Identifying Nanoscale Structure–Function Relationships Using Multimodal Atomic Force Microscopy, Dimensionality Reduction, and Regression Techniques

2018 ◽  
Vol 9 (12) ◽  
pp. 3307-3314 ◽  
Author(s):  
Jessica Kong ◽  
Rajiv Giridharagopal ◽  
Jeffrey S. Harrison ◽  
David S. Ginger
Keyword(s):  
Atomic Force Microscopy ◽  
Dimensionality Reduction ◽  
Structure Function ◽  
Force Microscopy ◽  
Atomic Force ◽  
Regression Techniques ◽  
Nanoscale Structure

scholarly journals Sequence‐dependent nucleosome nanoscale structure characterized by atomic force microscopy

2019 ◽  
Vol 33 (10) ◽  
pp. 10916-10923 ◽  
Author(s):  
Tommy Stormberg ◽  
Micah Stumme-Diers ◽  
Yuri L. Lyubchenko
Keyword(s):  
Atomic Force Microscopy ◽  
Force Microscopy ◽  
Atomic Force ◽  
Sequence Dependent ◽  
Nanoscale Structure

scholarly journals Array atomic force microscopy for real-time multiparametric analysis

2019 ◽  
Vol 116 (13) ◽  
pp. 5872-5877 ◽  
Author(s):  
Qingqing Yang ◽  
Qian Ma ◽  
Kate M. Herum ◽  
Chonghe Wang ◽  
Nirav Patel ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Structure Function ◽  
Function Analysis ◽  
Atomic Scale ◽  
Beam Deflection ◽  
Emergent Properties ◽  
Multiscale Approach ◽  
Force Microscopy ◽  
Atomic Force ◽  
Wide Range

Nanoscale multipoint structure–function analysis is essential for deciphering the complexity of multiscale biological and physical systems. Atomic force microscopy (AFM) allows nanoscale structure–function imaging in various operating environments and can be integrated seamlessly with disparate probe-based sensing and manipulation technologies. Conventional AFMs only permit sequential single-point analysis; widespread adoption of array AFMs for simultaneous multipoint study is challenging owing to the intrinsic limitations of existing technological approaches. Here, we describe a prototype dispersive optics-based array AFM capable of simultaneously monitoring multiple probe–sample interactions. A single supercontinuum laser beam is utilized to spatially and spectrally map multiple cantilevers, to isolate and record beam deflection from individual cantilevers using distinct wavelength selection. This design provides a remarkably simplified yet effective solution to overcome the optical cross-talk while maintaining subnanometer sensitivity and compatibility with probe-based sensors. We demonstrate the versatility and robustness of our system on parallel multiparametric imaging at multiscale levels ranging from surface morphology to hydrophobicity and electric potential mapping in both air and liquid, mechanical wave propagation in polymeric films, and the dynamics of living cells. This multiparametric, multiscale approach provides opportunities for studying the emergent properties of atomic-scale mechanical and physicochemical interactions in a wide range of physical and biological networks.

scholarly journals Structural variability and dynamics in the ectodomain of an ancestral-type classical cadherin revealed by AFM imaging

2021 ◽  
Author(s):  
Shigetaka Nishiguchi ◽  
Hiroki Oda
Keyword(s):  
Atomic Force Microscopy ◽  
Structure Function ◽  
High Speed ◽  
Adhesive Properties ◽  
Force Microscopy ◽  
Type Iii ◽  
Atomic Force ◽  
Afm Imaging ◽  
Comparative Structure ◽  
Ancestral Type

Type III cadherin represents the ancestral form of classical cadherin in bilaterian metazoans. Drosophila possesses type III and type IVa cadherins, known as DN- and DE-cadherins, respectively. Mature DN- and DE-cadherins have 15 and 7 extracellular cadherin domain (EC) repeats, respectively, with DN-cadherin EC6–11 homologous to DE-cadherin EC1–6. These EC repeats contain predicted complete or partial Ca2+-free inter-EC linkers that potentially contribute to adhesion. Comparative structure-function studies of DN- and DE-cadherins may help us understand the ancestral and derived states of classical cadherin-mediated adhesion mechanisms. Here, using bead aggregation assays, we found that DN-cadherin EC1–11 and DE-cadherin EC1–6 exhibit Ca2+-dependent adhesive properties. Using high-speed atomic force microscopy (HS-AFM) imaging in solution, we showed that both DN- and DE-cadherin ectodomains share a common morphological framework consisting of a strand-like and a globule-like portion. Furthermore, the DN-cadherin EC repeats were highly variable, flexible in morphology, and with at least three bendable sites, one of which is located in EC6–11 and can act as a flexible hinge. Our findings provide insights into diversification of classical cadherin-mediated adhesion mechanisms. (180 words or less)

Atomic force microscopy study of the structure–function relationships of the biofilm-forming bacteriumStreptococcus mutans

2006 ◽  
Vol 17 (4) ◽  
pp. S1-S7 ◽  
Author(s):  
Sarah E Cross ◽  
Jens Kreth ◽  
Lin Zhu ◽  
Fengxia Qi ◽  
Andrew E Pelling ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Structure Function ◽  
Microscopy Study ◽  
Atomic Force Microscopy Study ◽  
Force Microscopy ◽  
Atomic Force
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