Scientists at Kanazawa University in Japan have developed a new high-speed atomic force microscopy techniques to understand better the structures and dynamics of some of life’s most ubiquitous and inscrutable molecules, intrinsically disordered proteins.
The development of protein crystallography during the 1930s and 1950s made a few protein structures visible unexpectedly, yet it slowly became apparent that many proteins lack a single set structure making them intractable to x-ray crystallography. As they are excessively thin for electron microscopy, the only viable alternatives for many of these inherently disordered proteins (IDPs) are nuclear magnetic resonance imaging and small-angle x-ray scattering.
Data collected from these techniques are averaged over ensembles and 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 to capture dynamics and protein structures.
In this new study, scientists applied their new technique to the study of several IDPs. They studied parameters defining the shape, size, and chain length of protein regions and a power-law relating the protein size to the protein length, and a quantitative description of the mica surface’s effect on protein dimensions.
The dynamics of the protein conformations caught due to the technique’s high-speed capabilities uncovered globules that appear and disappear and changes between completely unstructured and loosely folded conformations in segments up to 160 amino acids long.
Examining measles virus nucleoprotein specifically recognized the shape and measurements, and characteristics of the order-disorder transitions in the area responsible for molecular recognition, which permits infections to distinguish host factors so they can reproduce. They could likewise decide larger-scale structures of the virus’s phosphoprotein that are not available to nuclear magnetic resonance.
Scientists suggest that the formation of specific compact shapes observed may explain the resistance to proteolysis — protein breakdown.
Scientists noted, “As well as a powerful tool in its own right, when all molecular features revealed by HS-AFM are combined with the folded local structure given by NMR, the combined information allows a quantitative delineation of the structural and dynamic characters of IDPs, more realistically compared to the pictures depicted individually, as demonstrated for PNT [measles virus phosphoprotein].”
- Noriyuki Kodera et al. Structural and dynamics analysis of intrinsically disordered proteins by high-speed atomic force microscopy. Nature Nanotechnology, 2020; DOI: 10.1038/s41565-020-00798-9