Tag Archives: Chuo University

Watching motor proteins at work

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Researchers in the UK and in Japan have described these motor proteins as ‘swinging on monkey bars’,

A Sept. 14, 2015 news item on Nanowerk provides more information about the motor protein observations,

These proteins are vital to complex life, forming the transport infrastructure that allows different parts of cells to specialise in particular functions. Until now, the way they move has never been directly observed.

Researchers at the University of Leeds and in Japan used electron microscopes to capture images of the largest type of motor protein, called dynein, during the act of stepping along its molecular track.

A Sept 14, 2015 Leeds University press release, (also on EurekAlert*) which originated the news item, expands on the theme with what amounts to a transcript of sorts for the video (Note: Links have been removed),

Dr Stan Burgess, at the University of Leeds’ School of Molecular and Cellular Biology, who led the research team, said: “Dynein has two identical motors tied together and it moves along a molecular track called a microtubule. It drives itself along the track by alternately grabbing hold of a binding site, executing a power stroke, then letting go, like a person swinging on monkey bars.

“Previously, dynein movement had only been tracked by attaching fluorescent molecules to the proteins and observing the fluorescence using very powerful light microscopes. It was a bit like tracking vehicles from space with GPS. It told us where they were, their speed and for how long they ran, stopped and so on, but we couldn’t see the molecules in action themselves. These are the first images of these vital processes.”

An understanding of motor proteins is important to medical research because of their fundamental role in complex cellular life. Many viruses hijack motor proteins to hitch a ride to the nucleus for replication. Cell division is driven by motor proteins and so insights into their mechanics could be relevant to cancer research. Some motor neurone diseases are also associated with disruption of motor protein traffic.

The team at Leeds, working within the world-leading Astbury Centre for Structural Molecular Biology, combined purified microtubules with purified dynein motors and added the chemical fuel ATP (adenosine triphosphate) to power the motor.

Dr Hiroshi Imai, now Assistant Professor in the Department of Biological Sciences at Chuo University, Japan, carried out the experiments while working at the University of Leeds.

He explained: “We set the dyneins running along their tracks and then we froze them in ‘mid-stride’ by cooling them at about a million degrees a second, fast enough to prevent the water from forming ice crystals as it solidified. Then using a cryo-electron microscope we took many thousands of images of the motors caught during the act of stepping. By combining many images of individual motors, we were able to sharpen up our picture of the dynein and build up a dynamic idea of how it moved. It is a bit like figuring out how to swing along monkey bars by studying photographs of many people swinging on them.”

Dr Burgess said: “Our most striking discovery was the existence of a hinge between the long, thin stalk and the ‘grappling hook’, like the wrist between a human arm and hand. This allows a lot of variation in the angle of attachment of the motor to its track.

“Each of the two arms of a dynein motor protein is about 25 nanometres (0.000025 millimetre) long, while the binding sites it attaches to are only 8 nanometres apart. That means dynein can reach not only the next rung but the one after that and the one after that and appears to give it flexibility in how it moves along the ‘track’.”

Dynein is not only the biggest but also the most versatile of the motor proteins in living cells and, like all motor proteins, is vital to life. Motor proteins transport cargoes and hold many cellular components in position within the cell. For instance, dynein is responsible for carrying messages from the tips of active nerve cells back to the nucleus and these messages keep the nerve cells alive.

Co-author Peter Knight, Professor of Molecular Contractility in the University of Leeds’ School of Molecular and Cellular Biology, said: “If a cell is like a city, these are like the truckers on its road and rail networks. If you didn’t have a transport system, you couldn’t have specialised regions. Every part of the cell would be doing the same thing and that would mean you could not have complex life.”

“Dynein is the multi-purpose vehicle of cellular transport. Other motor proteins, called kinesins and myosins, are much smaller and have specific functions, but dynein can turn its hand to a lot of different of functions,” Professor Knight said.

For instance, in the motor neurone connecting the central nervous system to the big toe—which is a single cell a metre long— dynein provides the transport from the toe back to the nucleus. Another vital role is in the movement of cells.

Dr Burgess said: “During brain development, neurones must crawl into their correct position and dynein molecules in this instance grab hold of the nucleus and pull it along with the moving mass of the cell. If they didn’t, the nucleus would be left behind and the cytoplasm would crawl away.”

The study involved researchers from the University of Leeds and Japan’s Waseda and Osaka universities, as well as the Quantitative Biology Center at Japan’s Riken research institute and the Japan Science and Technology Agency (JST). The research was funded by the Human Frontiers Science Program and the Biotechnology and Biological Sciences Research Council (BBSRC).

Here’s a link to and a citation for the paper,

Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules by Hiroshi Imai, Tomohiro Shima, Kazuo Sutoh, Matthew L. Walker, Peter J. Knight, Takahide Kon, & Stan A. Burgess. Nature Communications 6, Article number: 8179  doi:10.1038/ncomms9179 Published 14 September 2015

This paper is open access.

*The EurekAlert link added Sept. 15, 2015 at 1200 hours PST.

Single-element quasicrystal created in laboratory for the first time

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There’s a background story which gives this breakthrough a fabulous aspect but, first, here’s the research breakthrough from a Dec. 24, 2013 news item on Nanowerk (Note: A link has been removed),

A research group led by Assistant Professor Kazuki Nozawa and Professor Yasushi Ishii from the Department of Physics, Faculty of Science and Engineering, Chuo University, Chief Researcher Masahiko Shimoda from the National Institute for Materials Science (NIMS) and Professor An-Pang Tsai from the Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, succeeded for the first time in the world in fabricating a three-dimensional structure of a quasicrystal composed of a single element, through joint research with a group led by Dr. Hem Raj Sharma from the University of Liverpool, the United Kingdom.

The Dec. 2, 2013 National Institute for Materials Science (NIMS; Japan) press release, which originated the news item, describes quasicrystals and the reasons why this particular achievement is such a breakthrough,

Quasicrystals are substances discovered in 1984 by Dr. Dan Shechtman (who was awarded the Nobel Prize in Chemistry in 2011). [emphasis mine] To date, quasicrystals have been found in more than one hundred kinds of alloy, polymer and nanoparticle systems. However, a quasicrystal composed of a single element has not been found yet. Quasicrystals have a beautiful crystalline structure which is closely related to the golden ratio, called a quasiperiodic structure. This structure is made of a pentagonal or decagonal atomic arrangement that is not found in ordinary periodic crystals (see the reference illustrations). Due to the complexity of the crystalline structure and chemical composition, much about quasicrystals is still veiled in mystery, including the mechanism for stabilizing a quasiperiodic structure and the novel properties of this unique type of crystalline structure. For these reasons, efforts have been made for a long time in the quest for a chemically simple type of quasicrystal composed only of a single element. The joint research group has recently succeeded in growing a crystal of lead with a quasiperiodic structure which is modeled on the structure of a substrate quasicrystal, by vapor-depositing lead atoms on the quasicrystal substrate of an existing alloy made of silver (Ag), indium (In) and ytterbium (Yb). Success using this approach had been reported for fabricating a single-element quasiperiodic film consisting of a single atomic layer (two-dimensional structure), but there had been no successful case of fabricating a single-element quasiperiodic structure consisting of multiple atomic layers (three-dimensional structure). This recent success by the joint research group is a significant step forward toward achieving single-element quasicrystals. It is also expected to lead to advancement in various fields, such as finding properties unique to quasiperiodic structures that cannot be found in periodic crystals and elucidating the mechanism of stabilization of quasiperiodic structures.

Here’s an image illustrating the researchers’ achievement,

Illustrations of the deposition structure of lead. The Tsai cluster in the substrate quasicrystal which is near the surface of the substrate is cut at the point where it contacts the surface. While lead usually has a face-centered cubic structure, it is deposited on the quasicrystal substrate in a manner that it recovers Tsai clusters which are cut near the surface of the substrate. This indicates that a crystal of lead is grown with the same structure as the structure of the quasicrystal substrate. (Courtesy National Institute for Materials Science, Japan)

Illustrations of the deposition structure of lead. The Tsai cluster in the substrate quasicrystal which is near the surface of the substrate is cut at the point where it contacts the surface. While lead usually has a face-centered cubic structure, it is deposited on the quasicrystal substrate in a manner that it recovers Tsai clusters which are cut near the surface of the substrate. This indicates that a crystal of lead is grown with the same structure as the structure of the quasicrystal substrate. (Courtesy National Institute for Materials Science, Japan)

I suggested earlier that this achievement has a fabulous quality and the Daniel Schechtman backstory is the reason. The winner of the 2011 Nobel Prize for Chemistry, Schechtman was reviled for years within his scientific community as Ian Sample notes in his Oct. 5, 2011 article on the announcement of Schechtman’s Nobel win written for the Guardian newspaper (Note: A link has been removed),

A scientist whose work was so controversial he was ridiculed and asked to leave his research group has won the Nobel Prize in Chemistry.

Daniel Shechtman, 70, a researcher at Technion-Israel Institute of Technology in Haifa, received the award for discovering seemingly impossible crystal structures in frozen gobbets of metal that resembled the beautiful patterns seen in Islamic mosaics.

Images of the metals showed their atoms were arranged in a way that broke well-establised rules of how crystals formed, a finding that fundamentally altered how chemists view solid matter.

…

On the morning of 8 April 1982, Shechtman saw something quite different while gazing at electron microscope images of a rapidly cooled metal alloy. The atoms were packed in a pattern that could not be repeated. Shechtman said to himself in Hebrew, “Eyn chaya kazo,” which means “There can be no such creature.”

The bizarre structures are now known as “quasicrystals” and have been seen in a wide variety of materials. Their uneven structure means they do not have obvious cleavage planes, making them particularly hard.

…

In an interview this year with the Israeli newspaper, Haaretz, Shechtman said: “People just laughed at me.” He recalled how Linus Pauling, a colossus of science and a double Nobel laureate, mounted a frightening “crusade” against him. After telling Shechtman to go back and read a crystallography textbook, the head of his research group asked him to leave for “bringing disgrace” on the team. “I felt rejected,” Shachtman said.

It takes a lot to persevere when most, if not all, of your colleagues are mocking and rejecting your work so bravo to Schechtman! And,bravo to the Japan-UK project researchers who have persevered to help solve at least part of a complex problem requiring that our basic notions of matter be rethought.

I encourage you to read Sample’s article in its entirety as it is well written and I’ve excerpted only bits of the story as it relates to a point I’m making in this post, i.e., perseverance in the face of extreme resistance.

Special coating eliminates need to de-ice airplanes

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There was a big airplane accident years ago where the chief pilot had failed to de-ice the wings just before take off. The plane took off from Dulles Airport (Washington, DC) and crashed minutes later killing the crew and passengers (if memory serves, everyone died).

I read the story in a book about sociolinguistics and work. When the ‘black box’ (a recorder that’s in all airplanes) was recovered, sociolinguists were included in the team that was tasked with trying to establish the cause(s). From the sociolinguists’ perspective, it came down to this. The chief pilot hadn’t flown from Washington, DC very often and was unaware that icing could be as prevalent there as it is more northern airports. He did de-ice the wings but the plane did not take off in its assigned time slot (busy airport). After several minutes and just prior to takeoff, the chief pilot’s second-in-command who was more familiar with Washington’s weather conditions gently suggested de-icing wings a second time and was ignored. (They reproduced some of the dialogue in the text I was reading.) The story made quite an impact on me since I’m very familiar with the phenomenon (confession: I’ve been on both sides of the equation) of comments in the workplace being ignored, although not with such devastating consequences. Predictably, the sociolinguists suggested changing the crew’s communication habits (always a good idea) but it never occurred to them (or to me at the time of reading the text) that technology might help provide an answer.

A Japanese research team (Riho Kamada, Chuo University;  Katsuaki Morita, The University of Tokyo; Koji Okamoto, The University of Tokyo; Akihito Aoki, Kanagawa Institute of Technology; Shigeo Kimura, Kanagawa Institute of Technology; Hirotaka Sakaue, Japan Aerospace Exploration Agency [JAXA]) presented an anti-icing (or de-icing) solution for airplanes at the 65th Annual Meeting of the APS* Division of Fluid Dynamics, November 18–20, 2012 in San Diego, California, from the Nov. 16, 2012 news release on EurekAlert,

To help planes fly safely through cold, wet, and icy conditions, a team of Japanese scientists has developed a new super water-repellent surface that can prevent ice from forming in these harsh atmospheric conditions. Unlike current inflight anti-icing techniques, the researchers envision applying this new anti-icing method to an entire aircraft like a coat of paint.

As airplanes fly through clouds of super-cooled water droplets, areas around the nose, the leading edges of the wings, and the engine cones experience low airflow, says Hirotaka Sakaue, a researcher in the fluid dynamics group at the Japan Aerospace Exploration Agency (JAXA). This enables water droplets to contact the aircraft and form an icy layer. If ice builds up on the wings it can change the way air flows over them, hindering control and potentially making the airplane stall. Other members of the research team are with the University of Tokyo, the Kanagawa Institute of Technology, and Chuo University.

Current anti-icing techniques include diverting hot air from the engines to the wings, preventing ice from forming in the first place, and inflatable membranes known as pneumatic boots, which crack ice off the leading edge of an aircraft’s wings. The super-hydrophobic, or water repelling, coating being developed by Sakaue, Katsuaki Morita – a graduate student at the University of Tokyo – and their colleagues works differently, by preventing the water from sticking to the airplane’s surface in the first place.

The researchers developed a coating containing microscopic particles of a Teflon-based material called polytetrafluoroethylene (PTFE), which reduces the energy needed to detach a drop of water from a surface. “If this energy is small, the droplet is easy to remove,” says Sakaue. “In other words, it’s repelled,” he adds.

The PTFE microscale particles created a rough surface, and the rougher it is, on a microscopic scale, the less energy it takes to detach water from that surface. The researchers varied the size of the PTFE particles in their coatings, from 5 to 30 micrometers, in order to find the most water-repellant size. By measuring the contact angle – the angle between the coating and the drop of water – they could determine how well a surface repelled water.

While this work isn’t occurring at the nanoscale, I thought I’d make an exception due to my interest in the subject.

*APS is the American Physical Society