Tag Archives: Philipp Kukura

Gold glue?

If you’re hoping for gold flecks in your glue, this is not going to satisfy you, given that it’s all at the nanoscale. An August 7, 2019 news item on Nanowerk briefly describes this gold glue (Note: A link has been removed),

It has long been known that gold can be used to do things that philosophers have never even dreamed of. The Institute of Nuclear Physics of the Polish Academy of Sciences in Cracow has confirmed the existence of ‘gold glue’: bonds involving gold atoms, capable of permanently bonding protein rings. Skilfully used by an international team of scientists, the bonds have made it possible to construct molecular nanocages with a structure so far unparalleled in nature or even in mathematics (Nature, “An ultra-stable gold-coordinated protein cage displaying reversible assembly”).

Caption: The ‘impossible’ sphere, i.e. a molecular nanocage of 24 protein rings, each of which has an 11-sided structure. The rings are connected by bonds with the participation of gold atoms, here marked in yellow. Depending on their position in the structure, not all gold atoms have to be used to attach adjacent proteins (an unused gold atom is marked in red). Credit: Source: UJ, IFJ PAN

An August 6, 2019 Polish Academy of Sciences press release (also on EurekAlert but published August 7, 2019), which originated the news item, expands on the theme,

The world of science has been interested in molecular cages for years. Not without reason. Chemical molecules, including those that would under normal conditions enter into chemical reactions, can be enclosed within their empty interiors. The particles of the enclosed compound, separated by the walls of the cage from the environment, have nothing to bond with. These cages can be therefore be used, for example, to transport drugs safely into a cancer cell, only releasing the drug when they are inside it.

Molecular cages are polyhedra made up of smaller ‘bricks’, usually protein molecules. The bricks can’t be of any shape. For example, if we wanted to build a molecular polyhedron using only objects with the outline of an equilateral triangle, geometry would limit us to only three solid figures: a tetrahedron, an octahedron or an icosahedron. So far, there have been no other structural possibilities.

“Fortunately, Platonic idealism is not a dogma of the physical world. If you accept certain inaccuracies in the solid figure being constructed, you can create structures with shapes that are not found in nature, what’s more, with very interesting properties,” says Dr. Tomasz Wrobel from the Cracow Institute of Nuclear Physics of the Polish Academy of Sciences (IFJ PAN).

Dr. Wrobel is one of the members of an international team of researchers who have recently carried out the ‘impossible’: they built a cage similar in shape to a sphere out of eleven-walled proteins. The main authors of this spectacular success are scientists from the group of Prof. Jonathan Heddle from the Malopolska Biotechnology Centre of the Jagiellonian University in Cracow and the Japanese RIKEN Institute in Wako. The work described in Nature magazine took place with the participation of researchers from universities in Osaka and Tsukuba (Japan), Durham (Great Britain), Waterloo (Canada) and other research centres.

Each of the walls of the new nanocages was formed by a protein ring from which eleven cysteine molecules stuck out at regular intervals. It was to the sulphur atom found in each cysteine molecule that the ‘glue’, i.e. the gold atom, was planned to be attached. In the appropriate conditions, it could bind with one more sulphur atom, in the cysteine of a next ring. In this way a permanent chemical bond would be formed between the two rings. But would the gold atom under these conditions really be able to form a bond between the rings?

“In the Spectroscopic Imaging Laboratory of IFJ PAS we used Raman spectroscopy and X-ray photoelectron spectroscopy to show that in the samples provided to us with the test nanocages, the gold really did form bonds with sulphur atoms in cysteines. In other words, in a difficult, direct measurement, we proved that gold ‘glue’ for bonding protein rings in cages really does exist,” explains Dr. Wrobel.

Each gold atom can be treated as a stand-alone clip that makes it possible to attach another ring. The road to the ‘impossible’ begins when we realize that we don’t always have to use all of the clips! So, although all the rings of the new nanocages are physically the same, depending on their place in the structure they connect with their neighbours with a different number of gold atoms, and thus function as polygons with different numbers of vertices. 24 nanocage walls presented by the researchers were held together by 120 gold atoms. The outer diameter of the cages was 22 nanometres and the inner diameter was 16 nm.

Using gold atoms as a binder for nanocages is also important due to its possible applications. In earlier molecular structures, proteins were glued together using many weak chemical bonds. The complexity of the bonds and their similarity to the bonds responsible for the existence of the protein rings themselves did not allow for precise control over the decomposition of the cages. This is not the case in the new structures. On the one hand, gold-bonded nanocages are chemically and thermally stable (for example, they withstand hours of boiling in water). On the other hand, however, gold bonds are sensitive to an increase in acidity. By its increase, the nanocage can be decomposed in a controlled way and the contents can be released into the environment. Since the acidity within cells is greater than outside them, gold-bonded nanocages are ideal for biomedical applications.

The ‘impossible’ nanocage is the presentation of a qualitatively new approach to the construction of molecular cages, with gold atoms in the role of loose clips. The demonstrated flexibility of the gold bonds will make it possible in the future to create nanocages with sizes and features precisely tailored to specific needs.

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

An ultra-stable gold-coordinated protein cage displaying reversible assembly by Ali D. Malay, Naoyuki Miyazaki, Artur Biela, Soumyananda Chakraborti, Karolina Majsterkiewicz, Izabela Stupka, Craig S. Kaplan, Agnieszka Kowalczyk, Bernard M. A. G. Piette, Georg K. A. Hochberg, Di Wu, Tomasz P. Wrobel, Adam Fineberg, Manish S. Kushwah, Mitja Kelemen, Primož Vavpetič, Primož Pelicon, Philipp Kukura, Justin L. P. Benesch, Kenji Iwasaki & Jonathan G. Heddle Nature volume 569, pages438–442 (2019) Issue Date: 16 May 2019 DOI: https://doi.org/10.1038/s41586-019-1185-4 Published online: 08 May 2019

This paper is behind a paywall.

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,