Flexibility is key in mechanism of biological self-assembly

March 17, 2017

A new study has modeled a crucial first step in the self-assembly of cellular structures such as drug receptors and other protein complexes, and found that the flexibility of the structures has a dramatic impact on how fast two such structures join together.

The study, published this week in the journal Proceedings of the National Academy of Sciences, explored what happens when two water-repelling surfaces connect to build more complex structures. Using molecular simulations, the researchers illustrated the mechanism by which the process occurs and explored factors that favor self-assembly.

A surprise finding was the sensitivity with which the surfaces' determined the rate at which the surfaces eventually came together, with more flexible surfaces favoring joining. "Flexibility is like a knob that nature can tune to control the self-assembly of molecules," said Pablo Debenedetti, senior author on the study and Princeton's Dean for Research. Debenedetti is the Class of 1950 Professor in Engineering and Applied Science and a professor of chemical and biological engineering.

Researchers have long been interested in how biological structures can self-assemble according to physical laws. Tapping the secrets of self-assembly could, for example, lead to new methods of building nanomaterials for future electronic devices. Self-assembled protein complexes are the basis not only of drug receptors but also many other , including that facilitate the transmission of signals in the brain.

The study illustrated the process by which two water-repelling, or hydrophobic, structures come together. At the start of the simulation, the two surfaces were separated by a watery environment. Researchers knew from previous studies that these surfaces, due to their hydrophobic nature, will push water molecules away until only a very few water molecules remain in the gap. The evaporation of these last few molecules allows the two surfaces to snap together.

The video will load shortly
Researchers at Princeton University used molecular simulations to look at how two surfaces come together, which happens during the self-assembly of biological molecules such as drug receptors. As the two surfaces come near to each other, their water-repelling (hydrophobic) nature triggers fluctuations in the number of water molecules in the gap, causing the water to evaporate and form into bubbles on the surfaces. The bubbles grow as more water molecules evaporate. Eventually two bubbles on either surface connect to form a gap-spanning tube, which expands and pushes away any remaining water until the two surfaces collide. The study found that the flexibility of the two surfaces is a key factor in how fast this process occurs. Credit: Y. E. Altabet and P. D. Debenedetti, Princeton University.

The new molecular simulation conducted at Princeton yielded a more detailed look at the mechanism behind this process. In the simulation, when the surfaces are sufficiently close to each other, their hydrophobic nature triggered fluctuations in the number of water molecules in the gap, causing the liquid water to evaporate and form bubbles on the surfaces. The bubbles grew as more evaporated. Eventually two bubbles on either surface connected to form a gap-spanning tube, which expanded and pushed away any remaining water until the two surfaces collided.

Biological surfaces, such as cellular membranes, are flexible, so the researchers explored how the surfaces' flexibility affected the process. The researchers tuned the flexibility of the surfaces by varying the strength of the coupling between the atoms. The stronger the coupling, the less each atom can wiggle relative to its neighbors.

The researchers found that the speed at which the two surfaces snap together depended greatly on flexibility. Small changes in flexibility led to large changes in the rate at which the surfaces stuck together. For example, two very flexible surfaces adhered in just nanoseconds, whereas two inflexible surfaces fused incredibly slowly, on the order of seconds.

Another finding was that the last step in the process, where the vapor tube expands, was critical for ensuring that the surfaces came together. In simulations where the tube failed to expand, the surfaces never joined. Flexibility was key to ensuring that the tube expanded, the researchers found. Making the material more flexible lowered the barriers to evaporation and stabilized the vapor tube, increasing the chances that the tube would expand.

The provides a foundation for understanding how biological structures assemble and function, according to Elia Altabet, a graduate student in Debenedetti's group, and first author on the study. "A deeper understanding of the formation and function of protein assemblies such as drug receptors and ion channels could inform the design of new drugs to treat diseases," he said.

Explore further: New understanding of the 'dewetting' process

More information: Y. Elia Altabet et al, Effect of material flexibility on the thermodynamics and kinetics of hydrophobically induced evaporation of water, Proceedings of the National Academy of Sciences (2017). DOI: 10.1073/pnas.1620335114

Related Stories

New understanding of the 'dewetting' process

November 9, 2015

When a material, typically a liquid, is confined by surfaces that it doesn't like, the material can be expelled from the confining region in a process called "dewetting."

Research clarifies the physics of water repelling surfaces

July 3, 2015

Researchers have gained valuable insights into the behaviour of water on strongly hydrophobic (water-repelling) surfaces. Understanding this behaviour should help scientists develop new types of surfaces with applications ...

Learning how to fine-tune nanofabrication

February 14, 2017

Daniel Packwood, Junior Associate Professor at Kyoto University's Institute for Integrated Cell-Material Sciences (iCeMS), is improving methods for constructing tiny "nanomaterials" using a "bottom-up" approach called "molecular ...

Researchers find that molecules sense curvature at the nanoscale

September 20, 2012

(Phys.org)—UCLA researchers, working in collaboration with colleagues at the University of Washington and Pennsylvania State University have used surface photochemical reactions to probe the critical role of substrate morphology ...

Recommended for you

Chemists ID catalytic 'key' for converting CO2 to methanol

March 23, 2017

Capturing carbon dioxide (CO2) and converting it to useful chemicals such as methanol could reduce both pollution and our dependence on petroleum products. So scientists are intensely interested in the catalysts that facilitate ...

Team refines filters for greener natural gas

March 23, 2017

Natural gas producers want to draw all the methane they can from a well while sequestering as much carbon dioxide as possible, and could use filters that optimize either carbon capture or methane flow. No single filter will ...

Argon is not the 'dope' for metallic hydrogen

March 23, 2017

Hydrogen is both the simplest and the most-abundant element in the universe, so studying it can teach scientists about the essence of matter. And yet there are still many hydrogen secrets to unlock, including how best to ...

Microbes could make drug production more efficient

March 23, 2017

Alkaloid-based pharmaceuticals derived from plants can be potent treatments for a variety of illnesses. But getting these powerful therapeutic agents from plants can take a long time and cost plenty of money, because it often ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.