3D structure–property correlations of electronic and energy materials by tomographic atomic force microscopy

ClpB belongs to the cellular disaggretase machinery involved in rescuing misfolded or aggregated proteins during heat or other cellular shocks. The function of this protein relies on the interconversion between different conformations in its native condition. A recent high-speed-atomic-force-microscopy (HS-AFM) experiment on ClpB from Thermus thermophilus shows four predominant conformational classes, namely, open, closed, spiral, and half-spiral. Analyses of AFM images provide only partial structural information regarding the molecular surface, and thus computational modeling of three-dimensional (3D) structures of these conformations should help interpret dynamical events related to ClpB functions. In this study, we reconstruct 3D models of ClpB from HS-AFM images in different conformational classes. We have applied our recently developed computational method based on a low-resolution representation of 3D structure using a Gaussian mixture model, combined with a Monte-Carlo sampling algorithm to optimize the agreement with target AFM images. After conformational sampling, we obtained models that reflect conformational variety embedded within the AFM images. From these reconstructed 3D models, we described, in terms of relative domain arrangement, the different types of ClpB oligomeric conformations observed by HS-AFM experiments. In particular, we highlighted the slippage of the monomeric components around the seam. This study demonstrates that such details of information, necessary for annotating the different conformational states involved in the ClpB function, can be obtained by combining HS-AFM images, even with limited resolution, and computational modeling.

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1P-182 Lipid membrane stabilized on a flat hydrogel substrate for atomic force microscopy(Biol & Artifi memb.:Structure & Property, The 47th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.49.s90_6 ◽

2009 ◽

Vol 49 (supplement) ◽

pp. S90-S91

Author(s):

Akihiko Takagi ◽

Hitomi Hokonohara ◽

Tomoji Kawai

Keyword(s):

Atomic Force Microscopy ◽

Annual Meeting ◽

Lipid Membrane ◽

Structure Property ◽

Force Microscopy ◽

Atomic Force ◽

Biophysical Society

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Multifractal analysis of human canine teeth at nano scale: atomic force microscopy studies

International Nano Letters ◽

10.1007/s40089-019-00293-7 ◽

2019 ◽

Vol 10 (1) ◽

pp. 15-22 ◽

Cited By ~ 1

Author(s):

Shahram Solaymani ◽

Ştefan Ţălu ◽

Mahmood Ghoranneviss ◽

Seyed Mohammad Elahi ◽

Azizollah Shafiekhani ◽

...

Keyword(s):

Atomic Force Microscopy ◽

Multifractal Analysis ◽

The Other ◽

Structure Property ◽

Statistical Parameters ◽

Force Microscopy ◽

Atomic Force ◽

Surface Micromorphology ◽

Structural Architecture ◽

Old Men

AbstractThe aim of the present study is to explore the 3-D micromorphology of human canine teeth materials using multifractal analysis through atomic force microscopy (AFM). The 3-D surfaces of ten extracted canine teeth of a group of 40 year old men were studied (enamel, inter enamel, inter dentin, and cementum) by AFM images in tapping mode and on square areas of 1 μm × 1 μm (512 × 512 points). The AFM images and surface multifractal analysis confirm the dependency of surface micromorphology to their structure–property of these materials across the length scales of the teeth structural architecture. Surface statistical parameters and hence, multifractal approach have been considered as reliable and sensitive tools for quantifying the 3-D surface microtexture changes of human canine teeth materials. The surface of inter dentin had the most irregular topography (the width spectrum Δα = 2.8361, value bigger than all the other Δα sample values), while the most regular topography (the width spectrum Δα = 2.6804, value lower than all the other sample values) was found in cementum. It has been concluded that multifractal analyses can be used as mathematical tools to explore the 3-D micromorphology of human canine teeth materials.

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1P203 Dependence of Purple Membrane Bump Curvature on pH and Ionic Strength Analyzed by Atomic Force Microscopy Combined with Solvent Exchange(13A. Biological & Artificial membrane: Structure & Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s174_5 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S174

Author(s):

Yasunori Yokoyama ◽

Kousuke Yamada ◽

Yousuke Higashi ◽

Satoshi Ozaki ◽

Haorang Wang ◽

...

Keyword(s):

Atomic Force Microscopy ◽

Ionic Strength ◽

Annual Meeting ◽

Membrane Structure ◽

Solvent Exchange ◽

Structure Property ◽

Artificial Membrane ◽

Force Microscopy ◽

Atomic Force ◽

Biophysical Society

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Atomic Force Microscopy Based Electric Modes in Characterization of Organic Photovoltaics

MRS Proceedings ◽

10.1557/opl.2013.87 ◽

2013 ◽

Vol 1500 ◽

Author(s):

Craig Wall ◽

Sergei Magonov ◽

Sergey Belikov ◽

John Alexander

Keyword(s):

Atomic Force Microscopy ◽

Organic Photovoltaics ◽

Nanometer Scale ◽

Structure Property ◽

Force Microscopy ◽

Atomic Force ◽

Combined Use ◽

Structure Property Relationship ◽

Electric Force Microscopy

ABSTRACTCapabilities of Atomic Force Microscopy in different modes including Electric Force Microscopy and Kelvin Force Microscopy are reviewed and illustrated on several samples including organic photovoltaics (P3HT/PCBM, PEDOT:PSS). Compositional mapping of these blends is enhanced with a combined use of the modes, and variations of local electric properties are detected down to the nanometer scale. The revealed morphology will assist in development of comprehensive models accounting for the structure-property relationship in solar cells and related devices.

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New Insights into Anthelmintic Mechanisms of Action of a Synthetic Peptide: An Ultrastructural and Nanomechanical Approach

Polymers ◽

10.3390/polym13142370 ◽

2021 ◽

Vol 13 (14) ◽

pp. 2370

Author(s):

Alexandra M. S. Soares ◽

Luciana M. R. Alencar ◽

Lucas P. Dias ◽

Ruana C. Lima ◽

Carolina Rocha Silva ◽

...

Keyword(s):

Atomic Force Microscopy ◽

Larval Development ◽

Synthetic Peptide ◽

3D Structure ◽

Gastrointestinal Nematode ◽

Antimicrobial Protein ◽

Egg Hatch ◽

Force Microscopy ◽

Nematode Parasites ◽

Atomic Force

Resistant nematodes are not affected by the most common drugs commercially available. In the search for new anthelmintics, peptides have been investigated. Here, a linear synthetic peptide named RcAlb-PepIII bioinspired from the antimicrobial protein Rc-2S-Alb was designed, synthesized, and tested against barber pole worm Haemonchus contortus. The physicochemical properties of the peptide, the 3D structure model, the egg hatch inhibition, and larval development inhibition of H. contortus were carried out. Additionally, the ultrastructure of the nematode after treatment with the peptide was evaluated by atomic force microscopy. The RcAlb-PepIII inhibited the larval development of H. contortus with an EC50 of 90 µM and did not affect egg hatch. Atomic force microscopy reveals the high affinity of RcAlb-PepIII with the cuticle of H. contortus in the L2 stage. It also shows the deposition of RcAlb-PepIII onto the surface of the cuticle, forming a structure similar to a film that reduces the roughness and mean square roughness (Rq) of it. In conclusion, the bioinspired RcAlb-PepIII has the potential to be used as a new anthelmintic compound to control gastrointestinal nematode parasites.

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