JUN 24, 2016 10:16 AM PDT

Scientists Get Closer to Knowing Why Water is Essential

WRITTEN BY: Carmen Leitch
Data published this week in Proceedings of the National Academy of Sciences is the most convincing evidence seen yet that proteins need water to properly move and fold. This evidence appreciably aids in our understanding of why and how water is so critical for life. There has been a lack of understanding how proteins and water relate and interact, and it’s been a topic of research interest for decades.
Dongping Zhong, the Robert Smith Professor of physics at The Ohio State University. Photo by Jo McCulty, courtesy of The Ohio State University.
A team at Ohio State University, led by physics Professor Dongping Zhong, has shown that when proteins fold, water molecules surrounding the proteins are actually pushing and pulling at them to fold the parts of the protein into a specific conformation. All of this happens at incredibly fast speeds. This team has shown previously that water molecules slow down when they flow around proteins, while still moving around 100 times faster than the protein.

This new study shows that water molecules directly interact with the side chains of the protein. Side chains are the parts of a protein that bind and unbind to each other to create the functional protein.
"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," explains Zhong.

"We believe we now have strong direct evidence that on ultrafast time scales (picoseconds, or trillionths of a second), water modulates protein fluctuations," he continues.
In this PNAS image, Molecular dynamics simulations after several typical inner-layer (red) and outer-layer (blue) water molecules with relaxation motions that correspond to the observed dissolution dynamics. At time ?1S (20 fs), only outer-layer water molecules locally relax. At time ?2S (130 fs), water molecules have significant rotational motions. But all water molecules remain in position, and the protein does not move much. By time ?3S (50 ps), all water molecules have made significant rearrangements and also exchanged with bulk water.
To visualize this relationship, the investigators took pictures using ultrafast laser pulses of water molecules flowing around a DNA polymerase. By inserting the amino acid tryptophan into the polymerase, they were able to measure how fast molecules of water moved around it because the tryptophan acted as a sort of optical probe they could precisely locate. Optical probes enable researchers to visualize cellular events with excellent spatial resolution and in real time.

Using simulations on computers at the Ohio Supercomputer Center, the scientists were able to determine that when the water moved a particular direction, nanoseconds later the protein folded.
Shown here from PNAS are three relaxation processes of hydration water and coupled tryptophan side chain in a potential energy basin with conformational substrates. The arrow indicates the constrained relaxation pathway with the initial outer-layer ultrafast relaxation (?1S), which is not coupled to the protein motion, and two water-driven water/side-chain relaxations (?2S and ?3S), which access only a limited region in the energy basin.
Proteins are only able to fold and unfold in a few ways because of the amino acids they are made of; water cannot just shape a protein any random way. “Here, we’ve shown that the final shape of a protein depends on two things: water and the amino acids 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,” Zhong explains.
 
Sources: The Ohio State University News Room via Science Daily, PNAS
 
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