Tag Archives: Pete Wilton

Motor proteins have a stiff-legged walk

An April 23, 2015 news item on Nanowerk calls to mind Monty Python and its Ministry of Silly Walks,

The ‘stiff-legged’ walk of a motor protein along a tightrope-like filament has been captured for the first time.

Because cells are divided in many parts that serve different functions some cellular goodies need to be transported from one part of the cell to another for it to function smoothly. There is an entire class of proteins called ‘molecular motors’, such as myosin 5, that specialise in transporting cargo using chemical energy as fuel.

Remarkably, these proteins not only function like nano-scale lorries, they also look like a two-legged creature that takes very small steps. But exactly how Myosin 5 did this was unclear.

For anyone unfamiliar with The Ministry of Silly Walks (from its Wikipedia entry; Note: Links have been removed),

“The Ministry of Silly Walks” is a sketch from the Monty Python comedy troupe’s television show Monty Python’s Flying Circus, season 2, episode 14, which is entitled “Face the Press”.

Here’s an image from the sketch, which perfectly illustrates a stiff-legged walk,

John Cleese as a Civil Servant in the Ministry of Silly Walks. Screenshot from Monty Python's Flying Circus episode, Dinsdale (Alternate episode title: Face the Press). Ministry_of_Silly_Walks.jpg ‎(300 × 237 pixels, file size: 14 KB, MIME type: image/jpeg) [downloaded from http://en.wikipedia.org/wiki/File:Ministry_of_Silly_Walks.jpg]

John Cleese as a Civil Servant in the Ministry of Silly Walks. Screenshot from Monty Python’s Flying Circus episode, Dinsdale (Alternate episode title: Face the Press). Ministry_of_Silly_Walks.jpg ‎(300 × 237 pixels, file size: 14 KB, MIME type: image/jpeg) [downloaded from http://en.wikipedia.org/wiki/File:Ministry_of_Silly_Walks.jpg]

As far as I can tell, the use of this image would fall under the notion of ‘fair dealing‘ as it’s called in Canada.

Getting back to the Nanowerk news item, it started life as a University of Oxford Science blog April 23, 2015 posting  by Pete Wilton (Note: A link has been removed),

The motion of myosin 5 has now been recorded by a team led by Oxford University scientists using a new microscopy technique that can ‘see’ tiny steps of tens of nanometres captured at up to 1000 frames per second. The findings are of interest for anyone trying to understand the basis of cellular function but could also help efforts aimed at designing efficient nanomachines.

‘Until now, we believed that the sort of movements or steps these proteins made were random and free-flowing because none of the experiments suggested otherwise,’ said Philipp Kukura of Oxford University’s Department of Chemistry who led the research recently reported in the journal eLife. ‘However, what we have shown is that the movements only appeared random; if you have the capability to watch the motion with sufficient speed and precision, a rigid walking pattern emerges.’

One of the key problems for those trying to capture proteins on a walkabout is that not only are these molecules small – with steps much smaller than the wavelength of light and therefore the resolution of most optical microscopes – but they are also move very quickly.

Philipp describes how the team had to move from the microscope equivalent of an iPhone camera to something more like the high speed cameras used to snap speeding bullets. Even with such precise equipment the team had to tag the ‘feet’ of the protein in order to precisely image its gait: one foot was tagged with a quantum dot, the other with a gold particle just 20 nanometres across. (Confusingly, technically speaking, these ‘feet’ are termed the ‘heads’ of the protein because they bind to the actin filament).

I recommend reading Wilton’s post in its entirety. Meanwhile, here’s a 12 secs. video illustrating the motor protein’s stiff-legged walk,

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

Structural dynamics of myosin 5 during processive motion revealed by interferometric scattering microscopy by Joanna Andrecka, Jaime Ortega Arroyo, Yasuharu Takagi, Gabrielle de Wit, Adam Fineberg, Lachlan MacKinnon, Gavin Young, James R Sellers, & Philipp Kukura. eLife 2015;4:e05413 DOI: http://dx.doi.org/10.7554/eLife.05413Published March 6, 2015

This paper is open access.

As for silly walks, there is more than one version of the sketch with John Cleese on YouTube but I was particularly taken with this public homage which took place in Brno (Czech Republic) in Jan. 2013,

Enjoy!

Molecular robots (nanobots/nanorobots): a promising start at Oxford University

‘Baby steps’ is how they are describing the motion and the breakthrough in functional molecular robots at the University of Oxford. From a Dec. 11, 2014 news item on phys.org,

A walking molecule, so small that it cannot be observed directly with a microscope, has been recorded taking its first nanometre-sized steps.

It’s the first time that anyone has shown in real time that such a tiny object – termed a ‘small molecule walker’ – has taken a series of steps. The breakthrough, made by Oxford University chemists, is a significant milestone on the long road towards developing ‘nanorobots’.

‘In the future we can imagine tiny machines that could fetch and carry cargo the size of individual molecules, which can be used as building blocks of more complicated molecular machines; imagine tiny tweezers operating inside cells,’ said Dr Gokce Su Pulcu of Oxford University’s Department of Chemistry. ‘The ultimate goal is to use molecular walkers to form nanotransport networks,’ she says.

A Dec. 10, 2014 University of Oxford science blog post by Pete Wilton, which originated the news item, describes one of the problem with nanorobots,

However, before nanorobots can run they first have to walk. As Su explains, proving this is no easy task.

For years now researchers have shown that moving machines and walkers can be built out of DNA. But, relatively speaking, DNA is much larger than small molecule walkers and DNA machines only work in water.

The big problem is that microscopes can only detect moving objects down to the level of 10–20 nanometres. This means that small molecule walkers, whose strides are 1 nanometre long, can only be detected after taking around 10 or 15 steps. It would therefore be impossible to tell with a microscope whether a walker had ‘jumped’ or ‘floated’ to a new location rather than taken all the intermediate steps.

The post then describes how the researchers solved the problem,

… Su and her colleagues at Oxford’s Bayley Group took a new approach to detecting a walker’s every step in real time. Their solution? To build a walker from an arsenic-containing molecule and detect its motion on a track built inside a nanopore.

Nanopores are already the foundation of pioneering DNA sequencing technology developed by the Bayley Group and spinout company Oxford Nanopore Technologies. Here, tiny protein pores detect molecules passing through them. Each base disrupts an electric current passed through the nanopore by a different amount so that the DNA base ‘letters’ (A, C, G or T) can be read.

In this new research, they used a nanopore containing a track formed of five ‘footholds’ to detect how a walker was moving across it.

‘We can’t ‘see’ the walker moving, but by mapping changes in the ionic current flowing through the pore as the molecule moves from foothold to foothold we are able to chart how it is stepping from one to the other and back again,’ Su explains.

To ensure that the walker doesn’t float away, they designed it to have ‘feet’ that stick to the track by making and breaking chemical bonds. Su says: ‘It’s a bit like stepping on a carpet with glue under your shoes: with each step the walker’s foot sticks and then unsticks so that it can move to the next foothold.’ This approach could make it possible to design a machine that can walk on a variety of surfaces.

There is a video illustrating the molecular walker’s motion, (courtesy University of Oxford),

There is as noted in Wilton’s post, more work to do,

It’s quite an achievement for such a tiny machine but, as Su is the first to admit, there are many more challenges to be overcome before programmable nanorobots are a reality.

‘At the moment we don’t have much control over which direction the walker moves in; it moves pretty randomly,’ Su tells me. ‘The protein track is a bit like a mountain slope; there’s a direction that’s easier to walk in so walkers will tend to go this way. We hope to be able to harness this preference to build tracks that direct a walker where we want it to go.’

The next challenge after that will be for a walker to make itself useful by, for instance, carrying a cargo: there’s already space for it to carry a molecule on its ‘head’ that it could then take to a desired location to accomplish a task.

Su comments: ‘We should be able to engineer a surface where we can control the movement of these walkers and observe them under a microscope through the way they interact with a very thin fluorescent layer. This would make it possible to design chips with different stations with walkers ferrying cargo between these stations; so the beginnings of a nanotransport system.’

These are the first tentative baby steps of a new technology, but they promise that there could be much bigger strides to come.

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

Continuous observation of the stochastic motion of an individual small-molecule walker by Gökçe Su Pulcu, Ellina Mikhailova, Lai-Sheung Choi, & Hagan Bayley. Nature Nanotechnology (2014) doi:10.1038/nnano.2014.264 Published online 08 December 2014

This paper is behind a paywall.