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In water droplets like those on early Earth, amino acids can assemble spontaneously into proteins

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Tiny droplets of sea spray form above crashing waves

One of the really tough conundrums about how life got started on Earth is the “water paradox”: Liquid water is necessary for life as we know it here on Earth, and yet a lot of chainlike molecules that all living things need (like proteins, RNA, and DNA) cannot link up spontaneously in liquid water. 

Let’s consider proteins.  Living organisms can’t make proteins without the help of … already-existing proteins.  So how could proteins possibly have arisen in reasonable amounts to help set up the beginning of life on Earth, somewhere between 4.4 and 3.8 billion years ago?

Well, it just got a whole lot easier to explain.  A research team at Purdue University led by chemistry professor R. Graham Cooks used a simple but clever setup to convincingly solve this conundrum and show how this could have happened — quite easily, actually — on the early Earth.  Their findings were reported October 3 in the Proceedings of the National Academy of Sciences.  (Behind a paywall, but I thank Dr. Cooks for kindly sending me a reprint so I could check it out.)

We’re confident that amino acids — the building blocks of proteins — were available on the early Earth because of a bunch of observations:

  • Stanley Miller’s famous 1953 experiment ran early-Earth gases methane, ammonia, hydrogen, and water vapor past an electrical discharge (sort of like lightning) in circulation for several days, and plentiful organic compounds were formed, among them aspartate, alanine, glycine, and probably other amino acids.
  • In 2018, more-complex amino acids that appear to have formed in the absence of any life were found deep beneath the seafloor in mantle-derived rocks.
  • We’ve also seen at least 80 different kinds of amino acids show up in meteorites now.

But protein formation?  Not so much.  There was one report in 2020 of the first protein being found in a meteorite, which generated some buzz but ultimately didn’t survive peer review and hasn’t appeared in any journal.  If it had, believe me, I’d have been all over that one. 

So we’ve been looking very hard for a demonstration of how proteins could have formed from amino acids somehow on the early Earth, but until now, no such luck.

Why is it so hard to make proteins out of amino acids in water?

In order to get started, a “condensation” reaction has to occur; that is, two amino acids need to link together and kick out a water molecule:

Two generic amino acids link together to form a dipeptide, with the loss of a water molecule

The two molecules on the left side are both the same kind of molecule: a generic amino acid.  All amino acids look like this, the only difference among them being the “R”.  “R” can be lots of different things, but life on Earth, with rare exceptions, only uses 20 specific things for “R”. 

To link two amino acids together, the “amino” (—NH2) end of one amino acid reacts with the “acid” (—COOH) end of another one.   This gives us OC—NH (the “peptide bond”, shown in red on the right above), and it also produces a water molecule (HOH, in blue).  But keep in mind that this reaction can also go backwards.  And within a body of water, this backward reaction happens way, way, way more often than the forward, just because there’s so dang much water around.

I wanted to find out exactly how obnoxiously difficult it is to make a peptide bond in water, so I used a couple of online tools called eQuilibrator and Calistry to help me out.  Let’s take the simplest amino acid — glycine — where the “R” is just a hydrogen (H) and try to link two of them together.  Under garden-variety conditions (for those keeping score at home: pH 7.5, 25°C, and 0.25 M salt), it turns out that when this reaction settles to its final equilibrium state, only two out of every 360 quadrillion glycine molecules will have paired up.  Sheesh, we’re never going to get life started this way.

As if things weren’t already hard enough, amino acids spend most of their time in the “zwitterionic” form at most pH levels you’d encounter on Earth, where they can’t even react with each other:

From pH 4 to pH 9 (not strongly acidic or basic), amino acids spend most of their time in zwitterionic form.  Acidic groups such as -COOH like to donate protons (H+) to basic groups such as -NH2, and that’s exactly what happens

This means that even the super-crappy equilibrium state mentioned above will take a really long time to reach.  Now you see what an uber-tough nut the “water paradox” is to crack. 

So people have concocted explanations to get around this problem in ways that would fit in with conditions on early Earth, proposing that amino acids could be coerced to link together in water under very special circumstances like near natural mineral or clay catalysts, special salts, etc.  But these things start to feel like reaches and don’t provide intuitively satisfying answers.

Intelligent-design people would be happy to hear me say that, I suppose, but now I have to burst their bubble.

Cooks’ group provided the part we’d been missing all along — small water droplets — and showed that linking amino acids together within them turns out not to be hard at all.  They made a dilute solution of glycine or alanine in water.  After two hours, nothing had happened, of course.  But when they made fine spray out of those very same solutions, glycine-glycine (Gly-Gly) or alanine-alanine (Ala-Ala) dipeptides formed in easily detectable amounts in a matter of milliseconds.

Their first crack at making the droplets was with nano-electrospray ionization, or nESI.  Here we suck electrons out of a liquid (a dilute solution of glycine in water, in this case) by applying a strong voltage between the emitter and the detector.  The liquid takes on a net positive charge, so it’s literally pulled over to the negatively charged detector plate as a mist:

  

Nano-electrospray ionization (nESI).  We can also run this by reversing the voltage and giving the liquid a net negative charge if we want to.  At right is a mass spectrometer opening.  The droplets spend a few milliseconds in flight, then go in there and can be analyzed for their chemical content.  (The late John B. Fenn won the 2002 Nobel Prize in Chemistry for developing this method.)

The drops get even smaller on their way over to the detector because the positive charges within them repel each other, and this makes the droplets break up.  Normally, nESI makes droplets that start out around 0.2 μm (millionths of a meter) wide and get smaller from there.

But now you might say, isn’t putting a charge onto the molecules kind of cheating, though?  That doesn’t routinely happen in nature!  And if you say that, you are right.  It’s not exactly fair.  Lots of people have made peptide bonds under crazy, non-Earth-like conditions.  Big deal.

So then they repeated the experiment without applying any voltage at all, making the spray by physically pushing the liquid through the emitter with a syringe.  The droplets weren’t quite as small, but it worked anyway.  The net charge hadn’t been responsible for the effect after all; it was all about the droplets. 

But it gets better.  They sprayed two glycine-containing mists together and ended up with not only Gly-Gly but also Gly-Gly-Gly and Gly-Gly-Gly-Gly.  When they sprayed two jets containg Gly-Gly together, they got Gly-Gly-Gly-Gly and Gly-Gly-Gly-Gly-Gly-Gly!  They mixed glycine and alanine sprays together and got mixed peptides like Gly-Gly-Ala, Ala-Gly-Ala, etc. 

Hey, this is getting protein-like! 

Presumably if you keep slamming peptide-containing droplets together, as in sea spray, waterfall mist, and the like, the peptides can keep getting longer and longer and give you some primitive protein material to work with.

But wait a second.  How could these reactions work so fast in little droplets of water but not at all in bulk water?  I mean, water is water, isn’t it?  The trick seems to be that they happen only at the surface of each droplet.  One side of that surface is all water, true, but the other side is air, with very little water.  It becomes a whole lot easier to make water — that is, to run a condensation reaction like

Gly + Gly → Gly-Gly + H2O

— when there is no water around.  On the surface of a droplet, these molecules can stay dissolved in water and yet have access to a place with no water.  And there, my friends, is your solution to the “water paradox”.

Were we talking about drops?

There are plenty of other reasons that reactions can behave very differently at an air-water interface, and I mention that because this is actually a pretty hot topic in chemistry now.  It’s known that the —OH groups of water molecules can stick up at the surface, not being part of the (weak) bonding network they would have within the liquid, and that alone provides a different environment:

About 20% of the water molecules at an air-water interface have an -OH sticking up

There’s even an electric field across the air-water interface, and while that isn’t at all well-understood, it certainly can influence chemical reactions quite a bit.

The Purdue researchers observed that smaller droplets are better, because smaller droplets have a higher surface-to-volume ratio, so that means more surface area to do reactions compared to the volume to be filled, and so products like Gly-Gly can get more concentrated and be easier to detect.  

Can water droplets in nature get so tiny?  Of course they can!  Any droplet suspended in air will evaporate completely over time, so within a spray or mist we can generally have a full range of droplet sizes at any one time.  

It should be pointed out that, incredibly enough, the total surface area of sea spray on Earth is actually larger than the planet’s entire air-sea interface!  Not to mention all the droplets in clouds, waterfalls, rapids, etc.  So this is a hugely significant venue for new classes of chemical reactions occurring in nature, many of which we probably don’t even know about yet.

The same principle that applies to proteins here could very well also apply to DNA, RNA, polysaccharides, phosphates, and anything else biologically important that forms by condensation.  Hopefully our Purdue team will give some of those things a try next! 

But for now, one more unfathomable step in the emergence of life on Earth just got a whole lot more fathomable.  It’s always mesmerizing to watch the waves crash on the shore, and maybe part of the reason why is that we’re looking at the very beginnings of where we came from.



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Science

Water droplets hold the secret ingredient for building life

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Credit: CC0 Public Domain

Purdue University chemists have uncovered a mechanism for peptide-forming reactions to occur in water—something that has puzzled scientists for decades.

“This is essentially the chemistry behind the origin of life,” said Graham Cooks, the Henry Bohn Hass Distinguished Professor of Analytical Chemistry in Purdue’s College of Science.”This is the first demonstration that primordial molecules, simple amino acids, spontaneously form peptides, the building blocks of life, in droplets of pure water. This is a dramatic discovery.”

This water-based chemistry, which leads to proteins and so to life on Earth, could also lead to the faster development of drugs to treat humanity’s most debilitating diseases. The team’s discovery was published in the journal Proceedings of the National Academy of Sciences.

For decades scientists have theorized that life on Earth began in the oceans. The chemistry, however, remained an enigma. Raw amino acids—something that meteorites delivered to early Earth daily—can react and latch together to form peptides, the building blocks of proteins and, eventually, life. Puzzlingly, the process requires the loss of a water molecule, which seems highly unlikely in a wet, aqueous or oceanic environment. For life to form, it needed water. But it also needed space away from the water.

Cooks, an expert in mass spectrometry and early Earth chemistry, and his team have uncovered the answer to the riddle: “Water isn’t wet everywhere.” On the margins, where the water droplet meets the atmosphere, incredibly rapid reactions can take place, transforming abiotic amino acids into the building blocks of life. Places where sea spray flies into the air and waves pound the land, or where fresh water burbles down a slope, were fertile landscapes for life’s potential evolution.

The chemists have spent more than 10 years using mass spectrometers to study chemical reactions in droplets containing water.

“The rates of reactions in droplets are anywhere from a hundred to a million times faster than the same chemicals reacting in bulk solution,” Cooks said.

The rates of these reactions make catalysts unnecessary, speeding up the reactions and, in the case of early Earth chemistry, making the evolution of life possible. Understanding how this process works has been the goal of decades of scientific research. The secret of how life arose on Earth can help scientists understand why it happened and inform the search for life on other planets, or even moons.

Understanding how amino acids built themselves up into proteins and, eventually, life-forms revolutionizes scientists’ understanding of chemical synthesis. That same chemistry could now aid synthetic chemists in speeding the reactions critical to discovering and developing new drugs and therapeutic treatments for diseases.

“If you walk through an academic campus at night, the buildings with the lights on are where synthetic chemists are working,” Cooks said. “Their experiments are so slow that they run for days or weeks at a time. This isn’t necessary, and using droplet chemistry, we have built an apparatus, which is being used at Purdue now, to speed up the synthesis of novel chemicals and potential new drugs.”

Scientists discover new ‘origins of life’ chemical reactions

More information:
Holden, Dylan T. et al, Aqueous microdroplets enable abiotic synthesis and chain extension of unique peptide isomers from free amino acids, Proceedings of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2212642119. doi.org/10.1073/pnas.2212642119
Provided by
Purdue University

Citation:
The fountain of life: Water droplets hold the secret ingredient for building life (2022, October 3)
retrieved 3 October 2022
from https://phys.org/news/2022-10-fountain-life-droplets-secret-ingredient.html

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Wobbling droplets in space confirm late professor’s theory

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Droplet driven at 1.6 Hz oscillating in the [2,0] mode on substrate F7 exhibits a freely moving contact line. Credit: J. McCraney et al, Physical Review Letters (2022). DOI: 10.1103/PhysRevLett.129.084501

At a time when astronomers around the world are reveling in new views of the distant cosmos, an experiment on the International Space Station has given Cornell researchers fresh insight into something a little closer to home: water.

Specifically, the space station’s microgravity environment illuminated the ways that water droplets oscillate and spread across solid surfaces—knowledge that could have very earthbound applications in 3D-printing, spray cooling, and manufacturing and coating operations.

The research team’s paper, “Oscillations of Drops with Mobile Contact Lines on the International Space Station: Elucidation of Terrestrial Inertial Droplet Spreading,” published Aug. 16 in Physical Review Letters. The lead author is Joshua McCraney, Ph.D.

The experiment and its findings, while successful, are also bittersweet. The paper’s co-senior author Paul Steen, the Maxwell M. Upson Professor in the Smith School of Chemical and Biomolecular Engineering in the College of Engineering, died in September 2020, just before the experiment was conducted.

“It’s sad that Paul didn’t get to see the experiments launch into space,” said co-senior author Susan Daniel, the Fred H. Rhodes Professor in the Smith School of Chemical and Biomolecular Engineering, and Steen’s longtime collaborator. “We hope that we did right by him in the end, and that the paper that we produced from the work would make him proud.”

Daniel began collaborating with Steen shortly after she first came to Cornell as an assistant professor in 2007. While her current research is focused on the biological interface of the coronavirus, her graduate work was in chemical interfaces and fluid mechanics—a field in which Steen was advancing a number of theoretical predictions based upon how droplets resonate when subjected to vibrations. The two researchers instantly connected.

“He knew the theory and made predictions, and I knew how to execute the experiments to test them,” Daniel said. “Basically, from the moment I got here in 2007 until he passed away, we worked on trying to understand how liquids and surfaces interact with each other, and how the contact line at the interface between them behaves under different conditions.”

Their collaboration resulted in a “photo album” of the dozens of possible shapes that an oscillated drop of water can take. Steen later expanded on that project by cataloging the droplets’ energy states as evidenced by those resonant shapes, organizing them into a “periodic table” classification.

In 2016, Steen and Daniel received a four-year grant from the National Science Foundation (NSF) and NASA’s Center for the Advancement of Science in Space to conduct fluid dynamics research aboard the International Space Station U.S. National Laboratory.

Space is an ideal place to study the behavior of fluids because of the radical reduction of gravity, which on the ISS is about one-millionth of its terrestrial level. This means that fluid-surface interactions which are so small-scale and speedy on Earth that they are practically invisible can be, in space, nearly 10 times larger—from microns to centimeters—and their duration slows nearly 30-fold.

“It’s harder to study these drop motions, experimentally and fundamentally, when you have gravity in your way,” Daniel said.

Steen and Daniel selected a few resonance shapes from their photo album that they wanted to explore in detail, with a focus on how a water droplet’s contact line—or outer edge—slides back and forth across a surface, driving the way the liquid will spread, a phenomenon that can be controlled by varying vibration frequencies.

The team prepared meticulous instructions for the astronauts to follow, compressing four years of planning into a several-minute experiment in which every second was tightly choreographed.

With the researchers monitoring and providing feedback in real time on the ground, the astronauts deposited 10 mL water droplets via a syringe onto nine different hydrophobic surfaces with varying degrees of roughness. They also forced pairs of droplets to coalesce together, and placed droplets onto an oscillator and tuned its vibrations to achieve the targeted resonance shapes. The water droplets’ wobbling and jiggling movements were filmed, and the researchers spent the next year analyzing the data.

That analysis ultimately confirmed Steen’s theories about the way a liquid’s density and surface tension control the contact line’s mobility, overcoming a surface’s roughness.

Daniel credits co-author Joshua Bostwick, Ph.D., a former student of Steen and now the Stanzione Collaboration associate professor at Clemson University, with ensuring that the experiment results squared with Steen’s theoretical predictions.

“Josh was able to carry on with the theoretical side of this work in Paul’s absence, which was not something I was ready to step into and do. It was nice to have him rejoin the team and help us make sure that we were able to extract everything we could from the data we collected,” Daniel said. “Now we can essentially use the theory that Paul created to make predictions, for example, in processes where you’re spraying droplets on surfaces, or in 3D-printing, or where liquids spread across a surface really quickly.”

Vanessa Kern, Ph.D. was also a co-author of the paper.

New periodic table of droplets could help solve crimes

More information:
J. McCraney et al, Oscillations of Drops with Mobile Contact Lines on the International Space Station: Elucidation of Terrestrial Inertial Droplet Spreading, Physical Review Letters (2022). DOI: 10.1103/PhysRevLett.129.084501
Provided by
Cornell University

Citation:
Wobbling droplets in space confirm late professor’s theory (2022, August 16)
retrieved 17 August 2022
from https://phys.org/news/2022-08-droplets-space-late-professor-theory.html

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New study solves mystery of how soft liquid droplets erode hard surfaces

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A new study led by University of Minnesota Twin Cities researchers shows why liquid droplets have the ability to erode hard surfaces, a discovery that could help engineers design more erosion-resistant materials. The above image shows the impact droplets can make on a granular, sandy surface (left) versus a hard, plaster (right) surface. Credit: Cheng Research Group, University of Minnesota

A first-of-its-kind study led by University of Minnesota Twin Cities researchers reveals why liquid droplets have the ability to erode hard surfaces. The discovery could help engineers design better, more erosion-resistant materials.

Using a newly developed technique, the researchers were able to measure hidden quantities such as the shear stress and pressure created by the impact of liquid droplets on surfaces, a phenomenon that has only ever been studied visually. 

The paper is published in Nature Communications.

Researchers have been studying the impact of droplets for years, from the way raindrops hit the ground to the transmission of pathogens such as COVID-19 in aerosols. It’s common knowledge that slow-dripping water droplets can erode surfaces over time. But why can something seemingly soft and fluid make such a huge impact on hard surfaces?

“There are similar sayings in both eastern and western cultures that ‘Dripping water hollows out stone,'” explained Xiang Cheng, senior author on the paper and an associate professor in the University of Minnesota Department of Chemical Engineering and Materials Science. “Such sayings intend to teach a moral lesson: ‘Be persistent. Even if you’re weak, when you keep doing something continuously, you will make an impact.’ But, when you have something so soft like droplets hitting something so hard like rocks, you can’t help wondering, ‘Why does the drop impact cause any damage at all?’ That question is what motivated our research.”






Watch a video demonstrating in slow motion how a water droplet impacts a sandy surface. Credit: University of Minnesota

In the past, droplet impact has only been analyzed visually using high-speed cameras. The University of Minnesota researchers’ new technique, called high-speed stress microscopy, provides a more quantitative way to study this phenomenon by directly measuring the force, stress, and pressure underneath liquid drops as they hit surfaces.

The researchers found that the force exerted by a droplet actually spreads out with the impacting drop—instead of being concentrated in the center of the droplet—and the speed at which the droplet spreads out exceeds the speed of sound at short times, creating a shock wave across the surface. Each droplet behaves like a small bomb, releasing its impact energy explosively and giving it the force necessary to erode surfaces over time.

Besides paving a new way to study droplet impact, this research could help engineers design more erosion-resistant surfaces for applications that must weather the outdoor elements. Cheng and his lab at the University of Minnesota Twin Cities already plan to expand this research to study how different textures and materials change the amount of force created by liquid droplets.

“For example, we paint the surface of a building or coat wind turbine blades to protect the surfaces,” Cheng said. “But over time, rain droplets could still cause damage via impact. So, our research after this paper is to see if we can reduce the amount of shear stress of droplets, which would allow us to design special surfaces that can mitigate the stress.”

In addition to Cheng, the research team included University of Minnesota chemical engineering Ph.D. student Ting-Pi Sun, University of Santiago, Chile Assistant Professor Leonardo Gordillo and undergraduate students Franco Álvarez-Novoa and Klebbert Andrade, and O’Higgins University, Chile Assistant Professor Pablo Gutiérrez.

Heat conduction is important for droplet dynamics

More information:
Stress distribution and surface shock wave of drop impact, Nature Communications (2022). DOI: 10.1038/s41467-022-29345-x
Provided by
University of Minnesota

Citation:
New study solves mystery of how soft liquid droplets erode hard surfaces (2022, March 31)
retrieved 31 March 2022
from https://phys.org/news/2022-03-mystery-soft-liquid-droplets-erode.html

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part may be reproduced without the written permission. The content is provided for information purposes only.



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Scientists Smash Temperature Record on Keeping ‘Freezing Cold’ Water in Liquid Form

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Scientists have just proven that the freezing temperature of water can be even lower than what we thought was possible.

Taking tiny droplets of water, up to just 150 nanometers in size, a team of engineers at the University of Houston has pushed the critical temperature threshold to -44 degrees Celsius (-47.2 degrees Fahrenheit) – and, more saliently, accurately measured it.

 

Not just a fun thing to brag about at engineering parties, this achievement can now help us to better understand how water freezes, which has implications for a range of scientific fields, from meteorology to cryopreservation.

“Experimental probing of the freezing temperature of few-nanometer water droplets has been an unresolved challenge,” says mechanical engineer Hadi Ghasemi of the University of Houston, Texas.

“Here, through newly developed metrologies, we have been able to probe freezing of water droplets from micron scale down to 2 nm scale.”

Most of us don’t think about water very much, because it’s so ubiquitous and essential for our very existence. But common H2O is actually pretty weird; it doesn’t behave like any other liquid. Even the way it freezes is weird: where other liquids increase in density as they cool, water actually becomes less dense as it freezes.

Water’s behavior has been fairly well characterized and studied. We know, for example, that it tends to nucleate, or form ice crystals, at a variety of temperatures, sometimes resisting the process as far as -38 degrees Celsius. Any colder, and even the most stubborn water molecules will stick together as ice.

 

Ghasemi and colleagues pushed that temperature downwards by placing nanodroplets of water on a soft surface, like a gel or a lipid. Then, they probed the droplets using electrical resistance metrology and Fourier transform infrared spectroscopy to take their temperature as they froze.

The soft interface between the surface and the tiny droplet seemed to play a role in the suppression of ice nucleation, possibly because of the way the interface generates a large pressure on the droplet.

This is because the freezing temperature of water drops as ambient pressure rises. The most pronounced effect was seen in a droplet of water just 2 nanometers across.

“We found that if a water droplet is in contact with a soft interface, freezing temperature could be significantly lower than hard surfaces,” Ghasemi explains.

“Also, a few-nanometer water droplet could avoid freezing down to -44 degrees Celsius if it is in contact with a soft interface.”

The way tiny water droplets freeze is vitally important to cryopreservation, since the freezing of tiny droplets within cells can cause those cells to rupture and die. Learning how to slow or halt that process could help scientists find ways to mitigate that effect.

 

It could also help us better understand how nucleation happens in the atmosphere, where microscopic droplets of water freeze. And it could also help us to better design technology that suffers from ice exposure, such as aircraft and wind turbines, the researchers said.

“The findings are in good agreement with predictions of classical nucleation theory. This understanding contributes to a greater knowledge of natural phenomena and rational design of anti-icing systems for aviation, wind energy, and infrastructures and even cryopreservation systems,” they write in their paper.

“The findings provide an understanding of various natural phenomena and provide a route for the design of superior anti-icing biomimetics or smooth liquid-infused surfaces.”

The research has been published in Nature Communications.

 

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