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New Mechanism Moves Biochemical Cargo and Points to Design

Years ago, my wife Amy and I adopted two children from an orphanage in Mexico. It was enlightening to glimpse the world through their young eyes.

I remember the first time we took them to a grocery store in the States. They were amazed by what they saw. They couldn’t believe how much food was in one place. They kept running up and down the aisles, shouting “Mas comida!”

As Americans, we take so many things for granted. For many of us, all we have to do is get in our cars, drive a few miles to a nearby grocery or retail store, and buy almost anything we need or, even, just want. Food and other basic necessities are never in short supply—at least, this statement would have been true before the COVID19 pandemic disrupted our economy and economies around the world.

The COVID19 pandemic served as a rude awakening for many of us, particularly in its early days. It felt surreal to go into grocery stores and see empty shelves. And it was frustrating—even discouragingto travel from store to store, unable to find life’s basic necessities.

Many factors contributed to the food shortage and scarcity of household items. The most significant contributor appears to have been the failure of the logistics systems that supply products to grocery stores and general merchandise retailers. For example, when centralized processing and manufacturing operations—which normally create efficiencies—experienced disruptions, they delayed the production of food items and other essential consumer products, such as sanitary supplies. But perhaps the biggest culprit was the rigidity of supply chains. Under normal circumstances, this rigidity creates efficiencies, but in the midst of the lockdowns it kept the system from responding to changing demands. So, even though adequate manufacturing capabilities still existed, foodstuff and essential items sat in warehouses or had to be dumped because the supply chains couldn’t be adapted rapidly enough to deliver the right amount of product to the right outlets as lockdown and restrictions changed the economic demand for many items.

Through this difficult experience, the COVID19 pandemic drove home a key lesson for manufacturers and distributors: It is one thing to be able to produce a product, but, if that product can’t be effectively sent to the right location in a timely manner, then shortages become inevitable and lives are disrupted.

Transport of Cell Cargo
Life scientists have discovered that cells face the same logistical challenges. Once biomolecular materials are produced by the cell’s biosynthetic operations (i.e., manufacturing systems), they have to be distributed to the appropriate cellular location. If not, it disrupts the cellular economy to the point that cell survival is threatened.

For this reason, cells employ elaborate mechanisms to transport biomolecular cargo from its point of origin to the required location(s) in the cell. These processes are energy-intensive and require highly specific protein-protein interactions.

Recently, a research team of biophysicists from Germany discovered that cells employ a heretofore unrecognized mechanism to transport cargo that relies on a physical process called diffusiophoresis.1 This process seems to be energy dependent but doesn’t require highly specific protein-protein interactions. Instead, it appears to be based solely on a physical mechanism. For this reason, cells appear to employ diffusiophoresis to support the general movement of materials throughout the cell. Because of its simplicity and generalized nature, the research team believes that this process played an important role in the origin of life, serving as the first transport mechanism in the earliest appearing and most primitive cells on Earth.

Not only does this discovery offer fundamental insight into the physical processes occurring inside the cell, but it also has provocative theological implications, suggesting that the universe has been designed in the just-right way for life to be possible.

Diffusiophoresis
The phenomenon of diffusiophoresis was first studied by physicists in the 1940s. Physical scientists observed that the concentration gradient in solution of one substance (say, A) causes the movement of another substance (B) in response to its (A) concentration gradient.

Diffusiophoresis is distinct from diffusion. During diffusion, a substance (whether dissolved compounds or colloidal particles) travels along a gradient, moving from areas of high concentration to low concentration.

In other words, during the process of diffusion, materials move along their own concentration gradient. During diffusiophoresis, materials move in response to another substance’s concentration gradient.

The Min System
To determine the role played by physical processes in moving molecular-scale cargo from one location to another in the cell, the team turned their attention to the Min system found in E. coli. This system has become a useful model for life scientists interested in studying molecular transport in the cell.

The Min system plays a role in the cell division process. Three proteins comprise the Min system: MinC, MinD, and MinE. These three proteins move from cell pole to cell pole, setting up a dynamic oscillation of their concentration throughout the cell. This back-and-forth flux prevents the cell division protein FtsZ from locating in the cell poles. Instead, this protein is forced to concentrate in the cell’s midplane. Once localized to the cell’s midplane, multiple copies of FtsZ assemble into a contractile ring. This ring appears to drive the cell division process by causing the cell to constrict and by recruiting other enzymes to construct the cell wall after cell division takes place.

To initiate the process, MinD first localizes to one of the cell’s poles. This protein binds ATP. When the binding event takes place, the MinD becomes anchored to the cell membrane. Once MinD becomes bound to the cell membrane, it causes other copies of the MinD protein with bound ATP to cluster to the same polar location. In turn, these clusters bind copies of the MinC protein, resulting in their activation. MinC inhibits the polymerization of FtsZ, preventing copies of this protein from inappropriately assembling the contractile ring near the cell poles.


Figure: The Activity of the Min System
Image credit: Wikipedia



If left unchecked, the MinDC complexes would spread from the poles to the midplane of the cell, preventing the formation of the FtsZ contractile ring at its desired location. The MinE protein prevents this spread from occurring. Copies of the MinE protein interact with MinD, resulting in the formation of a MinE ring near the poles adjacent to the MinD and MinC clusters. The MinE protein causes ATP molecules that are bound to MinD to hydrolyze, releasing the products ADP and a phosphate ion. The hydrolysis of ATP causes MinD to dissociate from the cell membrane and in the process, MinC becomes deactivated.

Over time, a MinE ring will progressively decrease the size of the MinD plus MinC complexes. The freed copies of MinD can’t re-bind ATP right away. The ADP resulting from the hydrolysis reaction must dissociate from MinD first. Because the copies of MinD are concentrated at one end of the cell, the freed MinD copies will diffuse along the concentration gradient to the opposite end of the cell. Once there, MinD will interact with ATP and become bound to the opposite pole. Once again, this binding leads to MinD cluster formation and the binding and activation of MinC. The copies of MinE will then migrate to the opposite pole (because of the concentration gradient), form a ring, and cause MinD to debind.

This back-and-forth process occurs repeatedly. The MinD, MinC, and MinE proteins move from cell pole to cell pole, setting up a dynamic spatial organization in the cell. The net effect is that the concentration of FtsZ builds up near the midplane of the cell.

Min System and Diffusiophoresis
The German investigators devised a clever experiment to test if nonspecific physical processes played a role in moving molecular cargo around the cell.

To accomplish this test, they assembled lipid bilayers that were attached to a solid support. In previous studies, life scientists have used supported lipid bilayers to study the movements of MinD, MinC, and MinE in vitro. These studies have shed important light on the dynamic behavior of the Min system in bacterial cells.

They also incorporated molecular “cargo” into the supported lipid bilayers. This cargo consisted of highly folded pieces of DNA (called DNA origami) that were attached to the protein streptavidin through a biotin bridge. Streptavidin binds strongly to biotin. The researchers took advantage of this property to anchor the DNA origami to the supported lipid bilayer by incorporating biotinylated lipids into the lipid bilayers. (These lipid molecules have the chemical compound biotin chemically bound to them.) In other words, the streptavidin was attached to the biotinylated lipids and to a biotinylated DNA origami.

They also took advantage of the binding properties of streptavidin to create molecular cargo of varying sizes. They used the biotin-streptavidin complexes as a type of molecular building block. By stringing together individual biotin-streptavidin complexes, they could vary the length of the “bridge” that anchored the DNA origami to the supported lipid bilayer and, in doing so, vary the cargo size.

The researchers noted that when they added ATP to the experimental system (which triggered the binding of MinD to the supported lipid bilayer), they observed a pattern of concentration waves for the MinC, MinD, and MinE proteins as they moved from region to region along the supported bilayer surface. They also observed that the molecular cargo (made up of the DNA origami anchored to the lipid bilayer via the biotinylated streptavidin bridge) formed a pattern of concentration waves that was anti-correlated to the concentration waves of the Min system proteins. As a result, the molecular cargo localized to the regions of the lipid bilayer became depleted in the Min proteins. The researchers also observed that the movement of the molecular cargo correlated with its size, with the larger cargo molecules moving a greater distance than the smaller ones.

By mathematically modeling the concentration waves, the research team concluded that diffusiophoresis drove the movement of the cargo. They speculate that the size dependence of the diffusiophoretic movements of the cargo stems from frictional interactions with the Min proteins. The larger the cargo, the greater the friction it experiences and, hence, the greater the distance it moves. The size dependence of the diffusiophoretic movement has another important consequence. The researchers observed that over time the molecular cargo eventually became sorted by size. In other words, diffusiophoresis created a spatial organization of the molecular cargo.

The Importance of Diffusiophoresis
Because the movement and the spatial organization of the molecular cargo is driven by a physical mechanism, the German scientists believe that diffusiophoresis may be a general mechanism used by cells to distribute and organize biomolecules throughout the cell—particularly for simpler prokaryotic cells. In fact, because of the minimal nature of the process, the researchers speculate that the first primitive cells on Earth may have used this mechanism to move and sort biomolecules. They write:

“Finally, simple as it is in comparison to eukaryotic, translational motor proteins, this mechanism could be interpreted as an alternative, more rudimentary mode of mechanochemical coupling and as such might be prevalent in prokaryotes and might have been present in early forms of life.”2

The researchers also believe that diffusiophoresis may serve a critical role for work in synthetic biology. Researchers working in this field pursue the creation of artificial, nonnatural life-forms, including protocells and minimal cells. Because the spatial and temporal organization of biomolecules appears to be critical for life, diffusiophoresis provides researchers with an accessible approach to attain biomolecular organization. The alternative would require synthetic biologists to design and engineer more complex systems, based on specific protein-protein interactions.

Diffusiophoresis and the Anthropic Principle
As a biochemist and Christian theist, I maintain the importance of this discovery extends beyond identifying and characterizing a previously unrecognized physical process occurring inside the cell. It leads to a provocative theological implication. It suggests that the universe has been designed in the just-right way for life to be possible.

In many respects, diffusiophoresis is an unusual—even, unanticipated—physical process. Diffusion makes intuitive sense. It isn’t surprising that materials will move along their own concentration gradient. But it is counterintuitive to think that the concentration gradient of a dissolved substance or a colloidal material could drive the diffusion of another substance. Yet, diffusiophoresis arises out of the laws of nature. It is a manifestation of the fundamental design of the universe. Diffusiophoresis appears to be a surface phenomenon. In the case of the Min system, the movement of the molecular cargo appears to be driven by frictional interactions at the surface of the Min proteins and the DNA origami tethered to the lipid bilayer. In other instances, the surface interaction involves the ions at the interfacial double layer between the colloidal particle and the bulk solution.

It is eerie to think that this odd physical phenomenon—which emerges from the fundamental laws of nature— appears to display the just-right and necessary characteristics that make possible the coherent movement of biomolecular materials inside cells, capable of creating the spatial and temporal molecular-scale organization required for life. By all indications this organization appears to be necessary for life—not just sophisticated prokaryotic and eukaryotic cells but even primitive, minimal cells. For this reason, we can’t justifiably conclude that evolutionary mechanisms adapted life to take advantage of diffusiophoresis. Instead, by all indications, it appears as if life wouldn’t be possible if diffusiophoresis didn’t exist. There does not appear to be any other simple mechanism that can generate spatial and temporal biomolecular organization in cells. Diffusion can’t. Over time, this process will obliterate organization, driving the concentration of biomolecules to equilibrium.

In other words, it appears that the anthropic principle extends into the realm of biochemistry. If it wasn’t for the just-right laws of nature, the unusual process of diffusiophoresis wouldn’t exist and neither would life.


Resources

The Anthropic Principle in Biochemistry and Biology

Simple Biological Rules Affirm Creation” by Fazale Rana (article)

Have Researchers Developed a Computer Algorithm that Explains the Origin of Life?” by Fazale Rana (article)

Molecular Logic of the Electron Transport Chain Supports Creation” by Fazale Rana (article)

Protein Amino Acids Form a ‘Just-Right’ Set of Biological Building Blocks” by Fazale Rana (article)

Is the Optimal Set of Protein Amino Acids Purposed by a Mind?” by Fazale Rana (article)

A Periodic Table for Protein Structures Reveals Biochemical Design” by Fazale Rana (article)

The Logic of DNA Replication Makes a Case for Intelligent Design” by Fazale Rana (article)

Biochemical Grammar Communicates the Case for Creation” by Fazale Rana (article)

Fatty Acids Are Beautiful” by Fazale Rana (article)

Spatial Organization of Bacteria

Bacteria: Ordered and Organized,” by Fazale Rana (article)

Bringing Order to the Case for Intelligent Design, Part 1” by Fazale Rana (article)

Bringing Order to the Case for Intelligent Design, Part 2” by Fazale Rana (article)

More Complex than Imagined, Part 1” by Fazale Rana (article)

More Complex than Imagined, Part 2” by Fazale Rana (article)

Bacteria More Complex than Imagined,” by Fazale Rana (article)


Endnotes

  1. Beatrice Ramm et al., “A Diffusiophoretic Mechanism for ATPDriven Transport without Motor Proteins,” Nature Physics (April 5, 2021): doi: 10.1038/s4157-021-01213-3.
  2. Ramm et al., “A Diffusiophoretic Mechanism.”
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