Stepwise unfolding of titin under force-clamp atomic force microscopy

Oberhauser, Andrés F.; Hansma, Paul K.; Carrión‐Vázquez, Mariano; Fernández, Julio M.

doi:10.1073/pnas.98.2.468

Cited by 316 publications

(255 citation statements)

References 19 publications

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“…1C). The sawtooth pattern is reminiscent of that seen upon unraveling tandem repeats of Ig domains in a single titin molecule (16,17). At the end of the stretch, the chromatin curve approaches that of the full-length naked DNA (dotted line), indicating that no histones remained attached to the DNA in such a way that they would alter DNA elasticity.…”

Section: Resultsmentioning

confidence: 79%

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

Brower-Toland

Smith

Yeh

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

448

465

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The dynamic structure of individual nucleosomes was examined by stretching nucleosomal arrays with a feedback-enhanced optical trap. Forced disassembly of each nucleosome occurred in three stages. Analysis of the data using a simple worm-like chain model yields 76 bp of DNA released from the histone core at low stretching force. Subsequently, 80 bp are released at higher forces in two stages: full extension of DNA with histones bound, followed by detachment of histones. When arrays were relaxed before the dissociated state was reached, nucleosomes were able to reassemble and to repeat the disassembly process. The kinetic parameters for nucleosome disassembly also have been determined.

show abstract

Section: Resultsmentioning

confidence: 79%

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

Brower-Toland

Smith

Yeh

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

448

465

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show abstract

“…Mechanical stability of this protein has been assessed experimentally in many studies [41][42][43][44]. The OVrCSU contact map for 1TIT consists of 198 contacts.…”

Section: Resultsmentioning

confidence: 99%

Criteria for folding in structure-based models of proteins

Wołek

Cieplak

2016

The Journal of Chemical Physics

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In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very low thermodynamic stability, especially when the contact map used is too sparse. We consider six different structure-based models and show that allowing for a small, but model-dependent, percentage of the native contacts not being established boosts the folding temperature substantially while affecting the time scales of folding only in a minor way. We also compare other properties of the six models. We show that the choice of the description of the backbone stiffness has a substantial effect on the values of characteristic temperatures that relate both to equilibrium and kinetic properties. Models without any backbone stiffness (like the self-organized polymer) are found to perform similar to those with the stiffness, including in the studies of stretching.

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“…39 In contrast to dynamic SMFS, the force-clamp SMFS technique provides direct access to the reaction kinetics of mechanically activated processes on the molecular level. 12,14,15,[40][41][42][43] By analyzing the recorded data with an Arrhenius kinetics model with a force-dependent activation barrier, the measured reaction rate constants can be used directly to calculate force and temperature-independent parameters, like the activation energy, the Arrhenius pre-factor and the width of the binding potential.…”

Section: Introductionmentioning

confidence: 99%

Mechanically induced silyl ester cleavage under acidic conditions investigated by AFM-based single-molecule force spectroscopy in the force-ramp mode

et al. 2014

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AFM-based dynamic single-molecule force spectroscopy was used to stretch carboxymethylated amylose (CMA) polymers, which have been covalently tethered between a silanized glass substrate and a silanized AFM tip via acid-catalyzed ester condensation at pH 2.0. Rupture forces were measured as a function of temperature and force loading rate in the force-ramp mode. The data exhibit significant statistical scattering, which is fitted with a maximum likelihood estimation (MLE) algorithm.Bond rupture is described with a Morse potential based Arrhenius kinetics model.The fit yields a bond dissociation energy D e ¼ 35 kJ mol À1 and an Arrhenius prefactor A ¼ 6.6 Â 10 4 s À1 . The bond dissociation energy is consistent with previous experiments under identical conditions, where the force-clamp mode was employed. However, the bi-exponential decay kinetics, which the force-clamp results unambiguously revealed, are not evident in the force-ramp data. While it is possible to fit the force-ramp data with a bi-exponential model, the fit parameters differ from the force-clamp experiments. Overall, single-molecule force spectroscopy in the force-ramp mode yields data whose information content is more limited than force-clamp data. It may, however, still be necessary and advantageous to perform force-ramp experiments. The number of successful events is often higher in the force-ramp mode, and competing reaction pathways may make force-clamp experiments impossible.

show abstract

Stepwise unfolding of titin under force-clamp atomic force microscopy

Cited by 316 publications

References 19 publications

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

Criteria for folding in structure-based models of proteins

Mechanically induced silyl ester cleavage under acidic conditions investigated by AFM-based single-molecule force spectroscopy in the force-ramp mode

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