scholarly journals Single-Molecule Dynamics of the DNA−EcoRII Protein Complexes Revealed with High-Speed Atomic Force Microscopy

Biochemistry ◽  
2009 ◽  
Vol 48 (44) ◽  
pp. 10492-10498 ◽  
Author(s):  
Jamie L. Gilmore ◽  
Yuki Suzuki ◽  
Gintautas Tamulaitis ◽  
Virginijus Siksnys ◽  
Kunio Takeyasu ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
High Speed ◽  
Protein Complexes ◽  
Force Microscopy ◽  
Atomic Force ◽  
Single Molecule Dynamics ◽  
Molecule Dynamics

scholarly journals Resolving the data asynchronicity in high-speed atomic force microscopy measurement via the Kalman Smoother

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shintaroh Kubo ◽  
Suguru Kato ◽  
Kazuyuki Nakamura ◽  
Noriyuki Kodera ◽  
Shoji Takada
Keyword(s):  
Atomic Force Microscopy ◽  
Kalman Filter ◽  
Single Molecule ◽  
High Speed ◽  
Ground Truth ◽  
Bayesian Filtering ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Kalman Smoother ◽  
Atomic Force

Abstract High-speed atomic force microscopy (HS-AFM) is a scanning probe microscopy that can capture structural dynamics of biomolecules in real time at single molecule level near physiological condition. Albeit much improvement, while scanning one frame of HS-AFM movies, biomolecules often change their conformations largely. Thus, the obtained frame images can be hampered by the time-difference, the asynchronicity, in the data acquisition. Here, to resolve this data asynchronicity in the HS-AFM movie, we developed Kalman filter and smoother methods, some of the sequential Bayesian filtering approaches. The Kalman filter/smoother methods use alternative steps of a short time-propagation by a linear dynamical system and a correction by the likelihood of AFM data acquired pixel by pixel. We first tested the method using a toy model of a diffusing cone, showing that the Kalman smoother method outperforms to reproduce the ground-truth movie. We then applied the Kalman smoother to a synthetic movie for conformational change dynamics of a motor protein, i.e., dynein, confirming the superiority of the Kalman smoother. Finally, we applied the Kalman smoother to two real HS-AFM movies, FlhAC and centralspindlin, reducing distortion and noise in the AFM movies. The method is general and can be applied to any HS-AFM movies.

scholarly journals Mobility of nucleosomes is regulated by their binding partners

2022 ◽  
Author(s):  
Daniel P Melters ◽  
Keir C Neuman ◽  
Tatini Rakshit ◽  
Yamini Dalal
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
High Speed ◽  
Diffusion Constant ◽  
Chromatin Accessibility ◽  
Chromatin Dynamics ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force

Chromatin accessibility is modulated in a variety of ways, both to create open and closed chromatin states which are critical for eukaryotic gene regulation. At the mechanistic single molecule level, how accessibility is regulated remains a fundamental question in the field. Here, we use single molecule tracking by high-speed atomic force microscopy to investigate this question using chromatin arrays and extend our findings into the nucleus. By high-speed atomic force microscopy, we tracked chromatin dynamics in real time and observed that the essential kinetochore protein CENP-C reduces the diffusion constant of CENP-A nucleosomes and the linker H1.5 protein restricts H3 nucleosome mobility. We subsequently interrogated how CENP-C modulates CENP-A chromatin dynamics in vivo. Overexpressing CENP-C resulted in reduced centromeric transcription and impaired loading of new CENP-A molecules. These data suggest a model in which inner kinetochore proteins are critically involved in modulating chromatin accessibility and consequently, noncoding transcription at human centromeres.

Quantum-dot antibody conjugation visualized at the single-molecule scale with high-speed atomic force microscopy

2018 ◽  
Vol 167 ◽  
pp. 267-274 ◽  
Author(s):  
Takayuki Umakoshi ◽  
Hikari Udaka ◽  
Takayuki Uchihashi ◽  
Toshio Ando ◽  
Miho Suzuki ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Quantum Dot ◽  
Single Molecule ◽  
High Speed ◽  
Force Microscopy ◽  
Atomic Force ◽  
Antibody Conjugation

Imaging Cellular and Viral Materials with Small Cantilevers Developed for High Speed Atomic Force Microscopy

2007 ◽  
Vol 1025 ◽  
Author(s):  
Georg Fantner ◽  
Tzvetan Ivanov ◽  
Katerina Ivanova ◽  
David Gray ◽  
Ivo W Rangelow ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Real Time ◽  
Single Molecule ◽  
High Speed ◽  
Biological Systems ◽  
Real Life ◽  
Biologically Relevant ◽  
Force Microscopy ◽  
Atomic Force ◽  
Resonance Frequencies

AbstractHigh speed atomic force microscopy (AFM) holds the promise of investigating dynamic systems in real time with single molecule resolution. With the big push towards understanding more complex systems such as cell mechanics or cell-cell and cell-virus interactions, a tool is required that can extract information about these processes in real time in a physiological environment. Atomic force microscopy has been successfully used for investigations of many biological systems and materials in real life conditions, but taking AFM images takes too long to follow many biologically relevant processes. Therefore, attempts have been made to develop high speed AFM by reengineering all the components of an AFM system and much progress has been made. To be useful for investigations of biological systems however, it is often essential to keep imaging forces low in order to get good image quality and not to damage the sample. In this paper we will discuss new small AFM cantilevers we've developed to combine high resonance frequencies for faster imaging with low spring constants for gentle imaging.

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