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

2021 ◽  
Vol 8 ◽  
Author(s):  
Sotaro Fuchigami ◽  
Toru Niina ◽  
Shoji Takada

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.

2021 ◽  
Author(s):  
Hiroki Koide ◽  
Noriyuki Kodera ◽  
Shveta Bisht ◽  
Shoji Takada ◽  
Tsuyoshi Terakawa

The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the so-called hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain contacts dsDNA has remained unknown, potentially due to its conformational plasticity. Here, we conducted atomic force microscopy imaging of the budding yeast condensin holo-complex and used this data as basis for coarse-grained molecular dynamics simulations to model the hinge structure in a transient open conformation. We then simulated the dsDNA binding to open and closed hinge conformations, predicting that dsDNA binds to the outside surface when closed and to the outside and inside surfaces when open. Our simulations also suggested that the hinge can close around dsDNA bound to the inside surface. The conformational change of the hinge domain might be essential for the dsDNA binding regulation and play important roles in condensin-mediated DNA-loop extrusion.


1997 ◽  
Vol 36 (4) ◽  
pp. 41-48 ◽  
Author(s):  
A. Cornelissen ◽  
M. G. Burnett ◽  
R. D. McCall ◽  
D. T. Goddard

This paper concerns the imaging of hydrous floc particles by Light Microscopy (LM), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM) and Atomic Force Microscopy (AFM). The use of a microscope technique means that visual structural information is obtained, in contrast with other techniques measuring particle characteristics. It was found that when a preparation technique was used that involves cryogenic freezing of the sample, before observation in the SEM, larger (1-100 μm) floc particles could be imaged without the loss of structural information normally caused by drying the sample. Damage caused by drying was not apparent with the TEM technique used. It was shown that the various microscope techniques produced compatible results, together covering a wide size range (10 nm-5mm). This indicates that major artefact formation due to sample preparation is unlikely. It was furthermore shown that when a micro-scale continuous flow system was used the reproducibility of the floc structure observed increased.


2006 ◽  
Vol 79 (5) ◽  
pp. 783-789 ◽  
Author(s):  
C. C. Wang ◽  
S. H. Wu ◽  
J. B. Donnet ◽  
T. K. Wang

Abstract The microdispersion state of carbon blacks in an emulsion SBR matrix has been observed by atomic force microscopy (AFM) and the images analyzed quantitatively. The fillers were well dispersed in the rubber samples. Different parameters, such as the surface fraction of fillers in images, particle size distance distributions, have been extracted and the main results are presented.


2015 ◽  
Vol 119 (48) ◽  
pp. 27118-27124 ◽  
Author(s):  
Julian Gelman Constantin ◽  
Marcelo A. Carignano ◽  
Horacio R. Corti ◽  
Igal Szleifer

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