BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics

Amyot, Romain; Flechsig, Holger

doi:10.1371/journal.pcbi.1008444

Cited by 61 publications

(87 citation statements)

References 28 publications

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“…A detailed explanation of the simulated AFM scanning method and on general BioAFMviewer applications is provided in our previous report. 15…”

Section: Resultsmentioning

confidence: 99%

“…We have previously demonstrated that manual search can efficiently reveal atomic protein structures from experimental hs-AFM images. 15 On the other hand, the initial orientation may correspond to a candidate fit obtained from global search. In both situations, the Quick Fit function can be used to obtain a further refinement of structure fitting.…”

Section: Local Search -Quick Fit Functionmentioning

confidence: 99%

“…In Figure 3 further applications are provided, including fitting of the actin-filament all-atom structure to an experimental Hs-AFM image (see SI for details), and those of the ClpB chaperone and F1-ATPase motor which we have previously considered in our first report of the software. 15…”

Section: Application To Experimental Afm Imagesmentioning

confidence: 99%

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Atomic reconstruction of biomolecular structures from AFM images and quantitative validation of experimental data using simulated AFM scanning

Amyot

Marchesi

et al. 2021

Preprint

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We provide the BioAFMviewer-Toolbox, an extension of our previously developed software platform for simulated AFM scanning of biomolecular structures and dy- namics. The focus was on developing a toolbox of methods which employ simulated AFM scanning combined with quantitative analysis to facilitate the interpretation of resolution-limited AFM images. The key advancement is the automatized fitting of biomolecular structures to experimental AFM images, which allows to reconstruct 3D atomistic structures from AFM surface scans. Moreover, several methods for detailed analysis and comparison of surface topographies in simulated and experimental AFM images are provided. We demonstrate the applicability of the developed tools in the interpretation of high-speed AFM observations of proteins. The toolbox is implemented into the versatile interactive interface of the BioAFMviewer, which is a free software package available at www.bioafmviewer.com.

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“…A detailed explanation of the simulated AFM scanning method and on general BioAFMviewer applications is provided in our previous report. 15…”

Section: Resultsmentioning

confidence: 99%

Section: Local Search -Quick Fit Functionmentioning

confidence: 99%

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Atomic reconstruction of biomolecular structures from AFM images and quantitative validation of experimental data using simulated AFM scanning

Amyot

Marchesi

et al. 2021

Preprint

Self Cite

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“…The assembled hexagonal model satisfied a lattice constant of 17.5 nm. Simulated scanning was performed using the BioAFMviewer software 38 , with a tip that had a probe sphere radius of 1.5 nm and a cone half angle of 10°. The computed AFM graphics was subjected to a Gaussian blur to emulate the averaged experimental AFM images.…”

Section: Methodsmentioning

confidence: 99%

An ultra-wide scanner for large-area high-speed atomic force microscopy with megapixel resolution

Marchesi

Umeda

Komekawa

et al. 2021

Sci Rep

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High-speed atomic force microscopy (HS-AFM) is a powerful tool for visualizing the dynamics of individual biomolecules. However, in single-molecule HS-AFM imaging applications, x,y-scanner ranges are typically restricted to a few hundred nanometers, preventing overview observation of larger molecular assemblies, such as 2-dimensional protein crystal growth or fibrillar aggregation. Previous advances in scanner design using mechanical amplification of the piezo-driven x,y-positioning system have extended the size of HS-AFM image frames to several tens of micrometer, but these large scanners may suffer from mechanical instabilities at high scan speeds and only record images with limited pixel numbers and comparatively low lateral resolutions (> 20–100 nm/pixel), complicating single-molecule analysis. Thus, AFM systems able to image large sample areas at high speeds and with nanometer resolution have still been missing. Here, we describe a HS-AFM sample-scanner system able to record large topographic images (≤ 36 × 36 µm2) containing up to 16 megapixels, providing molecular resolution throughout the image frame. Despite its large size, the flexure-based scanner features a high resonance frequency (> 2 kHz) and delivers stable operation even at high scans speeds of up to 7.2 mm/s, minimizing the time required for recording megapixel scans. We furthermore demonstrate that operating this high-speed scanner in time-lapse mode can simultaneously identify areas of spontaneous 2-dimensional Annexin A5 crystal growth, resolve the angular orientation of large crystalline domains, and even detect rare crystal lattice defects, all without changing scan frame size or resolution. Dynamic processes first identified from overview scans can then be further imaged at increased frame rates in reduced scan areas after switching to conventional HS-AFM scanning. The added ability to collect large-area, high-resolution images of complex samples within biological-relevant time frames extends the capabilities of HS-AFM from single-molecule imaging to the study of large dynamic molecular arrays. Moreover, large-area HS-AFM scanning can generate detailed structural data sets from a single scan, aiding the quantitative analysis of structurally heterogenous samples, including cellular surfaces.

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“…The collision-detection method is available as a tool “afmize” ( http://doi.org/10.5281/zenode.3362044 ). The BioAFMviewer, which provides the pseudo-AFM image via a similar method, is also available ( Amyot and Flechsig, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Case Report: Bayesian Statistical Inference of Experimental Parameters via Biomolecular Simulations: Atomic Force Microscopy

Fuchigami

Niina

Takada

2021

Front. Mol. Biosci.

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The atomic force microscopy (AFM) is a powerful tool for imaging structures of molecules bound on surfaces. To gain high-resolution structural information, one often superimposes structure models on the measured images. Motivated by high flexibility of biomolecules, we previously developed a flexible-fitting molecular dynamics (MD) method that allows protein structural changes upon superimposing. Since the AFM image largely depends on the AFM probe tip geometry, the fitting process requires accurate estimation of the parameters related to the tip geometry. Here, we performed a Bayesian statistical inference to estimate a tip radius of the AFM probe from a given AFM image via flexible-fitting molecular dynamics (MD) simulations. We first sampled conformations of the nucleosome that fit well the reference AFM image by the flexible-fitting with various tip radii. We then estimated an optimal tip parameter by maximizing the conditional probability density of the AFM image produced from the fitted structure.

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BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics

Cited by 61 publications

References 28 publications

Atomic reconstruction of biomolecular structures from AFM images and quantitative validation of experimental data using simulated AFM scanning

Atomic reconstruction of biomolecular structures from AFM images and quantitative validation of experimental data using simulated AFM scanning

An ultra-wide scanner for large-area high-speed atomic force microscopy with megapixel resolution

Case Report: Bayesian Statistical Inference of Experimental Parameters via Biomolecular Simulations: Atomic Force Microscopy

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