Scientists glimpse why life can't happen without water

June 20, 2016
water
Credit: George Hodan/public domain

Scientists are getting closer to directly observing how and why water is essential to life as we know it.

A study in this week's Proceedings of the National Academy of Sciences provides the strongest evidence yet that proteins—the large and that fold into particular shapes to enable biological reactions—can't fold themselves.

Rather, the work of folding is done by much smaller , which surround proteins and push and pull at them to make them fold a certain way in fractions of a second, like scores of tiny origami artists folding a giant sheet of paper at blazingly fast speeds.

Dongping Zhong, leader of the research group at The Ohio State University that made the discovery, called the study a "major step forward" in the understanding of water- interactions and said it answers a question that's been dogging research into for decades.

"For a long time, scientists have been trying to figure out how water interacts with proteins. This is a fundamental problem that relates to protein structure, stability, dynamics and—finally—function," said Zhong, who is the Robert Smith Professor of physics at Ohio State.

"We believe we now have strong direct evidence that on ultrafast time scales (picoseconds, or trillionths of a second), water modulates protein fluctuations," he concluded.

Zhong, who is also a professor of chemistry and biochemistry, and his team used ultrafast laser pulses to take snapshots of water molecules moving around a DNA polymerase, the kind of protein that helps DNA reproduce.

The key to getting a good view of the interaction was to precisely locate optical probes on the protein surface, he said. The researchers inserted molecules of the amino acid tryptophan into the protein as a probe, and measured how water moved around it.

Water molecules typically flow around each other at picosecond speeds, while proteins fold at nanosecond speeds—1,000 times slower. Previously, Zhong's group demonstrated that water molecules slow down when they encounter a protein. Water molecules are still moving 100 times faster than a protein when they connect with it, however.

In the new study, the researchers were able to determine that the water molecules directly touched the protein's "side chains," the portions of the that bind and unbind with each other to enable folding and function. The researchers were also able to note the timing of movement in the molecules.

Computer simulations at the Ohio Supercomputer Center (OSC) helped the researchers visualize what was going on: where the water moved a certain way, the protein folded nanoseconds later, as if the water molecules were nudging the protein into shape.

Water can't arbitrarily shape a protein, Zhong explained. Proteins can only fold and unfold in a few different ways depending on the amino acids they're made of.

"Here, we've shown that the final shape of a protein depends on two things: water and the themselves. We can now say that, on ultrafast time scales, the protein surface fluctuations are controlled by water fluctuations. Water molecules work together like a big network to drive the movement of proteins."

Explore further: How water molecules dance to activate proteins

More information: Dynamics and mechanism of ultrafast water–protein interactions, PNAS, www.pnas.org/cgi/doi/10.1073/pnas.1602916113

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7 comments

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eric96
3 / 5 (2) Jun 20, 2016
All life on land needs oxygen.
Protein and therefore life needs water.
It follows that life started in the ocean.
To have a food chain, you have to start with the smallest.
"There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth,[5] forming a biomass which exceeds that of all plants and animals"
Well is the brunt of the ecosystem.
"Scientists believe that phytoplankton contribute between 50 to 85 percent of the oxygen in Earth's atmosphere. "
" You can't make new proteins without DNA, and you can't make new DNA without proteins. So which came first, proteins or DNA?"
"Was RNA the first replicator?"
"How was RNA created?"
thingumbobesquire
1 / 5 (8) Jun 21, 2016
Yet another example that the theory of random change is in the mind of the beholder.
thingumbobesquire
1 / 5 (7) Jun 21, 2016
Analog Wave Forms Versus Digital "Information" Models of the Brain http://thingumbob...tal.html
antialias_physorg
4.2 / 5 (5) Jun 21, 2016
All life on land needs oxygen.
Protein and therefore life needs water.

Not logical. There's plenty of anerobic life (on land and nywhere else) which still requires water. Oxygen isn't the reason why watewr is required.

To have a food chain, you have to start with the smallest.

Life did not start with a food chain
Tektrix
5 / 5 (4) Jun 21, 2016
Yet another example that the theory of random change is in the mind of the beholder.


Looks like we've got another self-promoting crank on the boards. :(
torbjorn_b_g_larsson
4.2 / 5 (5) Jun 21, 2016
Yet another example that the theory of random change is in the mind of the beholder.


But we aren't discussing "noise as we know it", we are discussing "life as we know it".

Possibly that is a crank erroneous characterization of the process of evolution or "differential reproduction", which can be mechanistically simplified to ("non-random") selection acting on ("random") variation. [ https://en.wikipe...volution ; how hard can it be to find with google? ]

It would be like calling gravity "random falling" or quantum mechanics "random disturbances", fit science for cranks.
snerdguy
not rated yet Jun 27, 2016
The title belies the research. They are determining the role that water plays in life the way we understand it exists right now. But, whether or not life, or the self assembly of molecules and structures, could exist in a different liquid under a different set of conditions is something we don't know and will likely never know. We just keep on looking.

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