Correlation between the translational and rotational diffusion of rod-shaped nanocargo on a lipid membrane revealed by single-particle tracking

Revealing the diffusion dynamics of nanoparticles on a lipid membrane plays an important role in a better understanding of the cellular translocation process and provides a theoretical basis for the rational design of delivery cargo.

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Functional Characterization of an Electromagnetic Perceptive Protein

10.1101/2020.10.07.329946 ◽

2020 ◽

Author(s):

Sunayana Mitra ◽

Carlo Barnaba ◽

Jens Schmidt ◽

Galit Pelled ◽

Assaf A. Gilad

Keyword(s):

Particle Tracking ◽

Single Particle ◽

Total Internal Reflection ◽

Magnetic Stimulation ◽

New Technologies ◽

Cellular Function ◽

Single Particle Tracking ◽

Internal Reflection ◽

Total Internal Reflection Fluorescence ◽

Diffusion Dynamics

AbstractMagnetoreception, the response to geomagnetic fields is a well described phenomenon in nature. However, it is likely that convergent evolution led to different mechanisms in different organisms. One intriguing example is the unique Electromagnetic Perceptive Gene (EPG) from the glass catfish Kryptopterus vitreolus, that can remotely control cellular function, upon magnetic stimulation in in-vitro and in animal models. Here, we report for the first time the cellular location and orientation of the EPG protein. We utilized a differential labelling technique in determining that the EPG protein is a membrane anchored protein with an N-terminal extracellular domain. The kinetics and diffusion dynamics of the EPG protein in response to magnetic stimulation was also elucidated using single particle imaging and tracking. Pulse chase labelling and Total Internal Reflection Fluorescence (TIRF) imaging revealed an increase in EPG kinetics post magnetic stimulation activation at a single particle level. Trajectory analysis show notably different EPG protein kinetics before and after magnetic stimulation in both 2 (free vs bound particle) and 3 state (free vs intermediate vs bound particle) tracking models. These data serve to provide additional information that support and understand the underlying biophysical mechanisms behind EPG activation by magnetic stimulation. In conclusion, our results provide evidence for the basis of magnetoreception in EPG protein that would aid in future studies that seek to understand this novel mechanism. This study is important for understanding the phenomenon of magnetoreception as well as developing new technologies for magnetogenetics – the utilization of electromagnetic fields to remotely control cellular function.Graphical TOCElucidation of magnetoreception in a fish derived Electromagnetic Perceptive Gene (EPG), using genetic tagging and single particle tracking with Total Internal Reflection Fluorescence (TIRF) suggests changes in kinetics of membranal motion upon stimulation by magnetic field.

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Single-particle tracking discloses binding-mediated rocking diffusion of rod-shaped biological particles on lipid membranes

Chemical Science ◽

10.1039/c8sc04033h ◽

2019 ◽

Vol 10 (5) ◽

pp. 1351-1359 ◽

Cited By ~ 6

Author(s):

Zhongju Ye ◽

Hua Liu ◽

Fuyan Wang ◽

Xin Wang ◽

Lin Wei ◽

...

Keyword(s):

Particle Tracking ◽

Single Particle ◽

Lipid Membranes ◽

Lipid Membrane ◽

Single Particle Tracking ◽

Two Dimensional ◽

Biological Particles

Interestingly, on the lipid membrane, E.coli displays anomalous rocking diffusion, which might facilitate the subsequent survey of stronger association sites on the two-dimensional (2D) surface.

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Spot-On: robust model-based analysis of single-particle tracking experiments

10.1101/171983 ◽

2017 ◽

Cited By ~ 3

Author(s):

Anders S Hansen ◽

Maxime Woringer ◽

Jonathan B Grimm ◽

Luke D Lavis ◽

Robert Tjian ◽

...

Keyword(s):

Single Molecule ◽

Particle Tracking ◽

Single Particle ◽

Motion Blur ◽

Single Particle Tracking ◽

Modeling Framework ◽

Diffusion Constants ◽

Diffusion Dynamics ◽

Wide Range ◽

And Diffusion

ABSTRACTSingle-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce “Spot-On”, an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants.IMPACT STATEMENTSpot-On is an easy-to-use website that makes a rigorous and bias-corrected modeling framework for analysis of single-molecule tracking experiments available to all.

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Single Particle Tracking of Peptides-Modified Nanocargo on Lipid Membrane Revealing Bulk-Mediated Diffusion

Analytical Chemistry ◽

10.1021/acs.analchem.6b03420 ◽

2016 ◽

Vol 88 (24) ◽

pp. 11973-11977 ◽

Cited By ~ 15

Author(s):

Lin Wei ◽

Zhongju Ye ◽

Yueling Xu ◽

Bo Chen ◽

Edward S. Yeung ◽

...

Keyword(s):

Particle Tracking ◽

Single Particle ◽

Lipid Membrane ◽

Single Particle Tracking

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Robust model-based analysis of single-particle tracking experiments with Spot-On

eLife ◽

10.7554/elife.33125 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 60

Author(s):

Anders S Hansen ◽

Maxime Woringer ◽

Jonathan B Grimm ◽

Luke D Lavis ◽

Robert Tjian ◽

...

Keyword(s):

Particle Tracking ◽

Single Particle ◽

Cell Biology ◽

Motion Blur ◽

Single Particle Tracking ◽

Modeling Framework ◽

Diffusion Constants ◽

Diffusion Dynamics ◽

Wide Range ◽

And Diffusion

Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce ‘Spot-On’, an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants.

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Quantum dot conjugated nanobodies for multiplex imaging of protein dynamics at synapses

Nanoscale ◽

10.1039/c7nr09130c ◽

2018 ◽

Vol 10 (21) ◽

pp. 10241-10249 ◽

Cited By ~ 7

Author(s):

Souvik Modi ◽

Nathalie F. Higgs ◽

David Sheehan ◽

Lewis D. Griffin ◽

Josef T. Kittler

Keyword(s):

Cell Membrane ◽

Protein Dynamics ◽

Particle Tracking ◽

Single Particle ◽

Ex Vivo ◽

Optical Probe ◽

Single Particle Tracking ◽

Specific Probe ◽

Diffusion Dynamics

An anti-GFP nanobody conjugated QD optical probe was applied to study single particle trackingin vitroandex vivo. This small, highly specific probe recognized GFP when expressed at the cell membrane and reported diffusion dynamics of the underlying target protein.

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Information-Efficient, Off-Center Sampling Results in Improved Precision in 3D Single-Particle Tracking Microscopy

Entropy ◽

10.3390/e23050498 ◽

2021 ◽

Vol 23 (5) ◽

pp. 498

Author(s):

Chen Zhang ◽

Kevin Welsher

Keyword(s):

Fisher Information ◽

Particle Tracking ◽

Single Particle ◽

Biological Samples ◽

Tracking System ◽

Single Particle Tracking ◽

Uniform Sampling ◽

Single Dimension ◽

3D Localization ◽

Particle Localization

In this work, we present a 3D single-particle tracking system that can apply tailored sampling patterns to selectively extract photons that yield the most information for particle localization. We demonstrate that off-center sampling at locations predicted by Fisher information utilizes photons most efficiently. When performing localization in a single dimension, optimized off-center sampling patterns gave doubled precision compared to uniform sampling. A ~20% increase in precision compared to uniform sampling can be achieved when a similar off-center pattern is used in 3D localization. Here, we systematically investigated the photon efficiency of different emission patterns in a diffraction-limited system and achieved higher precision than uniform sampling. The ability to maximize information from the limited number of photons demonstrated here is critical for particle tracking applications in biological samples, where photons may be limited.

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