Correction of the viscous drag induced errors in macromolecular manipulation experiments using atomic force microscope

Liu, Runcong; Roman, Marisa B.; Yang, Guoliang

doi:10.1063/1.3436646

Cited by 19 publications

(16 citation statements)

References 16 publications

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Section: Methodsmentioning

confidence: 97%

“…The measured unfolding forces are underestimated in high‐viscosity solutions due to the viscous drag on the AFM cantilever 35–38. A way to remove this artifact has been recently reported 35. According to the this procedure the drag force can be computed as where v liquid is the pulling velocity, v tip is the velocity of the tip, b l and b c are viscous drag coefficients related to the liquid motion and the bending of the cantilever (tip motion), respectively.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Observing the osmophobic effect in action at the single molecule level

et al. 2011

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Protecting osmolytes are widespread small organic molecules able to stabilize the folded state of most proteins against various denaturing stresses in vivo. The osmophobic model explains thermodynamically their action through a preferential exclusion of the osmolyte molecules from the protein surface, thus favoring the formation of intrapeptide hydrogen bonds. Few works addressed the influence of protecting osmolytes on the protein unfolding transition state and kinetics. Among those, previous single molecule force spectroscopy experiments evidenced a complexation of the protecting osmolyte molecules at the unfolding transition state of the protein, in apparent contradiction with the osmophobic nature of the protein backbone. We present single-molecule evidence that glycerol, which is a ubiquitous protecting osmolyte, stabilizes a globular protein against mechanical unfolding without binding into its unfolding transition state structure. We show experimentally that glycerol does not change the position of the unfolding transition state as projected onto the mechanical reaction coordinate. Moreover, we compute theoretically the projection of the unfolding transition state onto two other common reaction coordinates, that is, the number of native peptide bonds and the weighted number of native contacts. To that end, we augment an analytic Ising-like protein model with support for group-transfer free energies. Using this model, we find again that the position of the unfolding transition state does not change in the presence of glycerol, giving further support to the conclusions based on the single-molecule experiments.

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Section: Methodsmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 99%

Observing the osmophobic effect in action at the single molecule level

et al. 2011

View full text Add to dashboard Cite

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“…In SI Sec. 5 we have analyzed possible errors from several sources: the finite force resolution of AFM cantilever, the non-negligible hydrodynamic drag on the cantilever at large pulling speeds (¿ 1 µm/s) [39][40][41], uncertainties arising from finite sampling of the rupture force distributions, and the apparatus response time. Based on this error analysis, we conclude that the estimation of the heterogeneity parameter ∆ from the experimental data is reliable in all the systems of Fig.…”

Section: Analysis Of Experimental Datamentioning

confidence: 99%

“…Since in experiments the magnitude of the rupture force is defined as the difference in the pre-rupture and post-rupture force levels, the drag creates a velocity-dependent artifact. The magnitude of the error in the measured rupture force depends also on velocity of the cantilever tip pre-rupture, and hence the stiffness of the sample: the softer the sample, the smaller the velocity difference of the tip pre-and post-rupture, and the smaller the error [39][40][41]. However in typical biomolecule rupture experiments the sample at the point of rupture is maximally extended, with large stiffness, and the tip velocity is much slower than the pulling velocity.…”

Section: Sensitivity Of the Heterogeneity Analysis To Experimental Armentioning

confidence: 99%

Directly measuring single-molecule heterogeneity using force spectroscopy

Hinczewski

Hyeon

Thirumalai

2016

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

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One of the most intriguing results of single-molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active conformations. The structural differences between these conformations may be subtle, but each distinct state can be remarkably long-lived, with interconversions between states occurring only at macroscopic timescales, fractions of a second or longer. Although we now have proof of functional heterogeneity in a handful of systems-enzymes, motors, adhesion complexes-identifying and measuring it remains a formidable challenge. Here, we show that evidence of this phenomenon is more widespread than previously known, encoded in data collected from some of the most well-established single-molecule techniques: atomic force microscopy or optical tweezer pulling experiments. We present a theoretical procedure for analyzing distributions of rupture/unfolding forces recorded at different pulling speeds. This results in a single parameter, quantifying the degree of heterogeneity, and also leads to bounds on the equilibration and conformational interconversion timescales. Surveying 10 published datasets, we find heterogeneity in 5 of them, all with interconversion rates slower than 10 s −1 . Moreover, we identify two systems where additional data at realizable pulling velocities is likely to find a theoretically predicted, but so far unobserved crossover regime between heterogeneous and nonheterogeneous behavior. The significance of this regime is that it will allow far more precise estimates of the slow conformational switching times, one of the least understood aspects of functional heterogeneity.biomolecule heterogeneity | atomic force microscope | optical tweezers | rupture force distribution | dynamic disorder O ne of the great problems in modern biology is to understand how the intrinsic diversity of cellular behaviors is shaped by factors outside of the genome. The causes of this heterogeneity are spread across multiple scales, from noise in biochemical reaction networks through epigenetic mechanisms like DNA methylation and histone modification (1). It might be natural to expect heterogeneity at the cellular level because of the bewildering array of time and length scales associated with the molecules of life that govern cell function. Surprisingly, even at the level of individual biomolecules, diversity in functional properties like rates of enzymatic catalysis (2-5) or receptor-ligand binding (6, 7) can occur. This diversity arises from the presence of many distinct functional states in the free-energy landscape, which correspond to long-lived active conformations of the biomolecule. Although the reigning paradigm in proteins and nucleic acids has been a single, folded native structure, well separated in free energy from any other conformations, possibilities about rugged landscapes with multiple native states have been explored for a long time (8-15). However, only with the revolutionary advan...

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“…The AFM force measurements on soft samples in fluid environments are affected by a hydrodynamic drag force, which results from the viscous friction of the cantilever with the surrounding fluid. This effect appears more significant when cantilever-tip velocities are above a few µm/s [4,[13][14][15]. Under such circumstances, the drag force is dependent upon factors including the stiffness, dimensions and velocity of the cantilever, the fluid viscosity, and the cantilever/tip-surface separation [4,13].…”

Section: Introductionmentioning

confidence: 99%

Numerical study of the hydrodynamic drag force in atomic force microscopy measurements undertaken in fluids

Méndez-Méndez

Alonso-Rasgado

Faria

et al. 2014

Micron

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When atomic force microscopy (AFM) is employed for in vivo study of immersed biological samples, the fluid medium presents additional complexities, not least of which is the hydrodynamic drag force due to viscous friction of the cantilever with the liquid. This force should be considered when interpreting experimental results and any calculated material properties. In this paper, a numerical model is presented to study the influence of the drag force on experimental data obtained from AFM measurements using computational fluid dynamics (CFD) simulation. The model provides quantification of the drag force in AFM measurements of soft specimens in fluids.The numerical predictions were compared with experimental data obtained using AFM with a V-shaped cantilever fitted with a pyramidal tip. Tip velocities ranging from 1.05 to 105 µm/s were employed in water, polyethylene glycol and glycerol with the platform approaching from a distance of 6000 nm. The model was also compared with an existing analytical model. Good agreement was observed between numerical results, experiments and analytical predictions. Accurate predictions were obtained without the need for extrapolation of experimental data. In addition, the model can be employed over the range of tip geometries and velocities typically utilized in AFM measurements.

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Correction of the viscous drag induced errors in macromolecular manipulation experiments using atomic force microscope

Cited by 19 publications

References 16 publications

Observing the osmophobic effect in action at the single molecule level

Observing the osmophobic effect in action at the single molecule level

Directly measuring single-molecule heterogeneity using force spectroscopy

Numerical study of the hydrodynamic drag force in atomic force microscopy measurements undertaken in fluids

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