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Protein Dynamics in Living Cells

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

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Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor

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Ranking Single Fluorescent Protein-Based Calcium Biosensor Performance by Molecular Dynamics Simulations.

Melike Berksoz¹, Canan Atilgan¹

¹Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey.

Journal of Chemical Information and Modeling

|December 27, 2024

Summary

Genetically encoded fluorescent biosensors (GEFBs) enable in vivo biological visualization. Molecular dynamics simulations reveal water distribution and hydrogen bonds predict biosensor performance, aiding structure optimization.

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Area of Science:

Biophysics
Molecular Biology
Biochemistry

Background:

Genetically encoded fluorescent biosensors (GEFBs) are vital for in vivo biological process visualization.
Single fluorescent protein (FP)-based biosensors offer simplicity but face challenges in structure optimization, particularly linker design.
Optimizing linkers between sensory domains (SD) and FPs is crucial for effective chromophore response.

Purpose of the Study:

To analyze the dynamic properties of calmodulin-based calcium biosensors using molecular dynamics simulations.
To identify key factors influencing the performance of single FP-based biosensors.
To establish predictive metrics for biosensor structure optimization.

Main Methods:

All-atom molecular dynamics simulations were employed.
Dynamic properties of calmodulin-based calcium biosensors with varying FP-SD interfaces were analyzed.
Water molecule distribution and hydrogen bond occupancies were compared between ligand-bound and ligand-free states.

Main Results:

Biosensor performance correlates with water molecule distribution around the chromophore.
Shifts in hydrogen bond occupancies between ligand-bound and ligand-free states predict biosensor efficacy.
FP-SD interaction interfaces significantly impact calcium binding-dependent fluorescence changes.

Conclusions:

Biosensor performance can be predicted by analyzing water distribution and hydrogen bond dynamics.
Molecular dynamics simulations provide insights into optimizing GEFB structure and function.
This work offers a computational approach to enhance the design of fluorescent biosensors.