How physics and biology work together to explore the mechanisms of life

Each of our cells has about 40 million pieces of machinery that help the cell survive. For a smooth action, the right proteins must be concentrated at a specific time and location. Standard cell biology tools are often unable to detect delicate distribution at tiny spatial resolutions. A new approach combining genetics and cell biology experiments with physical modeling was developed by researchers from the University of Geneva. They were able to explain the complex mechanisms of the formation of the protein gradients using the simulation techniques they used. Their model can be adapted to other biology systems. The results can be found in the Proceedings of the National Academy of Sciences.

Like a drop of ink in a glass of water, the proteins can diffuse and distribute throughout the cell. Monica Gotta, a professor in the Department of Cell Physiology, says that the formation of gradients is central to many cellular and organismsal functions.

A use of randomness.

The anterior side of the embryo is believed to be where the key regulator of cell division is located. What would happen if the smallest detail went awry? Monica Gotta was happy to have a physicist on her team, as the usual tools of biology were not enough to answer this question.

I created a statistical model of the formation of the proteins based on the knowledge of the process and new hypotheses.

The team was able to do simulations through time and in 3D. The model had to be compared with biological data. The first version of the model incorporated all known physical and biological elements of the system and introduced specific parameters to test several hypotheses. They used the embryos of a small worm to test the results of their simulations of possible physical and biological outcomes.

There are intricate interactions at play.

Thanks to the interplay between modeling and cell biology, the UNIGE researchers were able to determine how the PLK-1 gradient was established and maintained over time. To counteract its tendency to diffuse in the cell, PLK-1 must bind and unbind from MEX-5. MEX-5 has the ability to change its diffusivity depending on its position within the cell, which is essential to enrich PLK-1 where needed.

This study provides a unique quantitative model for understanding dynamic interactions between the different types of cells and can be adapted to other cells for which the complex mechanisms can't be tested with usual cell biology experiments.

More information: Modeling protein dynamics in embryos reveals that the PLK-1 gradient relies on weakly coupled reaction–diffusion mechanisms, Proceedings of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2114205119. Journal information: Proceedings of the National Academy of Sciences Citation: How physics and biology work together to explore the mechanisms of life (2022, March 7) retrieved 7 March 2022 from https://phys.org/news/2022-03-physics-biology-explore-mechanisms-life.html This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.