Kanazawa University NanoLSI Podcast: High-speed atomic force microscopy takes on intrinsically disordered proteins

High-speed atomic force microscopy takes on intrinsically disordered proteins

Transcript of this podcast

Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Toshio Ando at the Kanazawa University NanoLSI, alongside Sonia Longhi at Aix-Marseille University and CNRS in France.

The research described in this podcast was published in Nature Nanotechnology in November 2020

Kanazawa University NanoLSI website

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High-speed atomic force microscopy takes on intrinsically disordered proteins

Kanazawa University’s pioneering high-speed atomic force microscope technology has now shed light on the structure and dynamics of some of life’s most ubiquitous and inscrutable molecules – intrinsically disordered proteins. The study is reported in Nature Nanotechnology.

Our understanding of biological proteins does not always correlate with how common or important they are. Half of all proteins, molecules that play an integral role in cell processes, are intrinsically disordered, which means many of the standard techniques for probing biomolecules don’t work on them. Now researchers at Kanazawa University in Japan have shown that their home-grown high-speed atomic force microscopy technology can provide information not just on the structures of these proteins but also their dynamics.

Understanding how a protein is put together provides valuable clues to its functions. The development of protein crystallography in the 1930s and 1950s brought several protein structures into view for the first time, but it gradually became apparent that a large fraction of proteins lack a single set structure making them intractable to xray crystallography. As they are too thin for electron microscopy, the only viable alternatives for many of these intrinsically disordered proteins are nuclear magnetic resonance imaging and small angle xray scattering. Data collected from these techniques are averaged over ensembles and so give no clear indication of individual protein conformations or how often they occur. Atomic force microscopy on the other hand is capable of nanoscale resolution biological imaging at high-speed, so it can capture dynamics as well as protein structures.

So what kind of insights can high-speed AFM offer for these proteins? 

In this latest work researchers at Kanazawa University alongside collaborators in Japan, France and Italy applied the technique to study several intrinsically disordered proteins. They identified parameters defining the shape, size and chain length of protein regions, as well as a power law relating the protein size to the protein length. Not only that but they got a quantitative description of the effect of the mica surface on protein dimensions. The dynamics of the protein conformations captured thanks to the high-speed capabilities of the technique revealed globules that appear and disappear, and transformations between fully unstructured and loosely folded conformations in segments up to 160 amino acids long.

Studies of the measles virus nucleoprotein in particular helped identify not just the shape and dimensions but also characteristics of the order-disorder transitions in the region responsible for molecular recognition, which allows viruses to identify host factors so that they can reproduce. They could also determine larger scale structures of the virus’s phosphoprotein that are not accessible to nuclear magnetic resonance (which can only give an indication of distances between amino acids separated by less than 2 nm). The researchers suggest that the formation of certain compact shapes observed may explain the resistance to proteolysis – protein break

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