Image: Vladimir Kunetki
Protein-protein bonds play a vital role in crucial biological processes such as enzymatic reactions, antibody binding, and response to medication. Precisely understanding and characterizing these interactions is essential for evaluating the effectiveness of potential treatments. However, current methodologies have limitations either in providing detailed insights into individual interactions or in analyzing large quantities of these bonds.
In a recent publication in the Biophysical Journal, scientists introduced an enhanced technique for assessing the strength and durability of protein-protein bonds under conditions that mimic those within the human body. This method utilizes sound waves to separate bonded proteins, while DNA leashes hold the two proteins in proximity to facilitate their reconnection after the bond is broken. This innovation enables repeated testing of the same protein bonds up to 100 times, offering valuable information on how bond strength changes over time.
According to senior author Laurent Limozin, a biophysicist at the Centre National de la Recherche Scientifique (CNRS), “We aimed to propose a method that is versatile enough to be applied to different types of bonds, has reasonable throughput, and achieves high molecular precision, which is currently only attainable through sophisticated techniques like optical or magnetic tweezers that may be challenging for non-specialists.”
To achieve this, Limozin’s team collaborated with researchers from Marseille and Paris to combine two existing technologies: acoustic force spectroscopy, allowing simultaneous testing of numerous molecular pairs, and DNA scaffolds, enabling repeated testing of the same bonds.
During acoustic force spectroscopy, pairs of bonded proteins are examined within a chamber filled with liquid. The proteins are held in place by DNA scaffolds, with one DNA strand attaching the first protein to the chamber’s bottom and another strand attaching the second protein to a small silica bead. When the chamber is subjected to a soundwave, the force of the wave pulls the silica bead, along with the attached protein, away from the bottom of the chamber. If the force is sufficient, this pulling action breaks the bond between the two proteins. However, in this novel method, a third DNA strand acts as a leash, keeping the proteins close together after their bond is ruptured.
“The uniqueness of our approach lies in the addition of this leash, connecting the two strands in the middle and keeping the proteins together after the bond is broken,” explains Limozin. “Without this leash, detachment would be irreversible, but with it, you can repeat the measurement almost an unlimited number of times.”
To demonstrate the feasibility of the technique, the research team applied it to characterize two single-molecule interactions of biomedical significance: the bond between proteins and rapamycin, an immunosuppressive drug, and the bond between a single-domain antibody and an HIV-1 antigen.
Using a microscope, the researchers observed these cycles of bonding and breaking. The ability to test the same protein-protein bond multiple times is crucial for exploring variations among molecularly identical pairs. It also allows researchers to investigate how these interactions evolve as the molecules age, which is valuable for determining the half-life of drugs or antibodies.
“With this tool, we have the means to delve deeper and experimentally investigate ideas about molecular heterogeneity and aging,” notes Limozin. “We, as well as others, believe that characterizing these properties will be highly useful in designing future therapeutics that need to function in scenarios involving mechanical forces.”
Reference: “Combining DNA scaffolds and acoustic force spectroscopy to characterize individual protein bonds” by Yong Jian Wang, Claire Valotteau, Adrien Aimard, Lorenzo Villanueva, Dorota Kostrz, Maryne Follenfant, Terence Strick, Patrick Chames, Felix Rico, Charlie Gosse and Laurent Limozin, 7 June 2023, Biophysical Journal.
DOI: 10.1016/j.bpj.2023.05.004
The study received funding from AMIDEX Emergence Innovation, the Plan Cancer PhysCancer program, the European Research Council, the Human Frontier Science Program, and PSL University.
Table of Contents
Frequently Asked Questions (FAQs) about protein-protein bonds
What is the purpose of the study mentioned in the text?
The purpose of the study is to introduce an improved technique for evaluating the durability and robustness of protein-protein bonds under conditions that mimic those within the human body.
How does the method work?
The method combines acoustic force spectroscopy and DNA scaffolds. Sound waves are used to pull bonded proteins apart, while DNA leashes keep the proteins close together after their bond is ruptured, allowing for repeated testing of the same protein bonds.
Why is it important to test protein-protein bonds multiple times?
Testing the same protein-protein bond multiple times is crucial for exploring variations among identical pairs and understanding how these interactions change as the molecules age. This information is valuable for determining the efficacy and lifespan of drugs or antibodies.
What are the potential applications of this technique?
The technique can be applied to various types of bonds and has the potential to provide valuable insights into molecular heterogeneity, aging, and mechanical forces involved in molecular interactions. It can aid in designing future therapeutics that need to function under such conditions.
How is the method different from existing techniques?
This method combines the advantages of acoustic force spectroscopy, which allows for testing multiple molecular pairs simultaneously, and DNA scaffolds, which enable repeated testing of the same bonds. It offers high molecular precision comparable to sophisticated techniques like optical or magnetic tweezers, but with increased modularity and reasonable throughput.
More about protein-protein bonds
- Biophysical Journal: Link
- AMIDEX Emergence Innovation: Link
- Plan Cancer PhysCancer program: Link
- European Research Council: Link
- Human Frontier Science Program: Link
- PSL University: Link
5 comments
this study is a game-changer! being able to test protein bonds so many times gives us a deeper understanding of how they work. i’m excited to see how this research progresses and what new insights it brings.
this study is great cuz it helps us understand how protein bonds work inside our bodies. and the fact that they can test the same bonds multiple times is so useful for seeing how they change over time. love it!
can’t wait to read more about this research! it’s fascinating how they’re using DNA leashes to keep the proteins together after they’re pulled apart. i wonder what other applications this technique could have.
wow this sounds like a super cool way to test protein bonds using sound waves and DNA! i never thought about using sound before, but it makes sense. imagine all the new discoveries we can make with this method!
i’m not a scientist but this article was pretty easy to understand. it’s cool how they combined different technologies to come up with a new method. i hope it leads to better treatments and drugs in the future.