Automated detection of protein unfolding events in atomic force microscopy force curves

2016 ◽  
Vol 79 (11) ◽  
pp. 1105-1111 ◽  
Author(s):  
Xavier García-Massó ◽  
Matthias C. Huber ◽  
Jacqueline. Friedmann ◽  
Luis M. Gonzalez ◽  
Stefan M. Schiller ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Protein Unfolding ◽  
Automated Detection ◽  
Force Microscopy ◽  
Atomic Force ◽  
Force Curves

scholarly journals Surface Structure and Nanomechanical Properties of Shewanella putrefaciens Bacteria at Two pH values (4 and 10) Determined by Atomic Force Microscopy

2005 ◽  
Vol 187 (11) ◽  
pp. 3864-3868 ◽  
Author(s):  
Fabien Gaboriaud ◽  
Sidney Bailet ◽  
Etienne Dague ◽  
Frédéric Jorand
Keyword(s):  
Atomic Force Microscopy ◽  
A Priori ◽  
Linear Part ◽  
Shewanella Putrefaciens ◽  
Nonlinear Part ◽  
Force Microscopy ◽  
Nanomechanical Properties ◽  
Ph Values ◽  
Atomic Force ◽  
Force Curves

ABSTRACT The nanomechanical properties of gram-negative bacteria (Shewanella putrefaciens) were investigated in situ in aqueous solutions at two pH values, specifically, 4 and 10, by atomic force microscopy (AFM). For both pH values, the approach force curves exhibited subsequent nonlinear and linear regimens that were related to the progressive indentation of the AFM tip in the bacterial cell wall, including a priori polymeric fringe (nonlinear part), while the linear part was ascribed to compression of the plasma membrane. These results indicate the dynamic of surface ultrastructure in response to changes in pH, leading to variations in nanomechanical properties, such as the Young's modulus and the bacterial spring constant.

scholarly journals Atomic force microscopy of the morphology and mechanical behaviour of barnacle cyprid footprint proteins at the nanoscale

2009 ◽  
Vol 7 (43) ◽  
pp. 285-296 ◽  
Author(s):  
In Yee Phang ◽  
Nick Aldred ◽  
Xing Yi Ling ◽  
Jurriaan Huskens ◽  
Anthony S. Clare ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Sea Water ◽  
Persistence Length ◽  
Force Microscopy ◽  
Bond Model ◽  
Atomic Force ◽  
Extension Force ◽  
Force Curves ◽  
High Elongation ◽  
Glass Surfaces

Barnacles are a major biofouler of man-made underwater structures. Prior to settlement, cypris larvae explore surfaces by reversible attachment effected by a ‘temporary adhesive’. During this exploratory behaviour, cyprids deposit proteinaceous ‘footprints’ of a putatively adhesive material. In this study, footprints deposited by Balanus amphitrite cyprids were probed by atomic force microscopy (AFM) in artificial sea water (ASW) on silane-modified glass surfaces. AFM images obtained in air yielded better resolution than in ASW and revealed the fibrillar nature of the secretion, suggesting that the deposits were composed of single proteinaceous nanofibrils, or bundles of fibrils. The force curves generated in pull-off force experiments in sea water consisted of regions of gradually increasing force, separated by sharp drops in extension force manifesting a characteristic saw-tooth appearance. Following the relaxation of fibrils stretched to high strains, force–distance curves in reverse stretching experiments could be described by the entropic elasticity model of a polymer chain. When subjected to relaxation exceeding 500 ms, extended footprint proteins refolded, and again showed saw-tooth unfolding peaks in subsequent force cycles. Observed rupture and hysteresis behaviour were explained by the ‘sacrificial bond’ model. Longer durations of relaxation (>5 s) allowed more sacrificial bond reformation and contributed to enhanced energy dissipation (higher toughness). The persistence length for the protein chains ( L P ) was obtained. At high elongation, following repeated stretching up to increasing upper strain limits, footprint proteins detached at total stretched length of 10 µm.

Digital force-feedback for protein unfolding experiments using atomic force microscopy

2006 ◽  
Vol 18 (4) ◽  
pp. 044022 ◽  
Author(s):  
Christian A Bippes ◽  
Harald Janovjak ◽  
Alexej Kedrov ◽  
Daniel J Muller
Keyword(s):  
Atomic Force Microscopy ◽  
Protein Unfolding ◽  
Force Feedback ◽  
Force Microscopy ◽  
Atomic Force

scholarly journals A simple and efficient quasi 3-dimensional viscoelastic model and software for simulation of tapping-mode atomic force microscopy

2015 ◽  
Vol 6 ◽  
pp. 2233-2241 ◽  
Author(s):  
Santiago D Solares
Keyword(s):  
Atomic Force Microscopy ◽  
Computational Cost ◽  
Viscoelastic Model ◽  
Software Tool ◽  
Tapping Mode ◽  
3 Dimensional ◽  
Force Microscopy ◽  
Atomic Force ◽  
Standard Linear Solid ◽  
Force Curves

This paper introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretation of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tapping-mode imaging, for both of which the force curves exhibit the expected features. Finally, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.

On averaging force curves over heterogeneous surfaces in atomic force microscopy

2012 ◽  
Vol 121 ◽  
pp. 16-24 ◽  
Author(s):  
I. Sokolov ◽  
V. Kalaparthi ◽  
M. Kreshchuk ◽  
M.E. Dokukin
Keyword(s):  
Atomic Force Microscopy ◽  
Heterogeneous Surfaces ◽  
Force Microscopy ◽  
Atomic Force ◽  
Force Curves
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