−517.

    (5) Hann, E.; Kirkpatrick, N.; Kleanthous, C.; Smith, D. A.; Radford, S. E.; Brockwell, D. J. The effect of protein complexation on the mechanical stability of Im9. Biophys. J. 2007, 92, L79−L81.

    (6) Sadler, D. P.; Petrik, E.; Taniguchi, Y.; Pullen, J. R.; Kawakami, M.; Radford, S. E.; Brockwell, D. J. Identification of a mechanical rheostat in the hydrophobic core of Protein L. J. Mol. Biol. 2009, 393, 237−248.

    (7) Brujic, J.; Hermans, R. I.; Walther, K. A.; Fernandez, J. M. Singlemolecule force spectroscopy reveals signatures of glassy dynamics in the energy landscape of ubiquitin. Nat. Phys. 2006, 2, 282−286.

    (8) Garcia-Manyes, S.; Brujic,́ J.; Badilla, C. L.; Fernańdez, J. M.

    Force-clamp spectroscopy of single-protein monomers reveals the individual unfolding and folding pathways of I27 and ubiquitin.

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